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Fisch KM, Rosenthal SB, Mark A, Sasik R, Nasamran CA, Clifford R, Derebery MJ, Boussaty E, Jepsen K, Harris J, Friedman RA. The genomic landscape of Ménière's disease: a path to endolymphatic hydrops. BMC Genomics 2024; 25:646. [PMID: 38943082 PMCID: PMC11212243 DOI: 10.1186/s12864-024-10552-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Ménière's disease (MD) is a disorder of the inner ear that causes episodic bouts of severe dizziness, roaring tinnitus, and fluctuating hearing loss. To date, no targeted therapy exists. As such, we have undertaken a large whole genome sequencing study on carefully phenotyped unilateral MD patients with the goal of gene/pathway discovery and a move towards targeted intervention. This study was a retrospective review of patients with a history of Ménière's disease. Genomic DNA, acquired from saliva samples, was purified and subjected to whole genome sequencing. RESULTS Stringent variant calling, performed on 511 samples passing quality checks, followed by gene-based filtering by recurrence and proximity in molecular interaction networks, led to 481 high priority MD genes. These high priority genes, including MPHOSPH8, MYO18A, TRIOBP, OTOGL, TNC, and MYO6, were previously implicated in hearing loss, balance, and cochlear function, and were significantly enriched in common variant studies of hearing loss. Validation in an independent MD cohort confirmed 82 recurrent genes. Pathway analysis pointed to cell-cell adhesion, extracellular matrix, and cellular energy maintenance as key mediators of MD. Furthermore, the MD-prioritized genes were highly expressed in human inner ear hair cells and dark/vestibular cells, and were differentially expressed in a mouse model of hearing loss. CONCLUSION By enabling the development of model systems that may lead to targeted therapies and MD screening panels, the genes and variants identified in this study will inform diagnosis and treatment of MD.
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Affiliation(s)
- Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA.
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Adam Mark
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Roman Sasik
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Chanond A Nasamran
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Royce Clifford
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA
- Research Department, VA Hospitals, San Diego, CA, USA
| | | | - Ely Boussaty
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jeffrey Harris
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Rick A Friedman
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA.
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Rad A, Bartsch O, Bakhtiari S, Zhu C, Xu Y, Monteiro FP, Kok F, Vulto-van Silfhout AT, Kruer MC, Bowl MR, Vona B. Expanding the spectrum of phenotypes for MPDZ: Report of four unrelated families and review of the literature. Clin Genet 2024. [PMID: 38857973 DOI: 10.1111/cge.14563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/24/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024]
Abstract
MPDZ, a gene with diverse functions mediating cell-cell junction interactions, receptor signaling, and binding multivalent scaffold proteins, is associated with a spectrum of clinically heterogeneous phenotypes with biallelic perturbation. Despite its clinical relevance, the mechanistic underpinnings of these variants remain elusive, underscoring the need for extensive case series and functional investigations. In this study, we conducted a systematic review of cases in the literature through two electronic databases following the PRISMA guidelines. We selected nine studies, including 18 patients, with homozygous or compound heterozygous variants in MPDZ and added five patients from four unrelated families with novel MPDZ variants. To evaluate the role of Mpdz on hearing, we analyzed available auditory electrophysiology data from a knockout murine model (Mpdzem1(IMPC)J/em1(IMPC)J) generated by the International Mouse Phenotyping Consortium. Using exome and genome sequencing, we identified three families with compound heterozygous variants, and one family with a homozygous frameshift variant. MPDZ-related disease is clinically heterogenous with hydrocephaly, vision impairment, hearing impairment and cardiovascular disease occurring most frequently. Additionally, we describe two unrelated patients with spasticity, expanding the phenotypic spectrum. Our murine analysis of the Mpdzem1(IMPC)J/em1(IMPC)J allele showed severe hearing impairment. Overall, we expand understanding of MPDZ-related phenotypes and highlight hearing impairment and spasticity among the heterogeneous phenotypes.
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Affiliation(s)
- Aboulfazl Rad
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Oliver Bartsch
- Medical Care Centre Section Human Genetics and Institute of Human Genetics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, Arizona, USA
- Department of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
| | - Changlian Zhu
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Göteborg, Sweden
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Fernando Kok
- Medical Department, Mendelics Genomic Analysis, Sao Paulo, Brazil
- Neurogenetics, Neurology Department, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil
| | - Anneke T Vulto-van Silfhout
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, Arizona, USA
- Department of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
| | - Michael R Bowl
- UCL Ear Institute, University College London, London, UK
| | - Barbara Vona
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
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Yamoah EN, Pavlinkova G, Fritzsch B. The Development of Speaking and Singing in Infants May Play a Role in Genomics and Dementia in Humans. Brain Sci 2023; 13:1190. [PMID: 37626546 PMCID: PMC10452560 DOI: 10.3390/brainsci13081190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
The development of the central auditory system, including the auditory cortex and other areas involved in processing sound, is shaped by genetic and environmental factors, enabling infants to learn how to speak. Before explaining hearing in humans, a short overview of auditory dysfunction is provided. Environmental factors such as exposure to sound and language can impact the development and function of the auditory system sound processing, including discerning in speech perception, singing, and language processing. Infants can hear before birth, and sound exposure sculpts their developing auditory system structure and functions. Exposing infants to singing and speaking can support their auditory and language development. In aging humans, the hippocampus and auditory nuclear centers are affected by neurodegenerative diseases such as Alzheimer's, resulting in memory and auditory processing difficulties. As the disease progresses, overt auditory nuclear center damage occurs, leading to problems in processing auditory information. In conclusion, combined memory and auditory processing difficulties significantly impact people's ability to communicate and engage with their societal essence.
