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Tlili A, Mahfood M, Al Mutery A, Chouchen J. Genetic analysis of 106 sporadic cases with hearing loss in the UAE population. Hum Genomics 2024; 18:59. [PMID: 38844983 PMCID: PMC11157727 DOI: 10.1186/s40246-024-00630-8] [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: 02/03/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Hereditary hearing loss is a rare hereditary condition that has a significant presence in consanguineous populations. Despite its prevalence, hearing loss is marked by substantial genetic diversity, which poses challenges for diagnosis and screening, particularly in cases with no clear family history or when the impact of the genetic variant requires functional analysis, such as in the case of missense mutations and UTR variants. The advent of next-generation sequencing (NGS) has transformed the identification of genes and variants linked to various conditions, including hearing loss. However, there remains a high proportion of undiagnosed patients, attributable to various factors, including limitations in sequencing coverage and gaps in our knowledge of the entire genome, among other factors. In this study, our objective was to comprehensively identify the spectrum of genes and variants associated with hearing loss in a cohort of 106 affected individuals from the UAE. RESULTS In this study, we investigated 106 sporadic cases of hearing impairment and performed genetic analyses to identify causative mutations. Screening of the GJB2 gene in these cases revealed its involvement in 24 affected individuals, with specific mutations identified. For individuals without GJB2 mutations, whole exome sequencing (WES) was conducted. WES revealed 33 genetic variants, including 6 homozygous and 27 heterozygous DNA changes, two of which were previously implicated in hearing loss, while 25 variants were novel. We also observed multiple potential pathogenic heterozygous variants across different genes in some cases. Notably, a significant proportion of cases remained without potential pathogenic variants. CONCLUSIONS Our findings confirm the complex genetic landscape of hearing loss and the limitations of WES in achieving a 100% diagnostic rate, especially in conditions characterized by genetic heterogeneity. These results contribute to our understanding of the genetic basis of hearing loss and emphasize the need for further research and comprehensive genetic analyses to elucidate the underlying causes of this condition.
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Affiliation(s)
- Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 Room 107, P.O. Box: 27272, Sharjah, United Arab Emirates.
- Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates.
| | - Mona Mahfood
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 Room 107, P.O. Box: 27272, Sharjah, United Arab Emirates
| | - Abdullah Al Mutery
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 Room 107, P.O. Box: 27272, Sharjah, United Arab Emirates
| | - Jihen Chouchen
- Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
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2
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Luthfi M, Pandey RB, Su YC, Sompornpisut P. Deciphering molecular basis of pesticide-induced recurrent pregnancy loss: insights from transcriptomics analysis. Toxicol Mech Methods 2024; 34:527-544. [PMID: 38294000 DOI: 10.1080/15376516.2024.2307975] [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: 10/15/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
Recent studies have revealed a notable connection between pesticide exposure and Recurrent Pregnancy Loss (RPL), yet the precise molecular underpinning of this toxicity remains elusive. Through the alignment of Differentially Expressed Genes (DEGs) of healthy and RPL patients with the target genes of 9 pesticide components, we identified a set of 12 genes responsible for RPL etiology. Interestingly, biological process showed that besides RPL, those 12 genes also associated with preeclampsia and cardiovascular disease. Enrichment analysis showed the engagement of these genes associated with essential roles in the molecular transport of small molecules, as well as the aldosterone-regulated sodium reabsorption, endocrine and other factor-regulated calcium reabsorption, mineral absorption, ion homeostasis, and ion transport by P-type ATPases. Notably, the crosstalk targets between pesticide components played crucial roles in influencing RPL results, suggesting a role in attenuating pesticide agents that contribute to RPL. It is important to note that non-significant concentration of the pesticide components observed in both control and RPL samples should not prematurely undermine the potential for pesticides to induce RPL in humans. This study emphasizes the complexity of pesticide induced RPL and highlights avenues for further research and precautionary measures.
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Affiliation(s)
- Muhammad Luthfi
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Computational Chemistry, Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
| | - R B Pandey
- School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Pornthep Sompornpisut
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Computational Chemistry, Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
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3
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Sutton DC, Andrews JC, Dolezal DM, Park YJ, Li H, Eberl DF, Yamamoto S, Groves AK. Comparative exploration of mammalian deafness gene homologues in the Drosophila auditory organ shows genetic correlation between insect and vertebrate hearing. PLoS One 2024; 19:e0297846. [PMID: 38412189 PMCID: PMC10898740 DOI: 10.1371/journal.pone.0297846] [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: 07/21/2023] [Accepted: 01/13/2024] [Indexed: 02/29/2024] Open
Abstract
Johnston's organ, the Drosophila auditory organ, is anatomically very different from the mammalian organ of Corti. However, recent evidence indicates significant cellular and molecular similarities exist between vertebrate and invertebrate hearing, suggesting that Drosophila may be a useful platform to determine the function of the many mammalian deafness genes whose underlying biological mechanisms are poorly characterized. Our goal was a comprehensive screen of all known orthologues of mammalian deafness genes in the fruit fly to better understand conservation of hearing mechanisms between the insect and the fly and ultimately gain insight into human hereditary deafness. We used bioinformatic comparisons to screen previously reported human and mouse deafness genes and found that 156 of them have orthologues in Drosophila melanogaster. We used fluorescent imaging of T2A-GAL4 gene trap and GFP or YFP fluorescent protein trap lines for 54 of the Drosophila genes and found 38 to be expressed in different cell types in Johnston's organ. We phenotypically characterized the function of strong loss-of-function mutants in three genes expressed in Johnston's organ (Cad99C, Msp-300, and Koi) using a courtship assay and electrophysiological recordings of sound-evoked potentials. Cad99C and Koi were found to have significant courtship defects. However, when we tested these genes for electrophysiological defects in hearing response, we did not see a significant difference suggesting the courtship defects were not caused by hearing deficiencies. Furthermore, we used a UAS/RNAi approach to test the function of seven genes and found two additional genes, CG5921 and Myo10a, that gave a statistically significant delay in courtship but not in sound-evoked potentials. Our results suggest that many mammalian deafness genes have Drosophila homologues expressed in the Johnston's organ, but that their requirement for hearing may not necessarily be the same as in mammals.
