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Chen J, Lewis MA, Wai A, Yin L, Dawson SJ, Ingham NJ, Steel KP. A new mutation of Sgms1 causes gradual hearing loss associated with a reduced endocochlear potential. Hear Res 2024; 451:109091. [PMID: 39067415 DOI: 10.1016/j.heares.2024.109091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/04/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
Sgms1 encodes sphingomyelin synthase 1, an enzyme in the sphingosine-1-phosphate signalling pathway, and was previously reported to underlie hearing impairment in the mouse. A new mouse allele, Sgms1tm1a, unexpectedly showed normal Auditory Brainstem Response thresholds. We found that the Sgms1tm1a mutation led to incomplete knockdown of transcript to 20 % of normal values, which was enough to support normal hearing. The Sgms1tm1b allele was generated by knocking out exon 7, leading to a complete lack of detectable transcript in the inner ear. Sgms1tm1b homozygotes showed largely normal auditory brainstem response thresholds at first, followed by progressive loss of sensitivity until they showed severe impairment at 6 months old. The endocochlear potential was consistently reduced in Sgms1tm1b mutants at 3, 4 and 8 weeks old, to around 80 mV compared with around 120 mV in control littermates. The stria vascularis showed a characteristic irregularity of marginal cell surfaces and patchy loss of Kcnq1 expression at their apical membrane, and expression analysis of the lateral wall suggested that marginal cells were the most likely initial site of dysfunction in the mutants. Finally, significant association of auditory thresholds with DNA markers within and close to the human SGMS1 gene were found in the 1958 Birth Cohort, suggesting that SGMS1 variants may play a role in the range of hearing abilities in the human population.
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Affiliation(s)
- Jing Chen
- Wolfson Sensory, Pain and Regeneration Centre, King's College London, London SE1 1UL, United Kingdom
| | - Morag A Lewis
- Wolfson Sensory, Pain and Regeneration Centre, King's College London, London SE1 1UL, United Kingdom
| | - Alisa Wai
- Wolfson Sensory, Pain and Regeneration Centre, King's College London, London SE1 1UL, United Kingdom
| | - Lucia Yin
- Wolfson Sensory, Pain and Regeneration Centre, King's College London, London SE1 1UL, United Kingdom
| | - Sally J Dawson
- UCL Ear Institute, University College London, London WC1X 8EE, United Kingdom
| | - Neil J Ingham
- Wolfson Sensory, Pain and Regeneration Centre, King's College London, London SE1 1UL, United Kingdom
| | - Karen P Steel
- Wolfson Sensory, Pain and Regeneration Centre, King's College London, London SE1 1UL, United Kingdom.
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2
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Guan C, Shaikh M, Warnecke A, Vona B, Albert JT. A burden shared: The evolutionary case for studying human deafness in Drosophila. Hear Res 2024; 450:109047. [PMID: 38896942 DOI: 10.1016/j.heares.2024.109047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/09/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
Hearing impairment is the most prevalent sensory disease in humans and can have dramatic effects on the development, and preservation, of our cognitive abilities and social interactions. Currently 20 % of the world's population suffer from a form of hearing impairment; this is predicted to rise to 25 % by 2050. Despite this staggering disease load, and the vast damage it inflicts on the social, medical and economic fabric of humankind, our ability to predict, or prevent, the loss of hearing is very poor indeed. We here make the case for a paradigm shift in our approach to studying deafness. By exploiting more forcefully the molecular-genetic conservation between human hearing and hearing in morphologically distinct models, such as the fruit fly Drosophila melanogaster, we believe, a deeper understanding of hearing and deafness can be achieved. An understanding that moves beyond the surface of the 'deafness genes' to probe the underlying bedrock of hearing, which is shared across taxa, and partly shared across modalities. When it comes to understanding the workings (and failings) of human sensory function, a simple fruit fly has a lot to offer and a fly eye might sometimes be a powerful model for a human ear. Particularly the use of fly avatars, in which specific molecular (genetic or proteomic) states of humans (e.g. specific patients) are experimentally reproduced, in order to study the corresponding molecular mechanisms (e.g. specific diseases) in a controlled yet naturalistic environment, is a tool that promises multiple unprecedented insights. The use of the fly - and fly avatars - would benefit humans and will help enhance the power of other scientific models, such as the mouse.
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Affiliation(s)
- Chonglin Guan
- Sensory Physiology & Behaviour Group, Department for Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Str. 9-11, 26111 Oldenburg, Germany; Cluster of Excellence Hearing4all, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Str. 9-11, 26111 Oldenburg, Germany
| | - Muhammad Shaikh
- Ear Institute, University College London, 332 Gray's Inn Road, London, WC1 × 8EE, UK
| | - Athanasia Warnecke
- Hannover Medical School, Department of Otorhinolaryngology, Head & Neck Surgery, Hannover, Germany; Cluster of Excellence Hearing4all, MHH Hannover, Germany
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany; Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany.
| | - Joerg T Albert
- Sensory Physiology & Behaviour Group, Department for Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Str. 9-11, 26111 Oldenburg, Germany; Cluster of Excellence Hearing4all, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Str. 9-11, 26111 Oldenburg, Germany; Ear Institute, University College London, 332 Gray's Inn Road, London, WC1 × 8EE, UK.
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3
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James K, Oluwole OG. Leveraging human-mouse studies to advance the genetics of hearing impairment in Africa. J Gene Med 2024; 26:e3714. [PMID: 38949079 DOI: 10.1002/jgm.3714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 04/10/2024] [Accepted: 06/02/2024] [Indexed: 07/02/2024] Open
Abstract
Mouse models are used extensively to understand human pathobiology and mechanistic functions of disease-associated loci. However, in this review, we investigate the potential of using genetic mouse models to identify genetic markers that can disrupt hearing thresholds in mice and then target the hearing-enriched orthologues and loci in humans. Currently, little is known about the real prevalence of genes that cause hearing impairment (HI) in Africa. Pre-screening mouse cell lines to identify orthologues of interest has the potential to improve the genetic diagnosis for HI in Africa to a significant percentage, for example, 10-20%. Furthermore, the functionality of a candidate gene derived from mouse screening with heterogeneous genetic backgrounds and multi-omic approaches can shed light on the molecular, genetic heterogeneity and plausible mode of inheritance of a gene in hearing-impaired individuals especially in the absence of large families to investigate.
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Affiliation(s)
- Kili James
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Oluwafemi G Oluwole
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biomedical Research Centre, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Vijayakumar S, DiGuiseppi JA, Dabestani PJ, Ryan WG, Quevedo RV, Li Y, Diers J, Tu S, Fleegel J, Nguyen C, Rhoda LM, Imami AS, Hamoud ARA, Lovas S, McCullumsmith RE, Zallocchi M, Zuo J. In silico transcriptome screens identify epidermal growth factor receptor inhibitors as therapeutics for noise-induced hearing loss. SCIENCE ADVANCES 2024; 10:eadk2299. [PMID: 38896614 PMCID: PMC11186505 DOI: 10.1126/sciadv.adk2299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Noise-induced hearing loss (NIHL) is a common sensorineural hearing impairment that lacks U.S. Food and Drug Administration-approved drugs. To fill the gap in effective screening models, we used an in silico transcriptome-based drug screening approach, identifying 22 biological pathways and 64 potential small molecule treatments for NIHL. Two of these, afatinib and zorifertinib [epidermal growth factor receptor (EGFR) inhibitors], showed efficacy in zebrafish and mouse models. Further tests with EGFR knockout mice and EGF-morpholino zebrafish confirmed their protective role against NIHL. Molecular studies in mice highlighted EGFR's crucial involvement in NIHL and the protective effect of zorifertinib. When given orally, zorifertinib was found in the perilymph with favorable pharmacokinetics. In addition, zorifertinib combined with AZD5438 (a cyclin-dependent kinase 2 inhibitor) synergistically prevented NIHL in zebrafish. Our results underscore the potential for in silico transcriptome-based drug screening in diseases lacking efficient models and suggest EGFR inhibitors as potential treatments for NIHL, meriting clinical trials.
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Affiliation(s)
- Sarath Vijayakumar
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Joseph A. DiGuiseppi
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Parinaz Jila Dabestani
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - William G. Ryan
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA.
| | - Rene Vielman Quevedo
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Yuju Li
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Jack Diers
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Shu Tu
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Jonathan Fleegel
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Cassidy Nguyen
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Lauren M. Rhoda
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Ali Sajid Imami
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA.
| | | | - Sándor Lovas
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Robert E. McCullumsmith
- Department of Neurosciences, University of Toledo, Toledo, OH 43614, USA.
- Neurosciences Institute, ProMedica, Toledo, OH 43606, USA
| | - Marisa Zallocchi
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Jian Zuo
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, NE 68178, USA
- Ting Therapeutics, University of California San Diego, 9310 Athena Circle, San Diego, CA 92037, USA
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5
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Gwilliam K, Sperber M, Perry K, Rose KP, Ginsberg L, Paladugu N, Song Y, Milon B, Elkon R, Hertzano R. A cell type-specific approach to elucidate the role of miR-96 in inner ear hair cells. FRONTIERS IN AUDIOLOGY AND OTOLOGY 2024; 2:1400576. [PMID: 38826689 PMCID: PMC11141775 DOI: 10.3389/fauot.2024.1400576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Introduction Mutations in microRNA-96 (miR-96), a microRNA expressed within the hair cells (HCs) of the inner ear, result in progressive hearing loss in both mouse models and humans. In this study, we present the first HC-specific RNA-sequencing (RNA-seq) dataset from newborn Mir96Dmdo heterozygous, homozygous mutant, and wildtype mice. Methods Bulk RNA-seq was performed on HCs of newborn Mir96Dmdo heterozygous, homozygous mutant, and wildtype mice. Differentially expressed gene analysis was conducted on Mir96Dmdo homozygous mutant HCs compared to wildtype littermate controls, followed by GO term and protein-protein interaction analysis on these differentially expressed genes. Results We identify 215 upregulated and 428 downregulated genes in the HCs of the Mir96Dmdo homozygous mutant mice compared to their wildtype littermate controls. Many of the significantly downregulated genes in Mir96Dmdo homozygous mutant HCs have established roles in HC development and/or known roles in deafness including Myo15a, Myo7a, Ush1c, Gfi1, and Ptprq and have enrichment in gene ontology (GO) terms with biological functions such as sensory perception of sound. Interestingly, upregulated genes in Mir96Dmdo homozygous mutants, including possible miR-96 direct targets, show higher wildtype expression in supporting cells compared to HCs. Conclusion Our data further support a role for miR-96 in HC development, possibly as a repressor of supporting cell transcriptional programs in HCs. The HC-specific Mir96Dmdo RNA-seq data set generated from this manuscript are now publicly available in a dedicated profile in the gene expression analysis resource (gEAR-https://umgear.org/p?l=miR96).
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Affiliation(s)
- Kathleen Gwilliam
- Section on Omics and Translational Science of Hearing, Neurotology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, United States
| | - Michal Sperber
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katherine Perry
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Kevin P. Rose
- Section on Omics and Translational Science of Hearing, Neurotology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, United States
| | - Laura Ginsberg
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Nikhil Paladugu
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Beatrice Milon
- Section on Omics and Translational Science of Hearing, Neurotology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, United States
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronna Hertzano
- Section on Omics and Translational Science of Hearing, Neurotology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, United States
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
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6
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Liu Y, Zeng X, Zhang H. An Emerging Approach of Age-Related Hearing Loss Research: Application of Integrated Multi-Omics Analysis. Adv Biol (Weinh) 2024; 8:e2300613. [PMID: 38279573 DOI: 10.1002/adbi.202300613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/03/2024] [Indexed: 01/28/2024]
Abstract
As one of the most common otologic diseases in the elderly, age-related hearing loss (ARHL) usually characterized by hearing loss and cognitive disorders, which have a significant impact on the elderly's physical and mental health and quality of life. However, as a typical disease of aging, it is unclear why aging causes widespread hearing impairment in the elderly. As molecular biological experiments have been conducted for research recently, ARHL is gradually established at various levels with the application and development of integrated multi-omics analysis in the studies of ARHL. Here, the recent progress in the application of multi-omics analysis in the molecular mechanisms of ARHL development and therapeutic regimens, including the combined analysis of different omics, such as transcriptome, proteome, and metabolome, to screen for risk sites, risk genes, and differences in lipid metabolism, etc., is outlined and the integrated histological data further promote the profound understanding of the disease process as well as physiological mechanisms of ARHL. The advantages and disadvantages of multi-omics analysis in disease research are also discussed and the authors speculate on the future prospects and applications of this part-to-whole approach, which may provide more comprehensive guidance for ARHL and aging disease prevention and treatment.