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Affiliation(s)
- Ebenezer N. Yamoah
- Department of Physiology and Cell Biology, School of Medicine, University of Nevada, Reno, NV 89557, USA;
| | | | - Bernd Fritzsch
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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McNeill A. 2022: the year that was in the European Journal of Human Genetics. Eur J Hum Genet 2023; 31:131-133. [PMID: 36750730 PMCID: PMC9905485 DOI: 10.1038/s41431-023-01283-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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Abstract
Hearing loss (HL) is an etiologically heterogeneous disorder that affects around 5% of the world's population. There has been an exponential increase in the identification of genes and variants responsible for hereditary HL over recent years. Iran, a country located in the Middle East, has a high prevalence of consanguineous marriages, so heterogeneous diseases such as HL are more common. Comprehensive studies using different strategies from linkage analysis to next-generation sequencing, especially exome-sequencing, have achieved significant success in identifying possible pathogens in deaf Iranian families. About 12% of non-syndromic autosomal recessive HL genes investigated to date, were first identified in families from Iran. Variations of 56 genes have been observed in families with NSHL in Iran. Variants in GJB2, SLC26A4, MYO15A, MYO7A, CDH23, and TMC1 account for 16.5%, 16.25%, 13.5%, 9.35%, 6.9% and 4.92%, cases of NSHL, respectively. In summary, there are also different diagnostic rates between studies conducted in Iran. In the comprehensive investigations conducted by the Genetic Research Center of the University of Social Welfare and Rehabilitation Sciences over the past 20 years, the overall diagnosis rate is about 80% while there are other studies with lower diagnostic rates which could reflect differences in project designs, sampling, and accuracy and validity of the methods used. Furthermore, there are several syndromic HHLs in Iran including, Waardenburg syndrome, BOR syndrome, Brown-Vialetto-Van Laere syndrome, Wolfram syndrome, among which Pendred and Usher syndromes are well-studied. These results are of importance for further investigation and elucidation of the molecular basis of HHL in Iran.
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McNeill A. New year, new issue. Eur J Hum Genet 2022; 30:1-2. [PMID: 34848845 PMCID: PMC8738724 DOI: 10.1038/s41431-021-01014-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Alisdair McNeill
- grid.11835.3e0000 0004 1936 9262Department of Neuroscience, The University of Sheffield, Sheffield, UK ,grid.413991.70000 0004 0641 6082Sheffield Clinical Genetics Department, Sheffield Children’s Hospital NHS Foundation Trust, Sheffield, UK
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Affiliation(s)
- Anne-Françoise Roux
- grid.121334.60000 0001 2097 0141Laboratoire de Génétique Moléculaire, Univ Montpellier, CHU, Montpellier, France ,grid.121334.60000 0001 2097 0141INM, Univ Montpellier, Inserm, Montpellier, France
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Saleem IB, Masoud MS, Qasim M, Ali M, Ahmed ZM. Identification and Computational Analysis of Rare Variants of Known Hearing Loss Genes Present in Five Deaf Members of a Pakistani Kindred. Genes (Basel) 2021; 12:genes12121940. [PMID: 34946889 PMCID: PMC8702217 DOI: 10.3390/genes12121940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022] Open
Abstract
Hearing loss (HL) is the most common neurosensory defect in humans that affects the normal communication. Disease is clinically and genetically heterogeneous, rendering challenges for the molecular diagnosis of affected subjects. This study highlights the phenotypic and genetic complexity of inherited HL in a large consanguineous Pakistan kindred. Audiological evaluation of all affected individuals revealed varying degree of mild to profound sensorineural HL. Whole exome (WES) of four family members followed by Sanger sequencing revealed candidate disease-associated variants in five known deafness genes: GJB2 (c.231G>A; p.(Trp77 *)), SLC26A4 (c.1337A>G; p.(Gln446Arg)), CDH23 (c.2789C>T; p.(Pro930Leu)), KCNQ4 (c.1672G>A; p.(Val558Met)) and MPDZ (c.4124T>C; p.(Val1375Ala)). All identified variants replaced evolutionary conserved residues, were either absent or had low frequencies in the control databases. Our in silico and 3-Dimensional (3D) protein topology analyses support the damaging impact of identified variants on the encoded proteins. However, except for the previously established “pathogenic” and “likely pathogenic” categories for the c.231G>A (p.(Trp77 *)) allele of GJB2 and c.1377A>G (p.(Gln446Arg)) of SLC26A4, respectively, all the remaining identified variants were classified as “uncertain significance” based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant pathogenicity guidelines. Our study highlights the complexity of genetic traits in consanguineous families, and the need of combining the functional studies even with the comprehensive profiling of multiple family members to improve the genetic diagnosis in complex inbred families.
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Affiliation(s)
- Irum Badshah Saleem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (I.B.S.); (M.Q.)
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (I.B.S.); (M.Q.)
- Correspondence: (M.S.M.); (Z.M.A.)
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (I.B.S.); (M.Q.)
| | - Muhammad Ali
- Department of Animal Sciences, Quaid-e-Azam University, Islamabad 46000, Pakistan;
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Correspondence: (M.S.M.); (Z.M.A.)
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