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Affiliation(s)
- Daniel C. Sutton
- Graduate Program in Genetics & Genomics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jonathan C. Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Dylan M. Dolezal
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Ye Jin Park
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Huffington Center on Aging, One Baylor Plaza, Houston, Texas, United States of America
| | - Hongjie Li
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Huffington Center on Aging, One Baylor Plaza, Houston, Texas, United States of America
| | - Daniel F. Eberl
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Shinya Yamamoto
- Graduate Program in Genetics & Genomics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas, United States of America
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
| | - Andrew K. Groves
- Graduate Program in Genetics & Genomics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
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Pourtavakoli A, Ghafouri-Fard S, Eslami S, Brand S, Taheri M. Expression assay of calcium signaling related lncRNAs in autism. Mol Biol Rep 2024; 51:185. [PMID: 38265729 DOI: 10.1007/s11033-023-09182-x] [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: 10/27/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024]
Abstract
BACKGROUND Calcium signaling has essential roles in the neurodevelopmental processes and pathophysiology of related disorders for instance autism spectrum disorder (ASD). METHODS AND RESULTS We compared expression of SLC1A1, SLC25A12, RYR2 and ATP2B2, as well as related long non-coding RNAs, namely LINC01231, lnc-SLC25A12, lnc-MTR-1 and LINC00606 in the peripheral blood of patients with ASD with healthy children. Expression of SLC1A1 was lower in ASD samples compared with control samples (Expression ratio (95% CI) 0.24 (0.08-0.77), adjusted P value = 0.01). Contrary, expression of LINC01231 was higher in cases compared with control samples (Expression ratio (95% CI) 25.52 (4.19-154), adjusted P value = 0.0006) and in male cases compared with healthy males (Expression ratio (95% CI) 28.24 (1.91-418), adjusted P value = 0.0009). RYR2 was significantly over-expressed in ASD children compared with control samples (Expression ratio (95% CI) 4.5 (1.16-17.4), adjusted P value = 0.029). Then, we depicted ROC curves for SLC1A1, LINC01231, RYR2 and lnc-SLC25A12 transcripts showing diagnostic power of 0.68, 0.75, 0.67 and 0.59, respectively. CONCLUSION To sum up, the current study displays possible role of calcium related genes and lncRNAs in the development of ASD.
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Affiliation(s)
- Ashkan Pourtavakoli
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Solat Eslami
- Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Serge Brand
- Center for Affective, Stress and Sleep Disorders, Psychiatric Clinics, University of Basel, Basel, Switzerland
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
- Urology and Nephrology Research Centre, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Poggio E, Barazzuol L, Salmaso A, Milani C, Deligiannopoulou A, Cazorla ÁG, Jang SS, Juliá-Palacios N, Keren B, Kopajtich R, Lynch SA, Mignot C, Moorwood C, Neuhofer C, Nigro V, Oostra A, Prokisch H, Saillour V, Schuermans N, Torella A, Verloo P, Yazbeck E, Zollino M, Jech R, Winkelmann J, Necpal J, Calì T, Brini M, Zech M. ATP2B2 de novo variants as a cause of variable neurodevelopmental disorders that feature dystonia, ataxia, intellectual disability, behavioral symptoms, and seizures. Genet Med 2023; 25:100971. [PMID: 37675773 DOI: 10.1016/j.gim.2023.100971] [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: 05/12/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023] Open
Abstract
PURPOSE ATP2B2 encodes the variant-constrained plasma-membrane calcium-transporting ATPase-2, expressed in sensory ear cells and specialized neurons. ATP2B2/Atp2b2 variants were previously linked to isolated hearing loss in patients and neurodevelopmental deficits with ataxia in mice. We aimed to establish the association between ATP2B2 and human neurological disorders. METHODS Multinational case recruitment, scrutiny of trio-based genomics data, in silico analyses, and functional variant characterization were performed. RESULTS We assembled 7 individuals harboring rare, predicted deleterious heterozygous ATP2B2 variants. The alleles comprised 5 missense substitutions that affected evolutionarily conserved sites and 2 frameshift variants in the penultimate exon. For 6 variants, a de novo status was confirmed. Unlike described patients with hearing loss, the individuals displayed a spectrum of neurological abnormalities, ranging from ataxia with dystonic features to complex neurodevelopmental manifestations with intellectual disability, autism, and seizures. Two cases with recurrent amino-acid variation showed distinctive overlap with cerebellar atrophy-associated ataxia and epilepsy. In cell-based studies, all variants caused significant alterations in cytosolic calcium handling with both loss- and gain-of-function effects. CONCLUSION Presentations in our series recapitulate key phenotypic aspects of Atp2b2-mouse models and underline the importance of precise calcium regulation for neurodevelopment and cerebellar function. Our study documents a role for ATP2B2 variants in causing heterogeneous neurodevelopmental and movement-disorder syndromes.