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Affiliation(s)
- Yue Liu
- Department of Otolaryngology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China
- Department of Otolaryngology, Longgang E.N.T. Hospital and Shenzhen Key Laboratory of E.N.T, Institute of E.N.T., Shenzhen, 518172, China
- Department of Graduate and Scientific Research, Zunyi Medical University Zhuhai Campus, Zhuhai, 519041, China
| | - Xianhai Zeng
- Department of Otolaryngology, Longgang E.N.T. Hospital and Shenzhen Key Laboratory of E.N.T, Institute of E.N.T., Shenzhen, 518172, China
- Department of Graduate and Scientific Research, Zunyi Medical University Zhuhai Campus, Zhuhai, 519041, China
| | - Huasong Zhang
- Department of Otolaryngology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China
- Department of Otolaryngology, Longgang E.N.T. Hospital and Shenzhen Key Laboratory of E.N.T, Institute of E.N.T., Shenzhen, 518172, China
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7
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Mi D, Yanatori I, Zheng H, Kong Y, Hirayama T, Toyokuni S. Association of poly( rC)-binding protein-2 with sideroflexin-3 through TOM20 as an iron entry pathway to mitochondria. Free Radic Res 2024; 58:261-275. [PMID: 38599240 DOI: 10.1080/10715762.2024.2340711] [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: 11/02/2023] [Accepted: 03/15/2024] [Indexed: 04/12/2024]
Abstract
Iron is essential for all the lives and mitochondria integrate iron into heme and Fe-S clusters for diverse use as cofactors. Here, we screened mitochondrial proteins in KU812 human chronic myelogenous leukemia cells by glutathione S-transferase pulldown assay with PCBP2 to identify mitochondrial receptors for PCBP2, a major cytosolic Fe(II) chaperone. LC-MS analyses identified TOM20, sideroflexin-3 (SFXN3), SFXN1 and TOM70 in the affinity-score sequence. Stimulated emission depletion microscopy and proteinase-K digestion of mitochondria in HeLa cells revealed that TOM20 is located in the outer membrane of mitochondria whereas SFXN3 is located in the inner membrane. Although direct association was not observed between PCBP2 and SFXN3 with co-immunoprecipitation, proximity ligation assay demonstrated proximal localization of PCBP2 with TOM20 and there was a direct binding between TOM20 and SFXN3. Single knockdown either of PCBP2 and SFXN3 in K562 leukemia cells significantly decreased mitochondrial catalytic Fe(II) and mitochondrial maximal respiration. SFXN3 but not MFRN1 knockout (KO) in mouse embryonic fibroblasts decreased FBXL5 and heme oxygenase-1 (HO-1) but increased transferrin uptake and induced ferritin, indicating that mitochondrial iron entry through SFXN3 is distinct. MFRN1 KO revealed more intense mitochondrial Fe(II) deficiency than SFXN3 KO. Insufficient mitochondrial heme synthesis was evident under iron overload both with SFXN3 and MFRN KO, which was partially reversed by HO-1 inhibitor. Conversely, SFXN3 overexpression caused cytosolic iron deficiency with mitochondrial excess Fe(II), which further sensitized HeLa cells to RSL3-induced ferroptosis. In conclusion, we discovered a novel pathway of iron entry into mitochondria from cytosol through PCBP2-TOM20-SFXN3 axis.
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Affiliation(s)
- Danyang Mi
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Izumi Yanatori
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hao Zheng
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yingyi Kong
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tasuku Hirayama
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, Gifu, Japan
| | - Shinya Toyokuni
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Center for Low-temperature Plasma Sciences, Nagoya University, Nagoya, Japan
- Center for Integrated Sciences of Low-temperature Plasma Core Research (iPlasma Core), Tokai National Higher Education and Research System, Nagoya, Japan
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8
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Rincon Sabatino S, Sangaletti R, Griswold A, Dietrich WD, King CS, Rajguru SM. Transcriptional response to mild therapeutic hypothermia in noise-induced cochlear injury. Front Neurosci 2024; 17:1296475. [PMID: 38298897 PMCID: PMC10827921 DOI: 10.3389/fnins.2023.1296475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/18/2023] [Indexed: 02/02/2024] Open
Abstract
Introduction Prevention or treatment for acoustic injury has been met with many translational challenges, resulting in the absence of FDA-approved interventions. Localized hypothermia following noise exposure mitigates acute cochlear injury and may serve as a potential avenue for therapeutic approaches. However, the mechanisms by which hypothermia results in therapeutic improvements are poorly understood. Methods This study performs the transcriptomic analysis of cochleae from juvenile rats that experienced noise-induced hearing loss (NIHL) followed by hypothermia or control normothermia treatment. Results Differential gene expression results from RNA sequencing at 24 h post-exposure to noise suggest that NIHL alone results in increased inflammatory and immune defense responses, involving complement activation and cytokine-mediated signaling. Hypothermia treatment post-noise, in turn, may mitigate the acute inflammatory response. Discussion This study provides a framework for future research to optimize hypothermic intervention for ameliorating hearing loss and suggests additional pathways that could be targeted for NIHL therapeutic intervention.
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Affiliation(s)
| | - Rachele Sangaletti
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
| | - Anthony Griswold
- Department of Human Genetics, University of Miami, Coral Gables, FL, United States
| | - W. Dalton Dietrich
- The Miami Project to Cure Paralysis, University of Miami, Coral Gables, FL, United States
| | | | - Suhrud M. Rajguru
- Department of Biomedical Engineering, University of Miami, Coral Gables, FL, United States
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
- The Miami Project to Cure Paralysis, University of Miami, Coral Gables, FL, United States
- RestorEar Devices LLC, Bozeman, MT, United States
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9
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Warren B, Eberl D. What can insects teach us about hearing loss? J Physiol 2024; 602:297-316. [PMID: 38128023 DOI: 10.1113/jp281281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Over the last three decades, insects have been utilized to provide a deep and fundamental understanding of many human diseases and disorders. Here, we present arguments for insects as models to understand general principles underlying hearing loss. Despite ∼600 million years since the last common ancestor of vertebrates and invertebrates, we share an overwhelming degree of genetic homology particularly with respect to auditory organ development and maintenance. Despite the anatomical differences between human and insect auditory organs, both share physiological principles of operation. We explain why these observations are expected and highlight areas in hearing loss research in which insects can provide insight. We start by briefly introducing the evolutionary journey of auditory organs, the reasons for using insect auditory organs for hearing loss research, and the tools and approaches available in insects. Then, the first half of the review focuses on auditory development and auditory disorders with a genetic cause. The second half analyses the physiological and genetic consequences of ageing and short- and long-term changes as a result of noise exposure. We finish with complex age and noise interactions in auditory systems. In this review, we present some of the evidence and arguments to support the use of insects to study mechanisms and potential treatments for hearing loss in humans. Obviously, insects cannot fully substitute for all aspects of human auditory function and loss of function, although there are many important questions that can be addressed in an animal model for which there are important ethical, practical and experimental advantages.
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Affiliation(s)
- Ben Warren
- Neurogenetics Group, College of Life Sciences, University of Leicester, Leicester, UK
| | - Daniel Eberl
- Department of Biology, University of Iowa, Iowa City, IA, USA
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10
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Papin M, Bouchet AM, Chantôme A, Vandier C. Ether-lipids and cellular signaling: A differential role of alkyl- and alkenyl-ether-lipids? Biochimie 2023; 215:50-59. [PMID: 37678745 DOI: 10.1016/j.biochi.2023.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/17/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023]
Abstract
Ether-lipids (EL) are specific lipids bearing a characteristic sn-1 ether bond. Depending on the ether or vinyl-ether nature of this bond, they are present as alkyl- or alkenyl-EL, respectively. Among EL, alkenyl-EL, also referred as plasmalogens in the literature, attract most of the scientific interest as they are the predominant EL species in eukaryotic cells, thus less is known about alkyl-EL. EL have been implicated in various signaling pathways and alterations in their quantity are frequently observed in pathologies such as neurodegenerative and cardiovascular diseases or cancer. However, it remains unknown whether both alkyl- and alkenyl-EL play the same roles in these processes. This review summarizes the roles and mechanisms of action of EL in cellular signaling and tries to discriminate between alkyl- and alkenyl-EL. We also focus on the involvement of EL-mediated alterations of cellular signaling in diseases and discuss the potential interest for EL in therapy.
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Affiliation(s)
- Marion Papin
- Nutrition, Croissance, Cancer (N2C) UMR 1069, University of Tours, INSERM, 37000, Tours, France.
| | | | - Aurélie Chantôme
- Nutrition, Croissance, Cancer (N2C) UMR 1069, University of Tours, INSERM, 37000, Tours, France
| | - Christophe Vandier
- Nutrition, Croissance, Cancer (N2C) UMR 1069, University of Tours, INSERM, 37000, Tours, France; Lifesome Therapeutics, López de Hoyos 42, 28006, Madrid, Spain
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11
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Lewis MA, Schulte J, Matthews L, Vaden KI, Steves CJ, Williams FMK, Schulte BA, Dubno JR, Steel KP. Accurate phenotypic classification and exome sequencing allow identification of novel genes and variants associated with adult-onset hearing loss. PLoS Genet 2023; 19:e1011058. [PMID: 38011198 PMCID: PMC10718637 DOI: 10.1371/journal.pgen.1011058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/13/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
Adult-onset progressive hearing loss is a common, complex disease with a strong genetic component. Although to date over 150 genes have been identified as contributing to human hearing loss, many more remain to be discovered, as does most of the underlying genetic diversity. Many different variants have been found to underlie adult-onset hearing loss, but they tend to be rare variants with a high impact upon the gene product. It is likely that combinations of more common, lower impact variants also play a role in the prevalence of the disease. Here we present our exome study of hearing loss in a cohort of 532 older adult volunteers with extensive phenotypic data, including 99 older adults with normal hearing, an important control set. Firstly, we carried out an outlier analysis to identify genes with a high variant load in older adults with hearing loss compared to those with normal hearing. Secondly, we used audiometric threshold data to identify individual variants which appear to contribute to different threshold values. We followed up these analyses in a second cohort. Using these approaches, we identified genes and variants linked to better hearing as well as those linked to worse hearing. These analyses identified some known deafness genes, demonstrating proof of principle of our approach. However, most of the candidate genes are novel associations with hearing loss. While the results support the suggestion that genes responsible for severe deafness may also be involved in milder hearing loss, they also suggest that there are many more genes involved in hearing which remain to be identified. Our candidate gene lists may provide useful starting points for improved diagnosis and drug development.
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Affiliation(s)
- Morag A. Lewis
- Wolfson Centre for Age-Related Diseases, King’s College London, United Kingdom
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Jennifer Schulte
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Lois Matthews
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Kenneth I. Vaden
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Claire J. Steves
- Department of Twin Research and Genetic Epidemiology, King’s College London, School of Life Course and Population Sciences, London, United Kingdom
| | - Frances M. K. Williams
- Department of Twin Research and Genetic Epidemiology, King’s College London, School of Life Course and Population Sciences, London, United Kingdom
| | - Bradley A. Schulte
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Judy R. Dubno
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King’s College London, United Kingdom
- The Medical University of South Carolina, Charleston, South Carolina, United States of America
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Martelletti E, Ingham NJ, Steel KP. Reversal of an existing hearing loss by gene activation in Spns2 mutant mice. Proc Natl Acad Sci U S A 2023; 120:e2307355120. [PMID: 37552762 PMCID: PMC10450448 DOI: 10.1073/pnas.2307355120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/06/2023] [Indexed: 08/10/2023] Open
Abstract
Hearing loss is highly heterogeneous, but one common form involves a failure to maintain the local ionic environment of the sensory hair cells reflected in a reduced endocochlear potential. We used a genetic approach to ask whether this type of pathology can be reversed, using the Spns2tm1a mouse mutant known to show this defect. By activating Spns2 gene transcription at different ages after the onset of hearing loss, we found that an existing auditory impairment can be reversed to give close to normal thresholds for an auditory brainstem response (ABR), at least at low to mid stimulus frequencies. Delaying the activation of Spns2 led to less effective recovery of ABR thresholds, suggesting that there is a critical period for intervention. Early activation of Spns2 not only led to improvement in auditory function but also to protection of sensory hair cells from secondary degeneration. The genetic approach we have used to establish that this type of hearing loss is in principle reversible could be extended to many other diseases using available mouse resources.
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Affiliation(s)
- Elisa Martelletti
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, LondonSE1 1UL, United Kingdom
| | - Neil J. Ingham
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, LondonSE1 1UL, United Kingdom
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, LondonSE1 1UL, United Kingdom
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13
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Lachgar-Ruiz M, Morín M, Martelletti E, Ingham NJ, Preite L, Lewis MA, Serrão de Castro LS, Steel KP, Moreno-Pelayo MÁ. Insights into the pathophysiology of DFNA44 hearing loss associated with CCDC50 frameshift variants. Dis Model Mech 2023; 16:dmm049757. [PMID: 37165931 PMCID: PMC10445743 DOI: 10.1242/dmm.049757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 05/02/2023] [Indexed: 05/12/2023] Open
Abstract
Non-syndromic sensorineural hearing loss (SNHL) is the most common sensory disorder, and it presents a high genetic heterogeneity. As part of our clinical genetic studies, we ascertained a previously unreported mutation in CCDC50 [c.828_858del, p.(Asp276Glufs*40)] segregating with hearing impairment in a Spanish family with SNHL associated with the autosomal dominant deafness locus DFNA44, which is predicted to disrupt protein function. To gain insight into the mechanism behind DFNA44 mutations, we analysed two Ccdc50 presumed loss-of-function mouse mutants, which showed normal hearing thresholds up to 6 months of age, indicating that haploinsufficiency is unlikely to be the pathogenic mechanism. We then carried out in vitro studies on a set of artificial mutants and on the p.(Asp276Glufs*40) and p.(Phe292Hisfs*37) human mutations, and determined that only the mutants containing the six-amino-acid sequence CLENGL as part of their aberrant protein tail showed an abnormal distribution consisting of perinuclear aggregates of the CCDC50 protein (also known as Ymer). Therefore, we conclude that the CLENGL sequence is necessary to form these aggregates. Taken together, the in vivo and in vitro results obtained in this study suggest that the two identified mutations in CCDC50 exert their effect through a dominant-negative or gain-of-function mechanism rather than by haploinsufficiency.
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Affiliation(s)
- María Lachgar-Ruiz
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
| | - Matías Morín
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
| | - Elisa Martelletti
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Neil J. Ingham
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Lorenzo Preite
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Morag A. Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Luciana Santos Serrão de Castro
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Miguel Ángel Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
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14
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Denommé-Pichon AS, Collins SC, Bruel AL, Mikhaleva A, Wagner C, Vancollie VE, Thomas Q, Chevarin M, Weber M, Prada CE, Overs A, Palomares-Bralo M, Santos-Simarro F, Pacio-Míguez M, Busa T, Legius E, Bacino CA, Rosenfeld JA, Le Guyader G, Egloff M, Le Guillou X, Mencarelli MA, Renieri A, Grosso S, Levy J, Dozières B, Desguerre I, Vitobello A, Duffourd Y, Lelliott CJ, Thauvin-Robinet C, Philippe C, Faivre L, Yalcin B. YWHAE loss of function causes a rare neurodevelopmental disease with brain abnormalities in human and mouse. Genet Med 2023; 25:100835. [PMID: 36999555 DOI: 10.1016/j.gim.2023.100835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
PURPOSE Miller-Dieker syndrome is caused by a multiple gene deletion, including PAFAH1B1 and YWHAE. Although deletion of PAFAH1B1 causes lissencephaly unambiguously, deletion of YWHAE alone has not clearly been linked to a human disorder. METHODS Cases with YWHAE variants were collected through international data sharing networks. To address the specific impact of YWHAE loss of function, we phenotyped a mouse knockout of Ywhae. RESULTS We report a series of 10 individuals with heterozygous loss-of-function YWHAE variants (3 single-nucleotide variants and 7 deletions <1 Mb encompassing YWHAE but not PAFAH1B1), including 8 new cases and 2 follow-ups, added with 5 cases (copy number variants) from literature review. Although, until now, only 1 intragenic deletion has been described in YWHAE, we report 4 new variants specifically in YWHAE (3 splice variants and 1 intragenic deletion). The most frequent manifestations are developmental delay, delayed speech, seizures, and brain malformations, including corpus callosum hypoplasia, delayed myelination, and ventricular dilatation. Individuals with variants affecting YWHAE alone have milder features than those with larger deletions. Neuroanatomical studies in Ywhae-/- mice revealed brain structural defects, including thin cerebral cortex, corpus callosum dysgenesis, and hydrocephalus paralleling those seen in humans. CONCLUSION This study further demonstrates that YWHAE loss-of-function variants cause a neurodevelopmental disease with brain abnormalities.
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Affiliation(s)
- Anne-Sophie Denommé-Pichon
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France; European Reference Network, ERN-ITHACA.
| | - Stephan C Collins
- UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Ange-Line Bruel
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Anna Mikhaleva
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | | | - Quentin Thomas
- UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France; Department of Neurology, Dijon Bourgogne University Hospital, Dijon, France
| | - Martin Chevarin
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Mathys Weber
- UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France; Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and GIMI Institute, Dijon Bourgogne University Hospital, Dijon, France
| | - Carlos E Prada
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Alexis Overs
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - María Palomares-Bralo
- European Reference Network, ERN-ITHACA; Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Autonomous University of Madrid, IdiPAZ, Madrid, Spain; Rare Diseases Networking Biomedical Research Centre (CIBERER), Carlos III Institute, Madrid, Spain
| | - Fernando Santos-Simarro
- European Reference Network, ERN-ITHACA; Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Autonomous University of Madrid, IdiPAZ, Madrid, Spain; Rare Diseases Networking Biomedical Research Centre (CIBERER), Carlos III Institute, Madrid, Spain
| | - Marta Pacio-Míguez
- Rare Diseases Networking Biomedical Research Centre (CIBERER), Carlos III Institute, Madrid, Spain
| | - Tiffany Busa
- Department of Medical Genetics, CHU Timone Enfants, AP-HM, Marseille, France
| | - Eric Legius
- Laboratory for Neurofibromatosis Research, Department of Human Genetics, KU Leuven University Hospital, Belgium
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Baylor Genetics Laboratories, Houston, TX
| | - Gwenaël Le Guyader
- Genetics Department, Poitiers University Hospital, Poitiers, France; University of Poitiers, Poitiers, France
| | - Matthieu Egloff
- Genetics Department, Poitiers University Hospital, Poitiers, France; University of Poitiers, Poitiers, France; Experimental and Clinical Neurosciences Laboratory, INSERM, University of Poitiers, Poitiers, France
| | - Xavier Le Guillou
- Genetics Department, Poitiers University Hospital, Poitiers, France; University of Poitiers, Poitiers, France
| | | | - Alessandra Renieri
- Medical Genetics, Azienda Ospedaliero-Universitaria Senese, Siena, Italy; Medical Genetics, University of Siena, Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Salvatore Grosso
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy; U.O.C. Pediatria, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Jonathan Levy
- Genetics Department, Robert-Debré University Hospital, APHP, Paris, France
| | - Blandine Dozières
- Department of Pediatric Neurology and Metabolic Diseases, Robert Debré University Hospital, APHP, Paris, France
| | - Isabelle Desguerre
- Departments of Pediatric Neurology and Medical Genetics, Hôpital Necker-Enfants Malades, Université Paris Cité, Paris, France
| | - Antonio Vitobello
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France; European Reference Network, ERN-ITHACA
| | - Yannis Duffourd
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France
| | | | - Christel Thauvin-Robinet
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France; Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and GIMI Institute, Dijon Bourgogne University Hospital, Dijon, France
| | - Christophe Philippe
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France; European Reference Network, ERN-ITHACA; Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and GIMI Institute, Dijon Bourgogne University Hospital, Dijon, France
| | - Binnaz Yalcin
- UMR1231 GAD "Génétique des Anomalies du Développement", INSERM, FHU-TRANSLAD, University of Burgundy, Dijon, France.
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15
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Vijayakumar S, DiGuiseppi JA, Dabestani J, Ryan WG, Vielman Quevedo R, Li Y, Diers J, Tu S, Fleegel J, Nguyen C, Rhoda LM, Imami AS, Hamoud AAR, Lovas S, McCullumsmith R, Zallocchi M, Zuo J. In Silico Transcriptome-based Screens Identify Epidermal Growth Factor Receptor Inhibitors as Therapeutics for Noise-induced Hearing Loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544128. [PMID: 37333346 PMCID: PMC10274759 DOI: 10.1101/2023.06.07.544128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Noise-Induced Hearing Loss (NIHL) represents a widespread disease for which no therapeutics have been approved by the Food and Drug Administration (FDA). Addressing the conspicuous void of efficacious in vitro or animal models for high throughput pharmacological screening, we utilized an in silico transcriptome-oriented drug screening strategy, unveiling 22 biological pathways and 64 promising small molecule candidates for NIHL protection. Afatinib and zorifertinib, both inhibitors of the Epidermal Growth Factor Receptor (EGFR), were validated for their protective efficacy against NIHL in experimental zebrafish and murine models. This protective effect was further confirmed with EGFR conditional knockout mice and EGF knockdown zebrafish, both demonstrating protection against NIHL. Molecular analysis using Western blot and kinome signaling arrays on adult mouse cochlear lysates unveiled the intricate involvement of several signaling pathways, with particular emphasis on EGFR and its downstream pathways being modulated by noise exposure and Zorifertinib treatment. Administered orally, Zorifertinib was successfully detected in the perilymph fluid of the inner ear in mice with favorable pharmacokinetic attributes. Zorifertinib, in conjunction with AZD5438 - a potent inhibitor of cyclin dependent kinase 2 - produced synergistic protection against NIHL in the zebrafish model. Collectively, our findings underscore the potential application of in silico transcriptome-based drug screening for diseases bereft of efficient screening models and posit EGFR inhibitors as promising therapeutic agents warranting clinical exploration for combatting NIHL. Highlights In silico transcriptome-based drug screens identify pathways and drugs against NIHL.EGFR signaling is activated by noise but reduced by zorifertinib in mouse cochleae.Afatinib, zorifertinib and EGFR knockout protect against NIHL in mice and zebrafish.Orally delivered zorifertinib has inner ear PK and synergizes with a CDK2 inhibitor.
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16
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Lewis MA, Schulte J, Matthews L, Vaden KI, Steves CJ, Williams FMK, Schulte BA, Dubno JR, Steel KP. Accurate phenotypic classification and exome sequencing allow identification of novel genes and variants associated with adult-onset hearing loss. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.27.23289040. [PMID: 37163093 PMCID: PMC10168485 DOI: 10.1101/2023.04.27.23289040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Adult-onset progressive hearing loss is a common, complex disease with a strong genetic component. Although to date over 150 genes have been identified as contributing to human hearing loss, many more remain to be discovered, as does most of the underlying genetic diversity. Many different variants have been found to underlie adult-onset hearing loss, but they tend to be rare variants with a high impact upon the gene product. It is likely that combinations of more common, lower impact variants also play a role in the prevalence of the disease. Here we present our exome study of hearing loss in a cohort of 532 older adult volunteers with extensive phenotypic data, including 99 older adults with normal hearing, an important control set. Firstly, we carried out an outlier analysis to identify genes with a high variant load in older adults with hearing loss compared to those with normal hearing. Secondly, we used audiometric threshold data to identify individual variants which appear to contribute to different threshold values. We followed up these analyses in a second cohort. Using these approaches, we identified genes and variants linked to better hearing as well as those linked to worse hearing. These analyses identified some known deafness genes, demonstrating proof of principle of our approach. However, most of the candidate genes are novel associations with hearing loss. While the results support the suggestion that genes responsible for severe deafness may also be involved in milder hearing loss, they also suggest that there are many more genes involved in hearing which remain to be identified. Our candidate gene lists may provide useful starting points for improved diagnosis and drug development.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, SE1 1UL, UK
- The Medical University of South Carolina, SC, USA
| | | | | | | | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, School of Life Course and Population Sciences, London, UK
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, School of Life Course and Population Sciences, London, UK
| | | | - Judy R Dubno
- The Medical University of South Carolina, SC, USA
| | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, SE1 1UL, UK
- The Medical University of South Carolina, SC, USA
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17
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Lackner K, Sailer S, van Klinken JB, Wever E, Pras-Raves ML, Dane AD, Honsho M, Abe Y, Keller MA, Golderer G, Werner-Felmayer G, Fujiki Y, Vaz FM, Werner ER, Watschinger K. Alterations in ether lipid metabolism and the consequences for the mouse lipidome. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159285. [PMID: 36690320 DOI: 10.1016/j.bbalip.2023.159285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/18/2022] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
Alkylglycerol monooxygenase (AGMO) and plasmanylethanolamine desaturase (PEDS1) are enzymes involved in ether lipid metabolism. While AGMO degrades plasmanyl lipids by oxidative cleavage of the ether bond, PEDS1 exclusively synthesizes a specific subclass of ether lipids, the plasmalogens, by introducing a vinyl ether double bond into plasmanylethanolamine phospholipids. Ether lipids are characterized by an ether linkage at the sn-1 position of the glycerol backbone and they are found in membranes of different cell types. Decreased plasmalogen levels have been associated with neurological diseases like Alzheimer's disease. Agmo-deficient mice do not present an obvious phenotype under unchallenged conditions. In contrast, Peds1 knockout mice display a growth phenotype. To investigate the molecular consequences of Agmo and Peds1 deficiency on the mouse lipidome, five tissues from each mouse model were isolated and subjected to high resolution mass spectrometry allowing the characterization of up to 2013 lipid species from 42 lipid subclasses. Agmo knockout mice moderately accumulated plasmanyl and plasmenyl lipid species. Peds1-deficient mice manifested striking changes characterized by a strong reduction of plasmenyl lipids and a concomitant massive accumulation of plasmanyl lipids resulting in increased total ether lipid levels in the analyzed tissues except for the class of phosphatidylethanolamines where total levels remained remarkably constant also in Peds1 knockout mice. The rate-limiting enzyme in ether lipid metabolism, FAR1, was not upregulated in Peds1-deficient mice, indicating that the selective loss of plasmalogens is not sufficient to activate the feedback mechanism observed in total ether lipid deficiency.