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Affiliation(s)
- Elena Poggio
- Department of Biology, University of Padua, Padua, Italy
| | - Lucia Barazzuol
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Andrea Salmaso
- Department of Biology, University of Padua, Padua, Italy
| | - Celeste Milani
- Department of Biology, University of Padua, Padua, Italy
| | | | - Ángeles García Cazorla
- European Reference Network for Hereditary Metabolic Diseases (MetabERN), Madrid, Spain; Neurometabolic Unit and Synaptic Metabolism Laboratory, Neurology Department Sant Joan de Déu Hospital, IPR, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Se Song Jang
- Seoul National University (SNU) College of Medicine, Seoul, South Korea
| | - Natalia Juliá-Palacios
- Neurology Department, Neurometabolic Unit, Institut de Recerca, CIBERER and MetabERN, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Boris Keren
- APHP.Sorbonne Université, Department of Medical Genetics, Pitié-Salpêtrière University Hospital, and Centre de Référence Maladies Rares Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Robert Kopajtich
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sally Ann Lynch
- Department of Clinical Genetics, Temple Street Children's University Hospital, Dublin, Ireland
| | - Cyril Mignot
- APHP.Sorbonne Université, Department of Medical Genetics, Pitié-Salpêtrière University Hospital, and Centre de Référence Maladies Rares Déficiences Intellectuelles de Causes Rares, Paris, France
| | - Catherine Moorwood
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Christiane Neuhofer
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania, Luigi Vanvitelli, Napoli, Italy
| | - Anna Oostra
- Department of Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Virginie Saillour
- Laboratoire de biologie médicale multisites Seqoia - FMG2025, Paris, France
| | - Nika Schuermans
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Annalaura Torella
- Department of Precision Medicine, University of Campania, Luigi Vanvitelli, Napoli, Italy
| | - Patrick Verloo
- Department of Pediatric Neurology, Center for Inherited Metabolic Disorders and metabERN, University Hospital Ghent, Ghent, Belgium
| | - Elise Yazbeck
- Pediatric Neurology Department, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Paris Saclay, Bicêtre Hospital, Le Kremlin Bicêtre, France
| | - Marcella Zollino
- Unit of Medical Genetics, Section of Genomic Medicine, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Robert Jech
- Department of Neurology, Charles University in Prague, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Jan Necpal
- 2nd Department of Neurology, Faculty of Medicine, Comenius University, Bratislava, Slovakia; Department of Neurology, Zvolen Hospital, Zvolen, Slovakia
| | - Tito Calì
- Department of Biomedical Sciences, University of Padua, Padua, Italy; Centro Studi per la Neurodegenerazione (CESNE), University of Padua, Padua, Italy; Neuroscience Center (PNC), University of Padua, Padua, Italy
| | - Marisa Brini
- Department of Biology, University of Padua, Padua, Italy; Centro Studi per la Neurodegenerazione (CESNE), University of Padua, Padua, Italy
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Institute for Advanced Study, Technical University of Munich, Garching, Germany.
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Taheri M, Pourtavakoli A, Eslami S, Ghafouri-Fard S, Sayad A. Assessment of expression of calcium signaling related lncRNAs in epilepsy. Sci Rep 2023; 13:17993. [PMID: 37865723 PMCID: PMC10590428 DOI: 10.1038/s41598-023-45341-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023] Open
Abstract
Calcium signaling is a metabolic pathway that is essential in neurons development and can be involved in the pathobiology of epilepsy. We assessed expression of three mRNA coding gene (SLC1A1, SLC25A12, and ATP2B2) and three related long non-coding RNAs (LINC01231:1, lnc-SLC25A12-8:1 and lnc-MTR-1:1) from this pathway in 39 patients with refractory epilepsy and 71 healthy controls. Expression of all genes except for lnc-SLC25A12 was higher in total epileptic cases compared with controls (P values = 0.0002, < 0.0001, < 0.0001, 0.049 and 0.0005 for SLC1A1, SLC25A12, LINC01231, ATP2B2 and lnc-MTR-1, respectively. When we separately compared expression of genes among males and females, SLC1A1, SLC25A12, LINC01231 and lnc-MTR-1 showed up-regulation in male cases compared with male controls. Moreover, expressions of SLC1A1 and SLC25A12 were higher in female cases compared with female controls. Remarkably, SLC25A12 was found to have the highest sensitivity value (= 1) for differentiation of epileptic cases from controls. Moreover, lnc-MTR-1 and lnc-SLC25A12 were sensitive markers for such purpose (sensitivity values = 0.89 and 0.87, respectively). The highest value belonged to LINC01231 with the value of 0.76. Taken together, this study demonstrates dysregulation of calcium-signaling related genes in epileptic patients and suggests these genes as potential biomarkers for epilepsy.
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Affiliation(s)
- Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ashkan Pourtavakoli
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Solat Eslami
- Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran
- Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Arezou Sayad
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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7
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Tao Y, Lamas V, Du W, Zhu W, Li Y, Whittaker MN, Zuris JA, Thompson DB, Rameshbabu AP, Shu Y, Gao X, Hu JH, Pei C, Kong WJ, Liu X, Wu H, Kleinstiver BP, Liu DR, Chen ZY. Treatment of monogenic and digenic dominant genetic hearing loss by CRISPR-Cas9 ribonucleoprotein delivery in vivo. Nat Commun 2023; 14:4928. [PMID: 37582836 PMCID: PMC10427623 DOI: 10.1038/s41467-023-40476-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
Mutations in Atp2b2, an outer hair cell gene, cause dominant hearing loss in humans. Using a mouse model Atp2b2Obl/+, with a dominant hearing loss mutation (Oblivion), we show that liposome-mediated in vivo delivery of CRISPR-Cas9 ribonucleoprotein complexes leads to specific editing of the Obl allele. Large deletions encompassing the Obl locus and indels were identified as the result of editing. In vivo genome editing promotes outer hair cell survival and restores their function, leading to hearing recovery. We further show that in a double-dominant mutant mouse model, in which the Tmc1 Beethoven mutation and the Atp2b2 Oblivion mutation cause digenic genetic hearing loss, Cas9/sgRNA delivery targeting both mutations leads to partial hearing recovery. These findings suggest that liposome-RNP delivery can be used as a strategy to recover hearing with dominant mutations in OHC genes and with digenic mutations in the auditory hair cells, potentially expanding therapeutics of gene editing to treat hearing loss.
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Affiliation(s)
- Yong Tao
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles St., Boston, MA, 02114, USA
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Veronica Lamas
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles St., Boston, MA, 02114, USA
- Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Wan Du
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles St., Boston, MA, 02114, USA
| | - Wenliang Zhu
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles St., Boston, MA, 02114, USA
| | - Yiran Li
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles St., Boston, MA, 02114, USA
- C.S. Mott Children's Hospital, Ann Harbor, MI, USA
| | - Madelynn N Whittaker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General hospital, Boston, MA, 02114, USA
| | - John A Zuris
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David B Thompson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Arun Prabhu Rameshbabu
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles St., Boston, MA, 02114, USA
| | - Yilai Shu
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles St., Boston, MA, 02114, USA
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, NHC Key Laboratory of Hearing Medicine, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200031, China
| | - Xue Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Johnny H Hu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Charles Pei
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles St., Boston, MA, 02114, USA
| | - Wei-Jia Kong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Hao Wu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Massachusetts General hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| | - Zheng-Yi Chen
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA.
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles St., Boston, MA, 02114, USA.