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Affiliation(s)
- Katharina Lackner
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria.
| | - Sabrina Sailer
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria; Institute of Human Genetics, Medical University of Innsbruck, Peter-Mayr-Strasse 1, 6020 Innsbruck, Austria.
| | - Jan-Bert van Klinken
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Department of Human Genetics, Leiden University Medical Center (LUMC), Einthovenweg 20, Leiden, 2333, ZC, the Netherlands.
| | - Eric Wever
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Bioinformatics Laboratory, Department of Epidemiology & Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands.
| | - Mia L Pras-Raves
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Bioinformatics Laboratory, Department of Epidemiology & Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands.
| | - Adrie D Dane
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Bioinformatics Laboratory, Department of Epidemiology & Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands.
| | - Masanori Honsho
- Department of Neuroinflammation and Brain Fatigue Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan.
| | - Yuichi Abe
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan.
| | - Markus A Keller
- Institute of Human Genetics, Medical University of Innsbruck, Peter-Mayr-Strasse 1, 6020 Innsbruck, Austria.
| | - Georg Golderer
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria.
| | - Gabriele Werner-Felmayer
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria.
| | - Yukio Fujiki
- Institute of Rheological Functions of Food, Kyushu University Collaboration Program, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan; Graduate School of Science, University of Hyogo, Hyogo, Japan.
| | - Frédéric M Vaz
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam 1105, AZ, The Netherlands.
| | - Ernst R Werner
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria.
| | - Katrin Watschinger
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria.
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Chiereghin C, Robusto M, Lewis MA, Caetano S, Massa V, Castorina P, Ambrosetti U, Steel KP, Duga S, Asselta R, Soldà G. In-depth genetic and molecular characterization of diaphanous related formin 2 (DIAPH2) and its role in the inner ear. PLoS One 2023; 18:e0273586. [PMID: 36689403 PMCID: PMC9870134 DOI: 10.1371/journal.pone.0273586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Diaphanous related formins are regulatory cytoskeletal protein involved in actin elongation and microtubule stabilization. In humans, defects in two of the three diaphanous genes (DIAPH1 and DIAPH3) have been associated with different types of hearing loss. Here, we investigate the role of the third member of the family, DIAPH2, in nonsyndromic hearing loss, prompted by the identification, by exome sequencing, of a predicted pathogenic missense variant in DIAPH2. This variant occurs at a conserved site and segregated with nonsyndromic X-linked hearing loss in an Italian family. Our immunohistochemical studies indicated that the mouse ortholog protein Diaph2 is expressed during development in the cochlea, specifically in the actin-rich stereocilia of the sensory outer hair cells. In-vitro studies showed a functional impairment of the mutant DIAPH2 protein upon RhoA-dependent activation. Finally, Diaph2 knock-out and knock-in mice were generated by CRISPR/Cas9 technology and auditory brainstem response measurements performed at 4, 8 and 14 weeks. However, no hearing impairment was detected. Our findings indicate that DIAPH2 may play a role in the inner ear; further studies are however needed to clarify the contribution of DIAPH2 to deafness.
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Affiliation(s)
| | - Michela Robusto
- Experimental Therapeutics Program, IFOM ETS -The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Morag A. Lewis
- Wolfson Centre for Age-Related Diseases, King’s College London, London, United Kingdom
| | - Susana Caetano
- Wolfson Centre for Age-Related Diseases, King’s College London, London, United Kingdom
| | - Valentina Massa
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | | | - Umberto Ambrosetti
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano and Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, UO Audiologia, Milano, Italy
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King’s College London, London, United Kingdom
| | - Stefano Duga
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
- Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Milan, Italy
| | - Rosanna Asselta
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
- Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Milan, Italy
| | - Giulia Soldà
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
- Humanitas University, Department of Biomedical Sciences, Pieve Emanuele, Milan, Italy
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19
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Groza T, Gomez FL, Mashhadi HH, Muñoz-Fuentes V, Gunes O, Wilson R, Cacheiro P, Frost A, Keskivali-Bond P, Vardal B, McCoy A, Cheng TK, Santos L, Wells S, Smedley D, Mallon AM, Parkinson H. The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease. Nucleic Acids Res 2023; 51:D1038-D1045. [PMID: 36305825 PMCID: PMC9825559 DOI: 10.1093/nar/gkac972] [Citation(s) in RCA: 128] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/05/2022] [Accepted: 10/14/2022] [Indexed: 01/30/2023] Open
Abstract
The International Mouse Phenotyping Consortium (IMPC; https://www.mousephenotype.org/) web portal makes available curated, integrated and analysed knockout mouse phenotyping data generated by the IMPC project consisting of 85M data points and over 95,000 statistically significant phenotype hits mapped to human diseases. The IMPC portal delivers a substantial reference dataset that supports the enrichment of various domain-specific projects and databases, as well as the wider research and clinical community, where the IMPC genotype-phenotype knowledge contributes to the molecular diagnosis of patients affected by rare disorders. Data from 9,000 mouse lines and 750 000 images provides vital resources enabling the interpretation of the ignorome, and advancing our knowledge on mammalian gene function and the mechanisms underlying phenotypes associated with human diseases. The resource is widely integrated and the lines have been used in over 4,600 publications indicating the value of the data and the materials.
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Affiliation(s)
- Tudor Groza
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Federico Lopez Gomez
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Hamed Haseli Mashhadi
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Violeta Muñoz-Fuentes
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Osman Gunes
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Robert Wilson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
| | - Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Anthony Frost
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | | | - Bora Vardal
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Aaron McCoy
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Tsz Kwan Cheng
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Luis Santos
- Research Data Team, The Turing Institute, 96 Euston Rd, London NW1 2DB, UK
| | - Sara Wells
- Mary Lyon Centre at MRC Harwell, Harwell Campus OX11 7UE, UK
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Ann-Marie Mallon
- Research Data Team, The Turing Institute, 96 Euston Rd, London NW1 2DB, UK
| | - Helen Parkinson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Welcome Genome Campus, Hinxton CB10 1SD, UK
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20
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Thalmeier D, Miller G, Schneltzer E, Hurt A, Hrabě deAngelis M, Becker L, Müller CL, Maier H. Objective hearing threshold identification from auditory brainstem response measurements using supervised and self-supervised approaches. BMC Neurosci 2022; 23:81. [PMID: 36575380 PMCID: PMC9795643 DOI: 10.1186/s12868-022-00758-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 11/18/2022] [Indexed: 12/28/2022] Open
Abstract
Hearing loss is a major health problem and psychological burden in humans. Mouse models offer a possibility to elucidate genes involved in the underlying developmental and pathophysiological mechanisms of hearing impairment. To this end, large-scale mouse phenotyping programs include auditory phenotyping of single-gene knockout mouse lines. Using the auditory brainstem response (ABR) procedure, the German Mouse Clinic and similar facilities worldwide have produced large, uniform data sets of averaged ABR raw data of mutant and wildtype mice. In the course of standard ABR analysis, hearing thresholds are assessed visually by trained staff from series of signal curves of increasing sound pressure level. This is time-consuming and prone to be biased by the reader as well as the graphical display quality and scale.In an attempt to reduce workload and improve quality and reproducibility, we developed and compared two methods for automated hearing threshold identification from averaged ABR raw data: a supervised approach involving two combined neural networks trained on human-generated labels and a self-supervised approach, which exploits the signal power spectrum and combines random forest sound level estimation with a piece-wise curve fitting algorithm for threshold finding.We show that both models work well and are suitable for fast, reliable, and unbiased hearing threshold detection and quality control. In a high-throughput mouse phenotyping environment, both methods perform well as part of an automated end-to-end screening pipeline to detect candidate genes for hearing involvement. Code for both models as well as data used for this work are freely available.
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Affiliation(s)
- Dominik Thalmeier
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, München, Germany ,grid.4567.00000 0004 0483 2525Helmholtz AI, Helmholtz Zentrum München, München, Germany
| | - Gregor Miller
- grid.4567.00000 0004 0483 2525Institute of Experimental Genetics, Helmholtz Zentrum München, München, Germany
| | - Elida Schneltzer
- grid.4567.00000 0004 0483 2525Institute of Experimental Genetics, Helmholtz Zentrum München, München, Germany
| | - Anja Hurt
- grid.4567.00000 0004 0483 2525Institute of Experimental Genetics, Helmholtz Zentrum München, München, Germany
| | - Martin Hrabě deAngelis
- grid.4567.00000 0004 0483 2525Institute of Experimental Genetics, Helmholtz Zentrum München, München, Germany ,grid.452622.5German Center for Diabetes Research (DZD), Neuherberg, Germany ,grid.6936.a0000000123222966Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising, Germany
| | - Lore Becker
- grid.4567.00000 0004 0483 2525Institute of Experimental Genetics, Helmholtz Zentrum München, München, Germany
| | - Christian L. Müller
- grid.4567.00000 0004 0483 2525Institute of Computational Biology, Helmholtz Zentrum München, München, Germany ,grid.4567.00000 0004 0483 2525Helmholtz AI, Helmholtz Zentrum München, München, Germany ,grid.5252.00000 0004 1936 973XDepartment of Statistics, LMU München, München, Germany ,grid.430264.70000 0004 4648 6763Center for Computational Mathematics, Flatiron Institute, New York, USA
| | - Holger Maier
- grid.4567.00000 0004 0483 2525Institute of Experimental Genetics, Helmholtz Zentrum München, München, Germany
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21
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Mardani S, Almadani N, Garshasbi M. Compound heterozygous variants in SPNS2 cause sensorineural hearing loss. Eur J Med Genet 2022; 66:104658. [DOI: 10.1016/j.ejmg.2022.104658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022]
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22
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Gao G, Guo S, Zhang Q, Zhang H, Zhang C, Peng G. Kiaa1024L/Minar2 is essential for hearing by regulating cholesterol distribution in hair bundles. eLife 2022; 11:e80865. [PMID: 36317962 PMCID: PMC9714970 DOI: 10.7554/elife.80865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/31/2022] [Indexed: 12/05/2022] Open
Abstract
Unbiased genetic screens implicated a number of uncharacterized genes in hearing loss, suggesting some biological processes required for auditory function remain unexplored. Loss of Kiaa1024L/Minar2, a previously understudied gene, caused deafness in mice, but how it functioned in the hearing was unclear. Here, we show that disruption of kiaa1024L/minar2 causes hearing loss in the zebrafish. Defects in mechanotransduction, longer and thinner hair bundles, and enlarged apical lysosomes in hair cells are observed in the kiaa1024L/minar2 mutant. In cultured cells, Kiaa1024L/Minar2 is mainly localized to lysosomes, and its overexpression recruits cholesterol and increases cholesterol labeling. Strikingly, cholesterol is highly enriched in the hair bundle membrane, and loss of kiaa1024L/minar2 reduces cholesterol localization to the hair bundles. Lowering cholesterol levels aggravates, while increasing cholesterol levels rescues the hair cell defects in the kiaa1024L/minar2 mutant. Therefore, cholesterol plays an essential role in hair bundles, and Kiaa1024L/Minar2 regulates cholesterol distribution and homeostasis to ensure normal hearing.