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Bionda A, Cortellari M, Liotta L, Crepaldi P. The Shepherd and the Hunter: A Genomic Comparison of Italian Dog Breeds. Animals (Basel) 2023; 13:2438. [PMID: 37570247 PMCID: PMC10417656 DOI: 10.3390/ani13152438] [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: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Shepherd and hunting dogs have undergone divergent selection for specific tasks, resulting in distinct phenotypic and behavioural differences. Italy is home to numerous recognized and unrecognized breeds of both types, providing an opportunity to compare them genomically. In this study, we analysed SNP data obtained from the CanineHD BeadChip, encompassing 116 hunting dogs (representing 6 breeds) and 158 shepherd dogs (representing 9 breeds). We explored the population structure, genomic background, and phylogenetic relationships among the breeds. To compare the two groups, we employed three complementary methods for selection signature detection: FST, XP-EHH, and ROH. Our results reveal a clear differentiation between shepherd and hunting dogs as well as between gun dogs vs. hounds and guardian vs. herding shepherd dogs. The genomic regions distinguishing these groups harbour several genes associated with domestication and behavioural traits, including gregariousness (WBSRC17) and aggressiveness (CDH12 and HTT). Additionally, genes related to morphology, such as size and coat colour (ASIP and TYRP1) and texture (RSPO2), were identified. This comparative genomic analysis sheds light on the genetic underpinnings of the phenotypic and behavioural variations observed in Italian hunting and shepherd dogs.
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Affiliation(s)
- Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
| | - Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, University of Messina, Viale Palatucci 13, 98168 Messina, Italy;
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
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9
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Aldè M, Cantarella G, Zanetti D, Pignataro L, La Mantia I, Maiolino L, Ferlito S, Di Mauro P, Cocuzza S, Lechien JR, Iannella G, Simon F, Maniaci A. Autosomal Dominant Non-Syndromic Hearing Loss (DFNA): A Comprehensive Narrative Review. Biomedicines 2023; 11:1616. [PMID: 37371710 DOI: 10.3390/biomedicines11061616] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Autosomal dominant non-syndromic hearing loss (HL) typically occurs when only one dominant allele within the disease gene is sufficient to express the phenotype. Therefore, most patients diagnosed with autosomal dominant non-syndromic HL have a hearing-impaired parent, although de novo mutations should be considered in all cases of negative family history. To date, more than 50 genes and 80 loci have been identified for autosomal dominant non-syndromic HL. DFNA22 (MYO6 gene), DFNA8/12 (TECTA gene), DFNA20/26 (ACTG1 gene), DFNA6/14/38 (WFS1 gene), DFNA15 (POU4F3 gene), DFNA2A (KCNQ4 gene), and DFNA10 (EYA4 gene) are some of the most common forms of autosomal dominant non-syndromic HL. The characteristics of autosomal dominant non-syndromic HL are heterogenous. However, in most cases, HL tends to be bilateral, post-lingual in onset (childhood to early adulthood), high-frequency (sloping audiometric configuration), progressive, and variable in severity (mild to profound degree). DFNA1 (DIAPH1 gene) and DFNA6/14/38 (WFS1 gene) are the most common forms of autosomal dominant non-syndromic HL affecting low frequencies, while DFNA16 (unknown gene) is characterized by fluctuating HL. A long audiological follow-up is of paramount importance to identify hearing threshold deteriorations early and ensure prompt treatment with hearing aids or cochlear implants.
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Affiliation(s)
- Mirko Aldè
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Giovanna Cantarella
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Diego Zanetti
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Lorenzo Pignataro
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Ignazio La Mantia
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Luigi Maiolino
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Salvatore Ferlito
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Paola Di Mauro
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Salvatore Cocuzza
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Jérôme René Lechien
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Giannicola Iannella
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Francois Simon
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Antonino Maniaci
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
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10
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Calcium signaling and genetic rare diseases: An auditory perspective. Cell Calcium 2023; 110:102702. [PMID: 36791536 DOI: 10.1016/j.ceca.2023.102702] [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: 12/14/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
Deafness is a highly heterogeneous disorder which stems, for 50%, from genetic origins. Sensory transduction relies mainly on sensory hair cells of the cochlea, in the inner ear. Calcium is key for the function of these cells and acts as a fundamental signal transduction. Its homeostasis depends on three factors: the calcium influx, through the mechanotransduction channel at the apical pole of the hair cell as well as the voltage-gated calcium channel at the base of the cells; the calcium buffering via Ca2+-binding proteins in the cytoplasm, but also in organelles such as mitochondria and the reticulum endoplasmic mitochondria-associated membranes with specialized proteins; and the calcium extrusion through the Ca-ATPase pump, located all over the plasma membrane. In addition, the synaptic transmission to the central nervous system is also controlled by calcium. Genetic studies of inherited deafness have tremendously helped understand the underlying molecular pathways of calcium signaling. In this review, we discuss these different factors in light of the associated genetic diseases (syndromic and non-syndromic deafness) and the causative genes.
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11
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Kim KS, Koo HY, Bok J. Alternative splicing in shaping the molecular landscape of the cochlea. Front Cell Dev Biol 2023; 11:1143428. [PMID: 36936679 PMCID: PMC10018040 DOI: 10.3389/fcell.2023.1143428] [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: 01/13/2023] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
The cochlea is a complex organ comprising diverse cell types with highly specialized morphology and function. Until now, the molecular underpinnings of its specializations have mostly been studied from a transcriptional perspective, but accumulating evidence points to post-transcriptional regulation as a major source of molecular diversity. Alternative splicing is one of the most prevalent and well-characterized post-transcriptional regulatory mechanisms. Many molecules important for hearing, such as cadherin 23 or harmonin, undergo alternative splicing to produce functionally distinct isoforms. Some isoforms are expressed specifically in the cochlea, while some show differential expression across the various cochlear cell types and anatomical regions. Clinical phenotypes that arise from mutations affecting specific splice variants testify to the functional relevance of these isoforms. All these clues point to an essential role for alternative splicing in shaping the unique molecular landscape of the cochlea. Although the regulatory mechanisms controlling alternative splicing in the cochlea are poorly characterized, there are animal models with defective splicing regulators that demonstrate the importance of RNA-binding proteins in maintaining cochlear function and cell survival. Recent technological breakthroughs offer exciting prospects for overcoming some of the long-standing hurdles that have complicated the analysis of alternative splicing in the cochlea. Efforts toward this end will help clarify how the remarkable diversity of the cochlear transcriptome is both established and maintained.