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Affiliation(s)
- Ge Gao
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan UniversityShanghaiChina
| | - Shuyu Guo
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan UniversityShanghaiChina
| | - Quan Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan UniversityShanghaiChina
| | - Hefei Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan UniversityShanghaiChina
| | - Cuizhen Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan UniversityShanghaiChina
| | - Gang Peng
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan UniversityShanghaiChina
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23
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Induced Pluripotent Stem Cells, a Stepping Stone to In Vitro Human Models of Hearing Loss. Cells 2022; 11:cells11203331. [PMID: 36291196 PMCID: PMC9600035 DOI: 10.3390/cells11203331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 10/05/2022] [Accepted: 10/14/2022] [Indexed: 11/28/2022] Open
Abstract
Hearing loss is the most prevalent sensorineural impairment in humans. Yet despite very active research, no effective therapy other than the cochlear implant has reached the clinic. Main reasons for this failure are the multifactorial nature of the disorder, its heterogeneity, and a late onset that hinders the identification of etiological factors. Another problem is the lack of human samples such that practically all the work has been conducted on animals. Although highly valuable data have been obtained from such models, there is the risk that inter-species differences exist that may compromise the relevance of the gathered data. Human-based models are therefore direly needed. The irruption of human induced pluripotent stem cell technologies in the field of hearing research offers the possibility to generate an array of otic cell models of human origin; these may enable the identification of guiding signalling cues during inner ear development and of the mechanisms that lead from genetic alterations to pathology. These models will also be extremely valuable when conducting ototoxicity analyses and when exploring new avenues towards regeneration in the inner ear. This review summarises some of the work that has already been conducted with these cells and contemplates future possibilities.
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24
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Kochaj RM, Martelletti E, Ingham NJ, Buniello A, Sousa BC, Wakelam MJO, Lopez-Clavijo AF, Steel KP. The Effect of a Pex3 Mutation on Hearing and Lipid Content of the Inner Ear. Cells 2022; 11:cells11203206. [PMID: 36291074 PMCID: PMC9600510 DOI: 10.3390/cells11203206] [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: 08/19/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
Peroxisome biogenesis disorders (due to PEX gene mutations) are associated with symptoms that range in severity and can lead to early childhood death, but a common feature is hearing impairment. In this study, mice carrying Pex3 mutations were found to show normal auditory development followed by an early-onset progressive increase in auditory response thresholds. The only structural defect detected in the cochlea at four weeks old was the disruption of synapses below inner hair cells. A conditional approach was used to establish that Pex3 expression is required locally within the cochlea for normal hearing, rather than hearing loss being due to systemic effects. A lipidomics analysis of the inner ear revealed a local reduction in plasmalogens in the Pex3 mouse mutants, comparable to the systemic plasmalogen reduction reported in human peroxisome biogenesis disorders. Thus, mice with Pex3 mutations may be a useful tool to understand the physiological basis of peroxisome biogenesis disorders.
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Affiliation(s)
- Rafael M. Kochaj
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, UK
| | - Elisa Martelletti
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, UK
| | - Neil J. Ingham
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, UK
| | - Annalisa Buniello
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, UK
| | - Bebiana C. Sousa
- Lipidomics Facility, The BBSRC Babraham Institute, Cambridge CB22 3AT, UK
| | | | | | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, London SE1 1UL, UK
- Correspondence:
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25
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Taiber S, Gozlan O, Cohen R, Andrade LR, Gregory EF, Starr DA, Moran Y, Hipp R, Kelley MW, Manor U, Sprinzak D, Avraham KB. A Nesprin-4/kinesin-1 cargo model for nuclear positioning in cochlear outer hair cells. Front Cell Dev Biol 2022; 10:974168. [PMID: 36211453 PMCID: PMC9537699 DOI: 10.3389/fcell.2022.974168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/07/2022] [Indexed: 11/14/2022] Open
Abstract
Nuclear positioning is important for the functionality of many cell types and is mediated by interactions of cytoskeletal elements and nucleoskeleton proteins. Nesprin proteins, part of the linker of nucleoskeleton and cytoskeleton (LINC) complex, have been shown to participate in nuclear positioning in multiple cell types. Outer hair cells (OHCs) in the inner ear are specialized sensory epithelial cells that utilize somatic electromotility to amplify auditory signals in the cochlea. Recently, Nesprin-4 (encoded by Syne4) was shown to play a crucial role in nuclear positioning in OHCs. Syne4 deficiency in humans and mice leads to mislocalization of the OHC nuclei and cell death resulting in deafness. However, it is unknown how Nesprin-4 mediates the position of the nucleus, and which other molecular components are involved in this process. Here, we show that the interaction of Nesprin-4 and the microtubule motor kinesin-1 is mediated by a conserved 4 amino-acid motif. Using in vivo AAV gene delivery, we show that this interaction is critical for nuclear positioning and hearing in mice. Nuclear mislocalization and cell death of OHCs coincide with the onset of hearing and electromotility and are solely restricted to outer, but not inner, hair cells. Likewise, the C. elegans functional homolog of Nesprin-4, UNC-83, uses a similar motif to mediate interactions between migrating nuclei and kinesin-1. Overall, our results suggest that OHCs require unique cellular machinery for proper nuclear positioning at the onset of electromotility. This machinery relies on the interaction between Nesprin-4 and kinesin-1 motors supporting a microtubule cargo model for nuclear positioning.
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Affiliation(s)
- Shahar Taiber
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel,School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Oren Gozlan
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Roie Cohen
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Leonardo R. Andrade
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Ellen F. Gregory
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Daniel A. Starr
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rebecca Hipp
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD, United States
| | - Matthew W. Kelley
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD, United States
| | - Uri Manor
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - David Sprinzak
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel,*Correspondence: David Sprinzak, ; Karen B. Avraham,
| | - Karen B. Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel,*Correspondence: David Sprinzak, ; Karen B. Avraham,
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Imtiaz A. ARNSHL gene identification: past, present and future. Mol Genet Genomics 2022; 297:1185-1193. [DOI: 10.1007/s00438-022-01926-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 07/05/2022] [Indexed: 10/16/2022]
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Mutations in MINAR2 encoding membrane integral NOTCH2-associated receptor 2 cause deafness in humans and mice. Proc Natl Acad Sci U S A 2022; 119:e2204084119. [PMID: 35727972 PMCID: PMC9245706 DOI: 10.1073/pnas.2204084119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Discovery of deafness genes and elucidating their functions have substantially contributed to our understanding of hearing physiology and its pathologies. Here we report on DNA variants in MINAR2, encoding membrane integral NOTCH2-associated receptor 2, in four families underlying autosomal recessive nonsyndromic deafness. Neurologic evaluation of affected individuals at ages ranging from 4 to 80 y old does not show additional abnormalities. MINAR2 is a recently annotated gene with limited functional understanding. We detected three MINAR2 variants, c.144G > A (p.Trp48*), c.412_419delCGGTTTTG (p.Arg138Valfs*10), and c.393G > T, in 13 individuals with congenital- or prelingual-onset severe-to-profound sensorineural hearing loss (HL). The c.393G > T variant is shown to disrupt a splice donor site. We show that Minar2 is expressed in the mouse inner ear, with the protein localizing mainly in the hair cells, spiral ganglia, the spiral limbus, and the stria vascularis. Mice with loss of function of the Minar2 protein (Minar2tm1b/tm1b) present with rapidly progressive sensorineural HL associated with a reduction in outer hair cell stereocilia in the shortest row and degeneration of hair cells at a later age. We conclude that MINAR2 is essential for hearing in humans and mice and its disruption leads to sensorineural HL. Progressive HL observed in mice and in some affected individuals and as well as relative preservation of hair cells provides an opportunity to interfere with HL using genetic therapies.
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29
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Lewis MA, Schulte BA, Dubno JR, Steel KP. Investigating the characteristics of genes and variants associated with self-reported hearing difficulty in older adults in the UK Biobank. BMC Biol 2022; 20:150. [PMID: 35761239 PMCID: PMC9238072 DOI: 10.1186/s12915-022-01349-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Age-related hearing loss is a common, heterogeneous disease with a strong genetic component. More than 100 loci have been reported to be involved in human hearing impairment to date, but most of the genes underlying human adult-onset hearing loss remain unknown. Most genetic studies have focussed on very rare variants (such as family studies and patient cohort screens) or very common variants (genome-wide association studies). However, the contribution of variants present in the human population at intermediate frequencies is hard to quantify using these methods, and as a result, the landscape of variation associated with adult-onset hearing loss remains largely unknown. RESULTS Here we present a study based on exome sequencing and self-reported hearing difficulty in the UK Biobank, a large-scale biomedical database. We have carried out variant load analyses using different minor allele frequency and impact filters, and compared the resulting gene lists to a manually curated list of nearly 700 genes known to be involved in hearing in humans and/or mice. An allele frequency cutoff of 0.1, combined with a high predicted variant impact, was found to be the most effective filter setting for our analysis. We also found that separating the participants by sex produced markedly different gene lists. The gene lists obtained were investigated using gene ontology annotation, functional prioritisation and expression analysis, and this identified good candidates for further study. CONCLUSIONS Our results suggest that relatively common as well as rare variants with a high predicted impact contribute to age-related hearing impairment and that the genetic contributions to adult hearing difficulty may differ between the sexes. Our manually curated list of deafness genes is a useful resource for candidate gene prioritisation in hearing loss.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK.
| | | | - Judy R Dubno
- The Medical University of South Carolina, Charleston, SC, USA
| | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK
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O’Donnell J, Zheng J. Vestibular Hair Cells Require CAMSAP3, a Microtubule Minus-End Regulator, for Formation of Normal Kinocilia. Front Cell Neurosci 2022; 16:876805. [PMID: 35783105 PMCID: PMC9247359 DOI: 10.3389/fncel.2022.876805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022] Open
Abstract
Kinocilia are exceptionally long primary sensory cilia located on vestibular hair cells, which are essential for transmitting key signals that contribute to mammalian balance and overall vestibular system function. Kinocilia have a “9+2” microtubule (MT) configuration with nine doublet MTs surrounding two central singlet MTs. This is uncommon as most mammalian primary sensory cilia have a “9+0” configuration, in which the central MT pair is absent. It has yet to be determined what the function of the central MT pair is in kinocilia. Calmodulin-regulated spectrin-associated protein 3 (CAMSAP3) regulates the minus end of MTs and is essential for forming the central MT pair in motile cilia, which have the “9+2” configuration. To explore the role of the central MT pair in kinocilia, we created a conditional knockout model (cKO), Camsap3-cKO, which intended to eliminate CAMSAP3 in limited organs including the inner ear, olfactory bulb, and kidneys. Immunofluorescent staining of vestibular organs demonstrated that CAMSAP3 proteins were significantly reduced in Camsap3-cKO mice and that aged Camsap3-cKO mice had significantly shorter kinocilia than their wildtype littermates. Transmission electron microscopy showed that aged Camsap3-cKO mice were in fact missing that the central MT pair in kinocilia more often than their wildtype counterparts. In the examination of behavior, wildtype and Camsap3-cKO mice performed equally well on a swim assessment, right-reflex test, and evaluation of balance on a rotarod. However, Camsap3-cKO mice showed slightly altered gaits including reduced maximal rate of change of paw area and a smaller paw area in contact with the surface. Although Camsap3-cKO mice had no differences in olfaction from their wildtype counterparts, Camsap3-cKO mice did have kidney dysfunction that deteriorated their health. Thus, CAMSAP3 is important for establishing and/or maintaining the normal structure of kinocilia and kidney function but is not essential for normal olfaction. Our data supports our hypothesis that CAMSAP3 is critical for construction of the central MT pair in kinocilia, and that the central MT pair may be important for building long and stable axonemes in these kinocilia. Whether shorter kinocilia might lead to abnormal vestibular function and altered gaits in older Camsap3-cKO mice requires further investigation.