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Affiliation(s)
- Kwan Soo Kim
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hei Yeun Koo
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinwoong Bok
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
- *Correspondence: Jinwoong Bok,
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12
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Souza Bomfim GH, Giacomello M, Lacruz RS. PMCA Ca 2+ clearance in dental enamel cells depends on the magnitude of cytosolic Ca 2. FASEB J 2023; 37:e22679. [PMID: 36515675 PMCID: PMC11006021 DOI: 10.1096/fj.202201291r] [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: 08/08/2022] [Revised: 10/31/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022]
Abstract
Enamel formation (amelogenesis) is a two-step process whereby crystals partially grow during the secretory stage followed by a significant growth expansion during the maturation stage concurrent with an increase in vectorial Ca2+ transport. This requires tight regulation of cytosolic Ca2+ (c Ca2+ ) concentration in the enamel forming ameloblasts by controlling Ca2+ influx (entry) and Ca2+ extrusion (clearance). Gene and protein expression studies suggest that the plasma membrane Ca2+ -ATPases (PMCA1-4) are likely involved in c Ca2+ extrusion in ameloblasts, yet no functional analysis of these pumps has been reported nor whether their activity changes across amelogenesis. PMCAs have high Ca2+ affinity and low Ca2+ clearance which may be a limiting factor in their contribution to enamel formation as maturation stage ameloblasts handle high Ca2+ loads. We analyzed PMCA function in rat secretory and maturation ameloblasts by blocking or potentiating these pumps. Low/moderate elevations in c Ca2+ measured using the Ca2+ probe Fura-2-AM show that secretory ameloblasts clear Ca2+ faster than maturation stage cells through PMCAs. This process was completely inhibited by an external alkaline (pH 9.0) solution or was significantly delayed by the PMCA blockers vanadate and caloxin 1b1. Eliciting higher c Ca2+ transients via the activation of the ORAI1 Ca2+ channel showed that the PMCAs of maturation ameloblasts were more efficient. Inhibiting PMCAs decreased the rate of Ca2+ influx via ORAI1 but potentiation with forskolin had no effect. Our findings suggest that PMCAs are functional Ca2+ pumps during amelogenesis regulating c Ca2+ upon low and/or moderate Ca2+ stimulus in secretory stage, thus participating in amelogenesis.
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Affiliation(s)
| | - Marta Giacomello
- Department of Biology, University of Padova, Padua, Italy
- Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Rodrigo S. Lacruz
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, USA
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13
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Klimara MJ, Nishimura C, Wang D, Kolbe DL, Schaefer AM, Walls WD, Frees KL, Smith RJH, Azaiez H. De novo variants are a common cause of genetic hearing loss. Genet Med 2022; 24:2555-2567. [PMID: 36194208 PMCID: PMC9729384 DOI: 10.1016/j.gim.2022.08.028] [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: 06/29/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/06/2022] Open
Abstract
PURPOSE De novo variants (DNVs) are a well-recognized cause of genetic disorders. The contribution of DNVs to hearing loss (HL) is poorly characterized. We aimed to evaluate the rate of DNVs in HL-associated genes and assess their contribution to HL. METHODS Targeted genomic enrichment and massively parallel sequencing were used for molecular testing of all exons and flanking intronic sequences of known HL-associated genes, with no exclusions on the basis of type of HL or clinical features. Segregation analysis was performed, and previous reports of DNVs in PubMed and ClinVar were reviewed to characterize the rate, distribution, and spectrum of DNVs in HL. RESULTS DNVs were detected in 10% (24/238) of trios for whom segregation analysis was performed. Overall, DNVs were causative in at least ∼1% of probands for whom a genetic diagnosis was resolved, with marked variability based on inheritance mode and phenotype. DNVs of MITF were most common (21% of DNVs), followed by GATA3 (13%), STRC (13%), and ACTG1 (8%). Review of reported DNVs revealed gene-specific variability in contribution of DNV to the mutational spectrum of HL-associated genes. CONCLUSION DNVs are a relatively common cause of genetic HL and must be considered in all cases of sporadic HL.
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Affiliation(s)
- Miles J Klimara
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Carla Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Donghong Wang
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Diana L Kolbe
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Amanda M Schaefer
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - William D Walls
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Kathy L Frees
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA.
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA.
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14
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Morisawa K, Sato T, Shimoyamada M, Mizuno R, Ohashi H, Watanabe-Hisazumi H, Takeshima K, Kojima A, Sato S, Hasegawa T, Takahashi T. Adapted whole-body surveillance for von Hippel-Lindau-associated tumors in 3p deletion syndrome with VHL deletion: A case report. Pediatr Blood Cancer 2022; 69:e29732. [PMID: 35441425 DOI: 10.1002/pbc.29732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 03/28/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Kazumi Morisawa
- Department of Pediatrics, Saitama City Hospital, Saitama, Japan.,Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Takeshi Sato
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | | | - Ryuichi Mizuno
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Japan
| | | | | | - Atsuhiro Kojima
- Department of Neurosurgery, Saitama City Hospital, Saitama, Japan
| | - Seiji Sato
- Department of Pediatrics, Saitama City Hospital, Saitama, Japan
| | - Tomonobu Hasegawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Takao Takahashi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
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15
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Pourtavakoli A, Ghafouri-Fard S. Calcium signaling in neurodevelopment and pathophysiology of autism spectrum disorders. Mol Biol Rep 2022; 49:10811-10823. [PMID: 35857176 DOI: 10.1007/s11033-022-07775-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/05/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Autism spectrum disorder (ASD) covers a group of neurodevelopmental disorders with complex genetic background. Several genetic mutations, epigenetic alterations, copy number variations and single nucleotide polymorphisms have been reported that cause ASD or modify its phenotype. Among signaling pathways that influence pathogenesis of ASD, calcium signaling has a prominent effect. METHODS We searched PubMed and Google Scholar databases with key words "Calcium signaling" and "Autism spectrum disorder". CONCLUSION This type of signaling has essential roles in the cell physiology. Endoplasmic reticulum and mitochondria are the key organelles involved in this signaling. It is vastly accepted that organellar disorders intensely influence the central nervous system (CNS). Several lines of evidence indicate alterations in the function of calcium channels in polygenic disorders affecting CNS. In the current review, we describe the role of calcium signaling in normal function of CNS and pathophysiology of ASD.
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Affiliation(s)
- Ashkan Pourtavakoli
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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16
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Searching for the Molecular Basis of Partial Deafness. Int J Mol Sci 2022; 23:ijms23116029. [PMID: 35682719 PMCID: PMC9181477 DOI: 10.3390/ijms23116029] [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: 03/31/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
Hearing is an important human sense for communicating and connecting with others. Partial deafness (PD) is a common hearing problem, in which there is a down-sloping audiogram. In this study, we apply a practical system for classifying PD patients, used for treatment purposes, to distinguish two groups of patients: one with almost normal hearing thresholds at low frequencies (PDT-EC, n = 20), and a second group with poorer thresholds at those same low frequencies (PDT-EAS, n = 20). After performing comprehensive genetic testing with a panel of 237 genes, we found that genetic factors can explain a significant proportion of both PDT-EC and PDT-EAS hearing losses, accounting, respectively, for approx. one-fifth and one-half of all the cases in our cohort. Most of the causative variants were located in dominant and recessive genes previously linked to PD, but more than half of the variants were novel. Among the contributors to PDT-EC we identified OSBPL2 and SYNE4, two relatively new hereditary hearing loss genes with a low publication profile. Our study revealed that, for all PD patients, a postlingual hearing loss more severe in the low-frequency range is associated with a higher detection rate of causative variants. Isolating a genetic cause of PD is important in terms of prognosis, therapeutic effectiveness, and risk of recurrence.
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17
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Bassani S, Beelen E, Rossel M, Voisin N, Morgan A, Arribat Y, Chatron N, Chrast J, Cocca M, Delprat B, Faletra F, Giannuzzi G, Guex N, Machavoine R, Pradervand S, Smits JJ, van de Kamp JM, Ziegler A, Amati F, Marlin S, Kremer H, Locher H, Maurice T, Gasparini P, Girotto G, Reymond A. Variants in USP48 encoding ubiquitin hydrolase are associated with autosomal dominant non-syndromic hereditary hearing loss. Hum Mol Genet 2021; 30:1785-1796. [PMID: 34059922 DOI: 10.1093/hmg/ddab145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
Non-Syndromic Hereditary Hearing Loss (NSHHL) is a genetically heterogeneous sensory disorder with about 120 genes already associated. Through exome sequencing and data aggregation, we identified a family with six affected individuals and one unrelated NSHHL patient with predicted-to-be deleterious missense variants in USP48. We also uncovered an eighth patient presenting unilateral cochlear nerve aplasia and a de novo splice variant in the same gene. USP48 encodes a ubiquitin carboxyl-terminal hydrolase under evolutionary constraint. Pathogenicity of the variants is supported by in vitro assays that showed that the mutated proteins are unable to hydrolyze tetra-ubiquitin. Correspondingly, three-dimensional representation of the protein containing the familial missense variant affects a loop that controls binding to ubiquitin. Consistent with a contribution of USP48 to auditory function, immunohistology showed that the encoded protein is expressed in the developing human inner ear, specifically in the spiral ganglion neurons, outer sulcus, interdental cells of the spiral limbus, stria vascularis, Reissner's membrane, and in the transient Kolliker's organ that is essential for auditory development. Engineered zebrafish knocked-down for usp48, the USP48 ortholog, presented with a delayed development of primary motor neurons, less developed statoacoustic neurons innervating the ears, decreased swimming velocity and circling swimming behavior indicative of vestibular dysfunction and hearing impairment. Corroboratingly, acoustic startle response assays revealed a significant decrease of auditory response of zebrafish lacking usp48 at 600 Hz and 800 Hz wavelengths. In conclusion, we describe a novel autosomal dominant NSHHL gene through a multipronged approach combining exome sequencing, animal modeling, immunohistology and molecular assays.
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Affiliation(s)
- Sissy Bassani
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Edward Beelen
- Department of Otorhinolaryngology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Norine Voisin
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Anna Morgan
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health, IRCCS, Burlo Garofolo, Trieste, Italy
| | - Yoan Arribat
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Chatron
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Massimiliano Cocca
- Institute for Maternal and Child Health, IRCCS, Burlo Garofolo, Trieste, Italy
| | | | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS, Burlo Garofolo, Trieste, Italy
| | - Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Roxane Machavoine
- Centre de référence Surdités Génétiques, Hôpital Necker, Institut Imagine, Paris, France
| | - Sylvain Pradervand
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Jeroen J Smits
- Department of Otorhinolaryngology and Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jiddeke M van de Kamp
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Alban Ziegler
- Centre de référence Surdités Génétiques, Hôpital Necker, Institut Imagine, Paris, France
| | - Francesca Amati
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Sandrine Marlin
- Centre de référence Surdités Génétiques, Hôpital Necker, Institut Imagine, Paris, France
| | - Hannie Kremer
- Department of Otorhinolaryngology and Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heiko Locher
- Department of Otorhinolaryngology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tangui Maurice
- MMDN, Univ Montpellier, EPHE, INSERM, Montpellier, France
| | - Paolo Gasparini
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health, IRCCS, Burlo Garofolo, Trieste, Italy
| | - Giorgia Girotto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health, IRCCS, Burlo Garofolo, Trieste, Italy
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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18
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Chen T, Rohacek AM, Caporizzo M, Nankali A, Smits JJ, Oostrik J, Lanting CP, Kücük E, Gilissen C, van de Kamp JM, Pennings RJE, Rakowiecki SM, Kaestner KH, Ohlemiller KK, Oghalai JS, Kremer H, Prosser BL, Epstein DJ. Cochlear supporting cells require GAS2 for cytoskeletal architecture and hearing. Dev Cell 2021; 56:1526-1540.e7. [PMID: 33964205 PMCID: PMC8137675 DOI: 10.1016/j.devcel.2021.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022]
Abstract
In mammals, sound is detected by mechanosensory hair cells that are activated in response to vibrations at frequency-dependent positions along the cochlear duct. We demonstrate that inner ear supporting cells provide a structural framework for transmitting sound energy through the cochlear partition. Humans and mice with mutations in GAS2, encoding a cytoskeletal regulatory protein, exhibit hearing loss due to disorganization and destabilization of microtubule bundles in pillar and Deiters' cells, two types of inner ear supporting cells with unique cytoskeletal specializations. Failure to maintain microtubule bundle integrity reduced supporting cell stiffness, which in turn altered cochlear micromechanics in Gas2 mutants. Vibratory responses to sound were measured in cochleae from live mice, revealing defects in the propagation and amplification of the traveling wave in Gas2 mutants. We propose that the microtubule bundling activity of GAS2 imparts supporting cells with mechanical properties for transmitting sound energy through the cochlea.