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Affiliation(s)
- Josephine O’Donnell
- Department of Otolaryngology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jing Zheng
- Department of Otolaryngology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Knowles Hearing Center, Northwestern University, Evanston, IL, United States
- *Correspondence: Jing Zheng,
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Maudoux A, Vitry S, El-Amraoui A. Vestibular Deficits in Deafness: Clinical Presentation, Animal Modeling, and Treatment Solutions. Front Neurol 2022; 13:816534. [PMID: 35444606 PMCID: PMC9013928 DOI: 10.3389/fneur.2022.816534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
The inner ear is responsible for both hearing and balance. These functions are dependent on the correct functioning of mechanosensitive hair cells, which convert sound- and motion-induced stimuli into electrical signals conveyed to the brain. During evolution of the inner ear, the major changes occurred in the hearing organ, whereas the structure of the vestibular organs remained constant in all vertebrates over the same period. Vestibular deficits are highly prevalent in humans, due to multiple intersecting causes: genetics, environmental factors, ototoxic drugs, infections and aging. Studies of deafness genes associated with balance deficits and their corresponding animal models have shed light on the development and function of these two sensory systems. Bilateral vestibular deficits often impair individual postural control, gaze stabilization, locomotion and spatial orientation. The resulting dizziness, vertigo, and/or falls (frequent in elderly populations) greatly affect patient quality of life. In the absence of treatment, prosthetic devices, such as vestibular implants, providing information about the direction, amplitude and velocity of body movements, are being developed and have given promising results in animal models and humans. Novel methods and techniques have led to major progress in gene therapies targeting the inner ear (gene supplementation and gene editing), 3D inner ear organoids and reprograming protocols for generating hair cell-like cells. These rapid advances in multiscale approaches covering basic research, clinical diagnostics and therapies are fostering interdisciplinary research to develop personalized treatments for vestibular disorders.
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Affiliation(s)
- Audrey Maudoux
- Unit Progressive Sensory Disorders, Pathophysiology and Therapy, Institut Pasteur, Institut de l'Audition, Université de Paris, INSERM-UMRS1120, Paris, France.,Center for Balance Evaluation in Children (EFEE), Otolaryngology Department, Assistance Publique des Hôpitaux de Paris, Robert-Debré University Hospital, Paris, France
| | - Sandrine Vitry
- Unit Progressive Sensory Disorders, Pathophysiology and Therapy, Institut Pasteur, Institut de l'Audition, Université de Paris, INSERM-UMRS1120, Paris, France
| | - Aziz El-Amraoui
- Unit Progressive Sensory Disorders, Pathophysiology and Therapy, Institut Pasteur, Institut de l'Audition, Université de Paris, INSERM-UMRS1120, Paris, France
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32
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Acharya A, Schrauwen I, Leal SM. Identification of autosomal recessive nonsyndromic hearing impairment genes through the study of consanguineous and non-consanguineous families: past, present, and future. Hum Genet 2022; 141:413-430. [PMID: 34291353 PMCID: PMC10416318 DOI: 10.1007/s00439-021-02309-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/24/2021] [Indexed: 10/20/2022]
Abstract
Hearing impairment (HI) is one of the most common sensory disabilities with exceptionally high genetic heterogeneity. Of genetic HI cases, 30% are syndromic and 70% are nonsyndromic. For nonsyndromic (NS) HI, 77% of the cases are due to autosomal recessive (AR) inheritance. ARNSHI is usually congenital/prelingual, severe-to-profound, affects all frequencies and is not progressive. Thus far, 73 ARNSHI genes have been identified. Populations with high rates of consanguinity have been crucial in the identification of ARNSHI genes, and 92% (67/73) of these genes were identified in consanguineous families. Recent changes in genomic technologies and analyses have allowed a shift towards ARNSHI gene discovery in outbred populations. The latter is crucial towards understanding the genetic architecture of ARNSHI in diverse and understudied populations. We present an overview of the 73 ARNSHI genes, the methods used to identify them, including next-generation sequencing which revolutionized the field, and new technologies that show great promise in advancing ARNSHI discoveries.
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Affiliation(s)
- Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA.
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA.
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33
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Lewis MA, Ingham NJ, Chen J, Pearson S, Di Domenico F, Rekhi S, Allen R, Drake M, Willaert A, Rook V, Pass J, Keane T, Adams DJ, Tucker AS, White JK, Steel KP. Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme. BMC Biol 2022; 20:67. [PMID: 35296311 PMCID: PMC8928630 DOI: 10.1186/s12915-022-01257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background Mice carrying targeted mutations are important for investigating gene function and the role of genes in disease, but off-target mutagenic effects associated with the processes of generating targeted alleles, for instance using Crispr, and culturing embryonic stem cells, offer opportunities for spontaneous mutations to arise. Identifying spontaneous mutations relies on the detection of phenotypes segregating independently of targeted alleles, and having a broad estimate of the level of mutations generated by intensive breeding programmes is difficult given that many phenotypes are easy to miss if not specifically looked for. Here we present data from a large, targeted knockout programme in which mice were analysed through a phenotyping pipeline. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Results Twenty-five lines out of 1311 displayed different deafness phenotypes that did not segregate with the targeted allele. We observed a variety of phenotypes by Auditory Brainstem Response (ABR) and behavioural assessment and isolated eight lines showing early-onset severe progressive hearing loss, later-onset progressive hearing loss, low frequency hearing loss, or complete deafness, with vestibular dysfunction. The causative mutations identified include deletions, insertions, and point mutations, some of which involve new genes not previously associated with deafness while others are new alleles of genes known to underlie hearing loss. Two of the latter show a phenotype much reduced in severity compared to other mutant alleles of the same gene. We investigated the ES cells from which these lines were derived and determined that only one of the 8 mutations could have arisen in the ES cell, and in that case, only after targeting. Instead, most of the non-segregating mutations appear to have occurred during breeding of mutant mice. In one case, the mutation arose within the wildtype colony used for expanding mutant lines. Conclusions Our data show that spontaneous mutations with observable effects on phenotype are a common side effect of intensive breeding programmes, including those underlying targeted mutation programmes. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01257-8.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England. .,Wellcome Sanger Institute, Hinxton, CB10 1SA, England.
| | - Neil J Ingham
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Jing Chen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | | | - Francesca Di Domenico
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Sohinder Rekhi
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Rochelle Allen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Matthew Drake
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Annelore Willaert
- Research Group of Experimental Oto-Rhino-Laryngology, Department of Neurosciences, KU Leuven - University of Leuven, Leuven, Belgium
| | - Victoria Rook
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Johanna Pass
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Thomas Keane
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - David J Adams
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Abigail S Tucker
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, England
| | | | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
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34
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The Road Traveled and Journey Ahead for the Genetics and Genomics of Tinnitus. Mol Diagn Ther 2022; 26:129-136. [PMID: 35167110 PMCID: PMC8942952 DOI: 10.1007/s40291-022-00578-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2022] [Indexed: 10/29/2022]
Abstract
The feasibility to unravel genetic and genomic signatures for disorders affecting the auditory system has accelerated since arriving in the post-genomics era roughly 20 years ago. Newly emerging studies have provided initial landmarks signaling heritability and thus, a genetic link, to severe tinnitus. Tinnitus, the phantom perception of ringing in the ears, is experienced by at least 15% of the adult population and can be extremely disabling. Despite its ubiquity, there is no cure for tinnitus and modalities offering relief are often of limited success. Because tinnitus is frequently reported in patients with acquired conductive or sensorineural hearing impairment, it has been widely accepted that tinnitus is secondary to and a symptom arising from hearing impairment. However, tinnitus has also been identified in the absence of auditory dysfunction and in young individuals, resulting in a debate about its origins. Genetics studies have identified severe tinnitus as a complex disorder arising from gene and environment interactions, refining its classification as a neurological disorder and, in at least a subset of patients, it appears not as a symptom of another health issue. This current opinion summarizes several recent studies that have challenged a long-accepted dogma and postulates how this information could eventually be used in the future to help patients. It is with great hope that this knowledge opens translational paths to provide relief for the many who suffer from the burden of tinnitus on a daily basis.
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Nolan LS, Chen J, Gonçalves AC, Bullen A, Towers ER, Steel KP, Dawson SJ, Gale JE. Targeted deletion of the RNA-binding protein Caprin1 leads to progressive hearing loss and impairs recovery from noise exposure in mice. Sci Rep 2022; 12:2444. [PMID: 35165318 PMCID: PMC8844073 DOI: 10.1038/s41598-022-05657-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022] Open
Abstract
Cell cycle associated protein 1 (Caprin1) is an RNA-binding protein that can regulate the cellular post-transcriptional response to stress. It is a component of both stress granules and neuronal RNA granules and is implicated in neurodegenerative disease, synaptic plasticity and long-term memory formation. Our previous work suggested that Caprin1 also plays a role in the response of the cochlea to stress. Here, targeted inner ear-deletion of Caprin1 in mice leads to an early onset, progressive hearing loss. Auditory brainstem responses from Caprin1-deficient mice show reduced thresholds, with a significant reduction in wave-I amplitudes compared to wildtype. Whilst hair cell structure and numbers were normal, the inner hair cell-spiral ganglion neuron (IHC-SGN) synapse revealed abnormally large post-synaptic GluA2 receptor puncta, a defect consistent with the observed wave-I reduction. Unlike wildtype mice, mild-noise-induced hearing threshold shifts in Caprin1-deficient mice did not recover. Oxidative stress triggered TIA-1/HuR-positive stress granule formation in ex-vivo cochlear explants from Caprin1-deficient mice, showing that stress granules could still be induced. Taken together, these findings suggest that Caprin1 plays a key role in maintenance of auditory function, where it regulates the normal status of the IHC-SGN synapse.
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Affiliation(s)
- Lisa S Nolan
- UCL Ear Institute, 332 Gray's Inn Road, London, WC1X 8EE, UK
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Jing Chen
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London, SE1 1UL, UK
| | | | - Anwen Bullen
- UCL Ear Institute, 332 Gray's Inn Road, London, WC1X 8EE, UK
| | - Emily R Towers
- UCL Ear Institute, 332 Gray's Inn Road, London, WC1X 8EE, UK
| | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Sally J Dawson
- UCL Ear Institute, 332 Gray's Inn Road, London, WC1X 8EE, UK.
| | - Jonathan E Gale
- UCL Ear Institute, 332 Gray's Inn Road, London, WC1X 8EE, UK.
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36
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CRISPR/Cas9-mediated pou4f3 knockout induces defects in the development of the zebrafish inner ear. JOURNAL OF BIO-X RESEARCH 2021. [DOI: 10.1097/jbr.0000000000000102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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37
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Botto C, Dalkara D, El-Amraoui A. Progress in Gene Editing Tools and Their Potential for Correcting Mutations Underlying Hearing and Vision Loss. Front Genome Ed 2021; 3:737632. [PMID: 34778871 PMCID: PMC8581640 DOI: 10.3389/fgeed.2021.737632] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
Blindness and deafness are the most frequent sensory disorders in humans. Whatever their cause - genetic, environmental, or due to toxic agents, or aging - the deterioration of these senses is often linked to irreversible damage to the light-sensing photoreceptor cells (blindness) and/or the mechanosensitive hair cells (deafness). Efforts are increasingly focused on preventing disease progression by correcting or replacing the blindness and deafness-causal pathogenic alleles. In recent years, gene replacement therapies for rare monogenic disorders of the retina have given positive results, leading to the marketing of the first gene therapy product for a form of childhood hereditary blindness. Promising results, with a partial restoration of auditory function, have also been reported in preclinical models of human deafness. Silencing approaches, including antisense oligonucleotides, adeno-associated virus (AAV)-mediated microRNA delivery, and genome-editing approaches have also been applied to various genetic forms of blindness and deafness The discovery of new DNA- and RNA-based CRISPR/Cas nucleases, and the new generations of base, prime, and RNA editors offers new possibilities for directly repairing point mutations and therapeutically restoring gene function. Thanks to easy access and immune-privilege status of self-contained compartments, the eye and the ear continue to be at the forefront of developing therapies for genetic diseases. Here, we review the ongoing applications and achievements of this new class of emerging therapeutics in the sensory organs of vision and hearing, highlighting the challenges ahead and the solutions to be overcome for their successful therapeutic application in vivo.