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Affiliation(s)
- Tingfang Chen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alex M Rohacek
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew Caporizzo
- Department of Physiology, Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amir Nankali
- The Caruso Department of Otolaryngology-Head and Neck Surgery, University of Southern California, Los Angeles, CA, USA
| | - Jeroen J Smits
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jaap Oostrik
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cornelis P Lanting
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Erdi Kücük
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jiddeke M van de Kamp
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Ronald J E Pennings
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Staci M Rakowiecki
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kevin K Ohlemiller
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - John S Oghalai
- The Caruso Department of Otolaryngology-Head and Neck Surgery, University of Southern California, Los Angeles, CA, USA
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Benjamin L Prosser
- Department of Physiology, Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas J Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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19
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Novel Variants in Hearing Loss Genes and Associations With Audiometric Thresholds in a Multi-ethnic Cohort of US Patients With Cochlear Implants. Otol Neurotol 2021; 41:978-985. [PMID: 32658404 DOI: 10.1097/mao.0000000000002671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
OBJECTIVES To investigate novel variants in hearing loss genes and clinical factors affecting audiometric outcomes of cochlear implant (CI) patients. BACKGROUND Approximately 50% of hearing loss has a genetic etiology, with certain genetic variants more prevalent in specific ethnic groups. Different variants and some clinical variables including inner ear malformations result in different prognoses or clinical outcomes after CI. METHODS Medical and genetic testing records of pediatric CI patients were reviewed for clinical variables. Minor allele frequencies of variants were obtained from Genome Aggregation Database (gnomAD) and variants were classified for pathogenicity. Standard statistical testing was done using Fisher's exact, Wilcoxon, and Spearman correlation tests. RESULTS Eighteen CI patients with genetic test results had pathogenic variants, including six patients with syndromic hearing loss and six patients with known GJB2 variants. Novel pathogenic variants were noted in CHD7, ADGRV1, and ARID1B, with variants in the latter two genes identified in Hispanic patients. Overall, carriage of genetic variants was associated with better pre-CI audiometric thresholds at 2000 Hz (p = 0.048). On the other hand, post-CI thresholds were significantly worse in patients with inner ear malformations, particularly in patients with atretic cochlear nerve canals. CONCLUSION Four novel pathogenic variants were identified, which contributes to knowledge of allelic spectrum for hearing loss especially in Hispanic patients. In this cohort, carriage of pathogenic variants particularly of GJB2 variants was associated with better pre-CI audiometric thresholds, while patients with inner ear malformations had worse post-CI audiometric thresholds.
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20
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Hwang SM, Lee JY, Park CK, Kim YH. The Role of TRP Channels and PMCA in Brain Disorders: Intracellular Calcium and pH Homeostasis. Front Cell Dev Biol 2021; 9:584388. [PMID: 33585474 PMCID: PMC7876282 DOI: 10.3389/fcell.2021.584388] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/06/2021] [Indexed: 12/19/2022] Open
Abstract
Brain disorders include neurodegenerative diseases (NDs) with different conditions that primarily affect the neurons and glia in the brain. However, the risk factors and pathophysiological mechanisms of NDs have not been fully elucidated. Homeostasis of intracellular Ca2+ concentration and intracellular pH (pHi) is crucial for cell function. The regulatory processes of these ionic mechanisms may be absent or excessive in pathological conditions, leading to a loss of cell death in distinct regions of ND patients. Herein, we review the potential involvement of transient receptor potential (TRP) channels in NDs, where disrupted Ca2+ homeostasis leads to cell death. The capability of TRP channels to restore or excite the cell through Ca2+ regulation depending on the level of plasma membrane Ca2+ ATPase (PMCA) activity is discussed in detail. As PMCA simultaneously affects intracellular Ca2+ regulation as well as pHi, TRP channels and PMCA thus play vital roles in modulating ionic homeostasis in various cell types or specific regions of the brain where the TRP channels and PMCA are expressed. For this reason, the dysfunction of TRP channels and/or PMCA under pathological conditions disrupts neuronal homeostasis due to abnormal Ca2+ and pH levels in the brain, resulting in various NDs. This review addresses the function of TRP channels and PMCA in controlling intracellular Ca2+ and pH, which may provide novel targets for treating NDs.
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Affiliation(s)
- Sung-Min Hwang
- Gachon Pain Center, Department of Physiology, Gachon University College of Medicine, Incheon, South Korea
| | - Ji Yeon Lee
- Gil Medical Center, Department of Anesthesiology and Pain Medicine, Gachon University, Incheon, South Korea
| | - Chul-Kyu Park
- Gachon Pain Center, Department of Physiology, Gachon University College of Medicine, Incheon, South Korea
| | - Yong Ho Kim
- Gachon Pain Center, Department of Physiology, Gachon University College of Medicine, Incheon, South Korea
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21
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Morgan A, Lenarduzzi S, Spedicati B, Cattaruzzi E, Murru FM, Pelliccione G, Mazzà D, Zollino M, Graziano C, Ambrosetti U, Seri M, Faletra F, Girotto G. Lights and Shadows in the Genetics of Syndromic and Non-Syndromic Hearing Loss in the Italian Population. Genes (Basel) 2020; 11:genes11111237. [PMID: 33105617 PMCID: PMC7690429 DOI: 10.3390/genes11111237] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
Hearing loss (HL), both syndromic (SHL) and non-syndromic (NSHL), is the most common sensory disorder, affecting ~460 million people worldwide. More than 50% of the congenital/childhood cases are attributable to genetic causes, highlighting the importance of genetic testing in this class of disorders. Here we applied a multi-step strategy for the molecular diagnosis of HL in 125 patients, which included: (1) an accurate clinical evaluation, (2) the analysis of GJB2, GJB6, and MT-RNR1 genes, (3) the evaluation STRC-CATSPER2 and OTOA deletions via Multiplex Ligation Probe Amplification (MLPA), (4) Whole Exome Sequencing (WES) in patients negative to steps 2 and 3. Our approach led to the characterization of 50% of the NSHL cases, confirming both the relevant role of the GJB2 (20% of cases) and STRC deletions (6% of cases), and the high genetic heterogeneity of NSHL. Moreover, due to the genetic findings, 4% of apparent NSHL patients have been re-diagnosed as SHL. Finally, WES characterized 86% of SHL patients, supporting the role of already know disease-genes. Overall, our approach proved to be efficient in identifying the molecular cause of HL, providing essential information for the patients’ future management.