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Affiliation(s)
- Catherine Botto
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aziz El-Amraoui
- Unit Progressive Sensory Disorders, Pathophysiology and Therapy, Institut Pasteur, Institut de l'Audition, Université de Paris, INSERM-UMRS1120, Paris, France
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38
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Trigila AP, Pisciottano F, Franchini LF. Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals. BMC Biol 2021; 19:244. [PMID: 34784928 PMCID: PMC8594068 DOI: 10.1186/s12915-021-01170-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 10/21/2021] [Indexed: 11/26/2022] Open
Abstract
Background Mammals possess unique hearing capacities that differ significantly from those of the rest of the amniotes. In order to gain insights into the evolution of the mammalian inner ear, we aim to identify the set of genetic changes and the evolutionary forces that underlie this process. We hypothesize that genes that impair hearing when mutated in humans or in mice (hearing loss (HL) genes) must play important roles in the development and physiology of the inner ear and may have been targets of selective forces across the evolution of mammals. Additionally, we investigated if these HL genes underwent a human-specific evolutionary process that could underlie the evolution of phenotypic traits that characterize human hearing. Results We compiled a dataset of HL genes including non-syndromic deafness genes identified by genetic screenings in humans and mice. We found that many genes including those required for the normal function of the inner ear such as LOXHD1, TMC1, OTOF, CDH23, and PCDH15 show strong signatures of positive selection. We also found numerous noncoding accelerated regions in HL genes, and among them, we identified active transcriptional enhancers through functional enhancer assays in transgenic zebrafish. Conclusions Our results indicate that the key inner ear genes and regulatory regions underwent adaptive evolution in the basal branch of mammals and along the human-specific branch, suggesting that they could have played an important role in the functional remodeling of the cochlea. Altogether, our data suggest that morphological and functional evolution could be attained through molecular changes affecting both coding and noncoding regulatory regions. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01170-6.
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Affiliation(s)
- Anabella P Trigila
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina
| | - Francisco Pisciottano
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina.,Current address: Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina
| | - Lucía F Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina.
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39
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Abstract
Compelling evidence indicates that some newborns harboring genetic variants associated with hearing loss might not be identified by current physiologic newborn hearing screening (NBHS) rendering current NBHS protocols suboptimal. Incorporating genomic sequencing into NBHS would improve clinical diagnosis and decrease time to early intervention efforts.
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Affiliation(s)
- Calli Ober Mitchell
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, NRB 160, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. https://twitter.com/CalliMitchell3
| | - Cynthia Casson Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, NRB 160, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, UK.
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40
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Guthrie OW, Bhatt IS. Nondeterministic nature of sensorineural outcomes following noise trauma. Biol Open 2021; 10:272549. [PMID: 34668520 PMCID: PMC8543023 DOI: 10.1242/bio.058696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 09/08/2021] [Indexed: 11/20/2022] Open
Abstract
Over 1.1 billion individuals are at risk for noise induced hearing loss yet there is no accepted therapy. A long history of research has demonstrated that excessive noise exposure will kill outer hair cells (OHCs). Such observations have fueled the notion that dead OHCs underlie hearing loss. Therefore, previous and current therapeutic approaches are based on preventing the loss of OHCs. However, the relationship between OHC loss and hearing loss is at best a modest correlation. This suggests that in addition to the death of OHCs, other mechanisms may regulate the type and degree of hearing loss. In the current study, we tested the hypothesis that permanent noise-induced-hearing loss is consequent to additional mechanisms beyond the noise dose and the death of OHCs. Hooded male rats were randomly divided into noise and control groups. Morphological and physiological assessments were conducted on both groups. The combined results suggest that beyond OHC loss, the surviving cochlear elements shape sensorineural outcomes, which can be nondeterministic. These findings provide the basis for individualized ototherapeutics that manipulate surviving cellular elements in order to bias cochlear function towards normal hearing even in the presence of dead OHCs. Summary: The current findings provide the basis for individualized ototherapeutics that manipulate surviving cellular elements in order to bias cochlear function towards normal hearing even in the presence of dead cells.
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Affiliation(s)
- O'neil W Guthrie
- Department of Communication Sciences & Disorders, Northern Arizona University, Flagstaff, AZ 86011, USA.,Cell & Molecular Pathology Laboratory, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Ishan S Bhatt
- Audiogenomics Research Laboratory, Department of Communication Sciences and Disorders, The University of Iowa, Iowa City, IA 52242, USA
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41
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Transcriptome-Wide Analysis Reveals a Role for Extracellular Matrix and Integrin Receptor Genes in Otic Neurosensory Differentiation from Human iPSCs. Int J Mol Sci 2021; 22:ijms221910849. [PMID: 34639189 PMCID: PMC8509699 DOI: 10.3390/ijms221910849] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 12/27/2022] Open
Abstract
We analyzed transcriptomic data from otic sensory cells differentiated from human induced pluripotent stem cells (hiPSCs) by a previously described method to gain new insights into the early human otic neurosensory lineage. We identified genes and biological networks not previously described to occur in the human otic sensory developmental cell lineage. These analyses identified and ranked genes known to be part of the otic sensory lineage program (SIX1, EYA1, GATA3, etc.), in addition to a number of novel genes encoding extracellular matrix (ECM) (COL3A1, COL5A2, DCN, etc.) and integrin (ITG) receptors (ITGAV, ITGA4, ITGA) for ECM molecules. The results were confirmed by quantitative PCR analysis of a comprehensive panel of genes differentially expressed during the time course of hiPSC differentiation in vitro. Immunocytochemistry validated results for select otic and ECM/ITG gene markers in the in vivo human fetal inner ear. Our screen shows ECM and ITG gene expression changes coincident with hiPSC differentiation towards human otic neurosensory cells. Our findings suggest a critical role of ECM-ITG interactions with otic neurosensory lineage genes in early neurosensory development and cell fate determination in the human fetal inner ear.
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42
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Kremer H. Novel gene discovery for hearing loss and other routes to increased diagnostic rates. Hum Genet 2021; 141:383-386. [PMID: 34599370 PMCID: PMC9034996 DOI: 10.1007/s00439-021-02374-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022]
Abstract
Despite decades of research, there is much to be learned about the genetic landscape of sensorineural hearing loss. Novel genes for hearing loss remain to be identified while ‘secrets’ of the known genes need to be uncovered. These ‘secrets’ include regulatory mechanisms of gene activity and novel aspects of gene structure. To obtain a more complete picture of the genetics of hearing loss, the available experimental and bioinformatic tools need to be fully exploited. This is also true for data resources such as ENCODE. For the inner ear, however, such data resources and analytical tools need to be developed or extended. Collaborative studies provide opportunities to achieve this and to optimally use those tools and resources that are already available. This will accelerate the discoveries that are necessary for improving molecular genetic diagnostics and genetic counselling and for the development of therapeutic strategies.
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Affiliation(s)
- Hannie Kremer
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands. .,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
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43
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Ingham NJ, Banafshe N, Panganiban C, Crunden JL, Chen J, Lewis MA, Steel KP. Inner hair cell dysfunction in Klhl18 mutant mice leads to low frequency progressive hearing loss. PLoS One 2021; 16:e0258158. [PMID: 34597341 PMCID: PMC8486144 DOI: 10.1371/journal.pone.0258158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/19/2021] [Indexed: 12/30/2022] Open
Abstract
Age-related hearing loss in humans (presbycusis) typically involves impairment of high frequency sensitivity before becoming progressively more severe at lower frequencies. Pathologies initially affecting lower frequency regions of hearing are less common. Here we describe a progressive, predominantly low-frequency recessive hearing impairment in two mutant mouse lines carrying different mutant alleles of the Klhl18 gene: a spontaneous missense mutation (Klhl18lowf) and a targeted mutation (Klhl18tm1a(KOMP)Wtsi). Both males and females were studied, and the two mutant lines showed similar phenotypes. Threshold for auditory brainstem responses (ABR; a measure of auditory nerve and brainstem neural activity) were normal at 3 weeks old but showed progressive increases from 4 weeks onwards. In contrast, distortion product otoacoustic emission (DPOAE) sensitivity and amplitudes (a reflection of cochlear outer hair cell function) remained normal in mutants. Electrophysiological recordings from the round window of Klhl18lowf mutants at 6 weeks old revealed 1) raised compound action potential thresholds that were similar to ABR thresholds, 2) cochlear microphonic potentials that were normal compared with wildtype and heterozygous control mice and 3) summating potentials that were reduced in amplitude compared to control mice. Scanning electron microscopy showed that Klhl18lowf mutant mice had abnormally tapering of the tips of inner hair cell stereocilia in the apical half of the cochlea while their synapses appeared normal. These results suggest that Klhl18 is necessary to maintain inner hair cell stereocilia and normal inner hair cell function at low frequencies.
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Affiliation(s)
- Neil J. Ingham
- Wolfson Centre for Age-Related Diseases, King’s College London, London, United Kingdom
| | - Navid Banafshe
- Wolfson Centre for Age-Related Diseases, King’s College London, London, United Kingdom
| | - Clarisse Panganiban
- Wolfson Centre for Age-Related Diseases, King’s College London, London, United Kingdom
| | - Julia L. Crunden
- Wolfson Centre for Age-Related Diseases, King’s College London, London, United Kingdom
| | - Jing Chen
- Wolfson Centre for Age-Related Diseases, King’s College London, London, United Kingdom
| | - Morag A. Lewis
- Wolfson Centre for Age-Related Diseases, King’s College London, London, United Kingdom
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King’s College London, London, United Kingdom
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Differential genetic diagnoses of adult post-lingual hearing loss according to the audiogram pattern and novel candidate gene evaluation. Hum Genet 2021; 141:915-927. [PMID: 34519870 PMCID: PMC9034979 DOI: 10.1007/s00439-021-02367-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
Ski-slope hearing loss (HL), which refers to increased auditory threshold at high frequencies, is common in adults. However, genetic contributions to this post-lingual HL remain largely unknown. Here, we prospectively investigated deafness-associated and novel candidate genes causing ski-slope HL. We analyzed 192 families with post-lingual HL via gene panel and/or exome sequencing. With an overall molecular diagnostic rate of 35.4% (68/192) in post-lingual HL, ski-slope HL showed a lower diagnostic rate (30.7%) compared with other conditions (40.7%). In patients who showed HL onset before the age of 40, genetic diagnostic probability was significantly lower for ski-slope HL than for other conditions. Further analysis of 51 genetically undiagnosed patients in the ski-slope HL group identified three variants in delta-like ligand 1 (DLL1), a Notch ligand, which presented in vitro gain-of-function effects on Notch downstream signaling. In conclusion, genetic diagnostic rates in post-lingual HL varied according to audiogram patterns with age-of-onset as a confounding factor. DLL1 was identified as a candidate gene causing ski-slope HL.
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Yague-Sanz C, Duval M, Larochelle M, Bachand F. Co-transcriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast. Nucleic Acids Res 2021; 49:8610-8624. [PMID: 34352089 PMCID: PMC8421224 DOI: 10.1093/nar/gkab654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/09/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription termination of protein-coding genes in eukaryotic cells usually relies on a tight coordination between the cleavage and polyadenylation of the pre-mRNA, and 5′-3′ degradation of the downstream nascent transcript. Here we investigated the contribution of the essential fission yeast endonuclease Pac1, a homolog of human Drosha that cleaves hairpin RNA structures, in triggering polyadenylation-independent transcription termination. Using ChIP-sequencing in Pac1-deficient cells, we found that Pac1 triggers transcription termination at snRNA and snoRNA genes as well as at specific protein-coding genes. Notably, we found that Pac1-dependent premature termination occurred at two genes encoding conserved transmembrane transporters whose expression were strongly repressed by Pac1. Analysis by genome editing indicated that a stem-loop structure in the nascent transcript directs Pac1-mediated cleavage and that the regions upstream and downstream of the Pac1 cleavage site in the targeted mRNAs were stabilized by mutation of nuclear 3′-5′ and 5′-3′ exonucleases, respectively. Our findings unveil a premature transcription termination pathway that uncouples co-transcriptional RNA cleavage from polyadenylation, triggering rapid nuclear RNA degradation.
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Affiliation(s)
- Carlo Yague-Sanz
- RNA Group, Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke J1E 4K8, Québec, Canada
| | - Maxime Duval
- RNA Group, Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke J1E 4K8, Québec, Canada
| | - Marc Larochelle
- RNA Group, Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke J1E 4K8, Québec, Canada
| | - François Bachand
- RNA Group, Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke J1E 4K8, Québec, Canada
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Cheatham MA. Spontaneous otoacoustic emissions are biomarkers for mice with tectorial membrane defects. Hear Res 2021; 409:108314. [PMID: 34332206 DOI: 10.1016/j.heares.2021.108314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/22/2021] [Accepted: 07/12/2021] [Indexed: 01/12/2023]
Abstract
Cochlear function depends on the operation of a coupled feedback loop, incorporating outer hair cells (OHCs), and structured to assure that inner hair cells (IHCs) convey frequency specific acoustic information to the brain, even at very low sound levels. Although our knowledge of OHC function and its contribution to cochlear amplification has expanded, the importance of the tectorial membrane (TM) to the processing of mechanical inputs has not been fully elucidated. In addition, there are a surprising number of genetic mutations that affect TM structure and that produce hearing loss in humans. By synthesizing old and new results obtained on several mouse mutants, we learned that animals with abnormal TMs are prone to generate spontaneous otoacoustic emissions (SOAE), which are uncommon in most wildtype laboratory animals. Because SOAEs are not produced in TM mutants or in humans when threshold shifts exceed approximately 25 dB, some degree of cochlear amplification is required. However, amplification by itself is not sufficient because normal mice are rarely spontaneous emitters. Since SOAEs reflect active cochlear operation, TM mutants are valuable for studying the oscillatory nature of the amplification process and the structures associated with its stabilization. Inasmuch as the mouse models were selected to mirror human auditory disorders, using SOAEs as a noninvasive clinical tool may assist the classification of individuals with genetic defects that influence the active mechanisms responsible for sensitivity and frequency selectivity, the hallmarks of mammalian hearing.
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Affiliation(s)
- Mary Ann Cheatham
- The Knowles Hearing Center, Roxelyn and Richard Pepper Department of Communication Sciences and Disorders, Northwestern University, 2-240 Frances Searle Building, 2240 Campus Drive, Evanston, IL 60208, USA.
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Xiao C, Rossignol F, Vaz FM, Ferreira CR. Inherited disorders of complex lipid metabolism: A clinical review. J Inherit Metab Dis 2021; 44:809-825. [PMID: 33594685 DOI: 10.1002/jimd.12369] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Over 80 human diseases have been attributed to defects in complex lipid metabolism. A majority of them have been reported recently in the setting of rapid advances in genomic technology and their increased use in clinical settings. Lipids are ubiquitous in human biology and play roles in many cellular and intercellular processes. While inborn errors in lipid metabolism can affect every organ system with many examples of genetic heterogeneity and pleiotropy, the clinical manifestations of many of these disorders can be explained based on the disruption of the metabolic pathway involved. In this review, we will discuss the physiological function of major pathways in complex lipid metabolism, including nonlysosomal sphingolipid metabolism, acylceramide metabolism, de novo phospholipid synthesis, phospholipid remodeling, phosphatidylinositol metabolism, mitochondrial cardiolipin synthesis and remodeling, and ether lipid metabolism as well as common clinical phenotypes associated with each.
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Affiliation(s)
- Changrui Xiao
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Francis Rossignol
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Carlos R Ferreira
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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Martín M, Modenutti CP, Gil Rosas ML, Peyret V, Geysels RC, Bernal Barquero CE, Sobrero G, Muñoz L, Signorino M, Testa G, Miras MB, Masini-Repiso AM, Calcaterra NB, Coux G, Carrasco N, Martí MA, Nicola JP. A Novel SLC5A5 Variant Reveals the Crucial Role of Kinesin Light Chain 2 in Thyroid Hormonogenesis. J Clin Endocrinol Metab 2021; 106:1867-1881. [PMID: 33912899 PMCID: PMC8208674 DOI: 10.1210/clinem/dgab283] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Indexed: 12/17/2022]
Abstract
CONTEXT Iodide transport defect (ITD) (Online Mendelian Inheritance in Man No. 274400) is an uncommon cause of dyshormonogenic congenital hypothyroidism due to loss-of-function variants in the SLC5A5 gene, which encodes the sodium/iodide symporter (NIS), causing deficient iodide accumulation in thyroid follicular cells. OBJECTIVE This work aims to determine the molecular basis of a patient's ITD clinical phenotype. METHODS The propositus was diagnosed with dyshormonogenic congenital hypothyroidism with minimal 99mTc-pertechnetate accumulation in a eutopic thyroid gland. The propositus SLC5A5 gene was sequenced. Functional in vitro characterization of the novel NIS variant was performed. RESULTS Sanger sequencing revealed a novel homozygous missense p.G561E NIS variant. Mechanistically, the G561E substitution reduces iodide uptake, because targeting of G561E NIS to the plasma membrane is reduced. Biochemical analyses revealed that G561E impairs the recognition of an adjacent tryptophan-acidic motif by the kinesin-1 subunit kinesin light chain 2 (KLC2), interfering with NIS maturation beyond the endoplasmic reticulum, and reducing iodide accumulation. Structural bioinformatic analysis suggests that G561E shifts the equilibrium of the unstructured tryptophan-acidic motif toward a more structured conformation unrecognizable to KLC2. Consistently, knockdown of Klc2 causes defective NIS maturation and consequently decreases iodide accumulation in rat thyroid cells. Morpholino knockdown of klc2 reduces thyroid hormone synthesis in zebrafish larvae leading to a hypothyroid state as revealed by expression profiling of key genes related to the hypothalamic-pituitary-thyroid axis. CONCLUSION We report a novel NIS pathogenic variant associated with dyshormonogenic congenital hypothyroidism. Detailed molecular characterization of G561E NIS uncovered the significance of KLC2 in thyroid physiology.
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Affiliation(s)
- Mariano Martín
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología–Consejo Nacional de Investigaciones Científicas y Técnicas, X5000HUA Córdoba, Argentina
| | - Carlos Pablo Modenutti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales–Consejo Nacional de Investigaciones Científicas y Técnicas, C1428EGA Buenos Aires, Argentina
| | - Mauco Lucas Gil Rosas
- Departamento de Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2000EZP Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario–Consejo Nacional de Investigaciones Científicas y Técnicas, S2000EZP Rosario, Argentina
| | - Victoria Peyret
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología–Consejo Nacional de Investigaciones Científicas y Técnicas, X5000HUA Córdoba, Argentina
| | - Romina Celeste Geysels
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología–Consejo Nacional de Investigaciones Científicas y Técnicas, X5000HUA Córdoba, Argentina
| | - Carlos Eduardo Bernal Barquero
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología–Consejo Nacional de Investigaciones Científicas y Técnicas, X5000HUA Córdoba, Argentina
| | - Gabriela Sobrero
- Programa Provincial de Pesquisa Neonatal, Hospital de Niños de la Santísima Trinidad de Córdoba, X5014AKK Córdoba, Argentina
| | - Liliana Muñoz
- Programa Provincial de Pesquisa Neonatal, Hospital de Niños de la Santísima Trinidad de Córdoba, X5014AKK Córdoba, Argentina
| | - Malvina Signorino
- Programa Provincial de Pesquisa Neonatal, Hospital de Niños de la Santísima Trinidad de Córdoba, X5014AKK Córdoba, Argentina
| | - Graciela Testa
- Programa Provincial de Pesquisa Neonatal, Hospital de Niños de la Santísima Trinidad de Córdoba, X5014AKK Córdoba, Argentina
| | - Mirta Beatriz Miras
- Programa Provincial de Pesquisa Neonatal, Hospital de Niños de la Santísima Trinidad de Córdoba, X5014AKK Córdoba, Argentina
| | - Ana María Masini-Repiso
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología–Consejo Nacional de Investigaciones Científicas y Técnicas, X5000HUA Córdoba, Argentina
| | - Nora Beatriz Calcaterra
- Departamento de Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2000EZP Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario–Consejo Nacional de Investigaciones Científicas y Técnicas, S2000EZP Rosario, Argentina
| | - Gabriela Coux
- Departamento de Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2000EZP Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario–Consejo Nacional de Investigaciones Científicas y Técnicas, S2000EZP Rosario, Argentina
| | - Nancy Carrasco
- Department of Cellular and Molecular Physiology, Yale School of Medicine, 06510 New Haven, Connecticut, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, 37232 Nashville, Tennessee, USA
| | - Marcelo Adrián Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales–Consejo Nacional de Investigaciones Científicas y Técnicas, C1428EGA Buenos Aires, Argentina
| | - Juan Pablo Nicola
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
- Centro de Investigaciones en Bioquímica Clínica e Inmunología–Consejo Nacional de Investigaciones Científicas y Técnicas, X5000HUA Córdoba, Argentina
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Dose-Dependent Pattern of Cochlear Synaptic Degeneration in C57BL/6J Mice Induced by Repeated Noise Exposure. Neural Plast 2021; 2021:9919977. [PMID: 34221004 PMCID: PMC8211526 DOI: 10.1155/2021/9919977] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/01/2021] [Accepted: 05/25/2021] [Indexed: 12/26/2022] Open
Abstract
It is widely accepted that even a single acute noise exposure at moderate intensity that induces temporary threshold shift (TTS) can result in permanent loss of ribbon synapses between inner hair cells and afferents. However, effects of repeated or chronic noise exposures on the cochlear synapses especially medial olivocochlear (MOC) efferent synapses remain elusive. Based on a weeklong repeated exposure model of bandwidth noise over 2-20 kHz for 2 hours at seven intensities (88 to 106 dB SPL with 3 dB increment per gradient) on C57BL/6J mice, we attempted to explore the dose-response mechanism of prolonged noise-induced audiological dysfunction and cochlear synaptic degeneration. In our results, mice repeatedly exposed to relatively low-intensity noise (88, 91, and 94 dB SPL) showed few changes on auditory brainstem response (ABR), ribbon synapses, or MOC efferent synapses. Notably, repeated moderate-intensity noise exposures (97 and 100 dB SPL) not only caused hearing threshold shifts and the inner hair cell ribbon synaptopathy but also impaired MOC efferent synapses, which might contribute to complex patterns of damages on cochlear function and morphology. However, repeated high-intensity (103 and 106 dB SPL) noise exposures induced PTSs mainly accompanied by damages on cochlear amplifier function of outer hair cells and the inner hair cell ribbon synaptopathy, rather than the MOC efferent synaptic degeneration. Moreover, we observed a frequency-dependent vulnerability of the repeated acoustic trauma-induced cochlear synaptic degeneration. This study provides a sight into the hypothesis that noise-induced cochlear synaptic degeneration involves both afferent (ribbon synapses) and efferent (MOC terminals) pathology. The pattern of dose-dependent pathological changes induced by repeated noise exposure at various intensities provides a possible explanation for the complicated cochlear synaptic degeneration in humans. The underlying mechanisms remain to be studied in the future.
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León Y, Magariños M, Varela-Nieto I. Ceramide Kinase Inhibition Blocks IGF-1-Mediated Survival of Otic Neurosensory Progenitors by Impairing AKT Phosphorylation. Front Cell Dev Biol 2021; 9:678760. [PMID: 34179008 PMCID: PMC8220815 DOI: 10.3389/fcell.2021.678760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022] Open
Abstract
Sphingolipids are bioactive lipid components of cell membranes with important signal transduction functions in health and disease. Ceramide is the central building block for sphingolipid biosynthesis and is processed to form structurally and functionally distinct sphingolipids. Ceramide can be phosphorylated by ceramide kinase (CERK) to generate ceramide-1-phosphate, a cytoprotective signaling molecule that has been widely studied in multiple tissues and organs, including the developing otocyst. However, little is known about ceramide kinase regulation during inner ear development. Using chicken otocysts, we show that genes for CERK and other enzymes of ceramide metabolism are expressed during the early stages of inner ear development and that CERK is developmentally regulated at the otic vesicle stage. To explore its role in inner ear morphogenesis, we blocked CERK activity in organotypic cultures of otic vesicles with a specific inhibitor. Inhibition of CERK activity impaired proliferation and promoted apoptosis of epithelial otic progenitors. CERK inhibition also compromised neurogenesis of the acoustic-vestibular ganglion. Insulin-like growth factor-1 (IGF-1) is a key factor for proliferation, survival and differentiation in the chicken otocyst. CERK inhibition decreased IGF-1-induced AKT phosphorylation and blocked IGF-1-induced cell survival. Overall, our data suggest that CERK is activated as a central element in the network of anti-apoptotic pro-survival pathways elicited by IGF-1 during early inner ear development.
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Affiliation(s)
- Yolanda León
- Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, Madrid, Spain.,Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Magariños
- Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, Madrid, Spain.,Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER, Unit 761, CIBER, ISCIII, Madrid, Spain
| | - Isabel Varela-Nieto
- Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, Madrid, Spain.,CIBERER, Unit 761, CIBER, ISCIII, Madrid, Spain
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