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Affiliation(s)
- Anna Morgan
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
- Correspondence:
| | - Stefania Lenarduzzi
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Beatrice Spedicati
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34125 Trieste, Italy
| | - Elisabetta Cattaruzzi
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Flora Maria Murru
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Giulia Pelliccione
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Daniela Mazzà
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Marcella Zollino
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, UOC Genetica, 00168 Rome, Italy;
- Istituto di Medicina Genomica, Università Cattolica Sacro Cuore, 00168 Rome, Italy
| | - Claudio Graziano
- Unit of Medical Genetics, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy; (C.G.); (M.S.)
| | - Umberto Ambrosetti
- Audiology and audiophonology, University of Milano/Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy;
| | - Marco Seri
- Unit of Medical Genetics, S. Orsola-Malpighi Hospital, 40138 Bologna, Italy; (C.G.); (M.S.)
| | - Flavio Faletra
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
| | - Giorgia Girotto
- Institute for Maternal and Child Health–IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (S.L.); (B.S.); (E.C.); (F.M.M.); (G.P.); (D.M.); (F.F.); (G.G.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34125 Trieste, Italy
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22
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de Bruijn SE, Smits JJ, Liu C, Lanting CP, Beynon AJ, Blankevoort J, Oostrik J, Koole W, de Vrieze E, Cremers CWRJ, Cremers FPM, Roosing S, Yntema HG, Kunst HPM, Zhao B, Pennings RJE, Kremer H. A RIPOR2 in-frame deletion is a frequent and highly penetrant cause of adult-onset hearing loss. J Med Genet 2020; 58:jmedgenet-2020-106863. [PMID: 32631815 PMCID: PMC8120656 DOI: 10.1136/jmedgenet-2020-106863] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/25/2020] [Accepted: 04/01/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Hearing loss is one of the most prevalent disabilities worldwide, and has a significant impact on quality of life. The adult-onset type of the condition is highly heritable but the genetic causes are largely unknown, which is in contrast to childhood-onset hearing loss. METHODS Family and cohort studies included exome sequencing and characterisation of the hearing phenotype. Ex vivo protein expression addressed the functional effect of a DNA variant. RESULTS An in-frame deletion of 12 nucleotides in RIPOR2 was identified as a highly penetrant cause of adult-onset progressive hearing loss that segregated as an autosomal dominant trait in 12 families from the Netherlands. Hearing loss associated with the deletion in 63 subjects displayed variable audiometric characteristics and an average (SD) age of onset of 30.6 (14.9) years (range 0-70 years). A functional effect of the RIPOR2 variant was demonstrated by aberrant localisation of the mutant RIPOR2 in the stereocilia of cochlear hair cells and failure to rescue morphological defects in RIPOR2-deficient hair cells, in contrast to the wild-type protein. Strikingly, the RIPOR2 variant is present in 18 of 22 952 individuals not selected for hearing loss in the Southeast Netherlands. CONCLUSION Collectively, the presented data demonstrate that an inherited form of adult-onset hearing loss is relatively common, with potentially thousands of individuals at risk in the Netherlands and beyond, which makes it an attractive target for developing a (genetic) therapy.
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Affiliation(s)
- Suzanne E de Bruijn
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Jeroen J Smits
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Chang Liu
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Cornelis P Lanting
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Andy J Beynon
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | | | - Jaap Oostrik
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Wouter Koole
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
| | - Erik de Vrieze
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Cor W R J Cremers
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Henricus P M Kunst
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
- Radboud Institute for Health Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Bo Zhao
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ronald J E Pennings
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Hannie Kremer
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
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23
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David D, Freixo JP, Fino J, Carvalho I, Marques M, Cardoso M, Piña-Aguilar RE, Morton CC. Comprehensive clinically oriented workflow for nucleotide level resolution and interpretation in prenatal diagnosis of de novo apparently balanced chromosomal translocations in their genomic landscape. Hum Genet 2020; 139:531-543. [PMID: 32030560 PMCID: PMC10501484 DOI: 10.1007/s00439-020-02121-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/28/2020] [Indexed: 12/27/2022]
Abstract
We present a comprehensive clinically oriented workflow for large-insert genome sequencing (liGS)-based nucleotide level resolution and interpretation of de novo (dn) apparently balanced chromosomal abnormalities (BCA) in prenatal diagnosis (PND). Retrospective or concomitant with conventional PND and liGS, molecular and newly developed clinically inspired bioinformatic tools (TAD-GConTool and CNV-ConTool) are applied to analyze and assess the functional and phenotypic outcome of dn structural variants (dnSVs). Retrospective analysis of four phenotype-associated dnSVs identified during conventional PND precisely reveal the genomic elements disrupted by the translocation breakpoints. Identification of autosomal dominant disease due to the disruption of ANKS1B and WDR26 by t(12;17)(q23.1;q21.33)dn and t(1;3)(q24.11;p25.3)dn breakpoints, respectively, substantiated the proposed workflow. We then applied this workflow to two ongoing prenatal cases with apparently balanced dnBCAs: 46,XX,t(16;17)(q24;q21.3)dn referred for increased risk on combined first trimester screening and 46,XY,t(2;19)(p13;q13.1)dn referred due to a previous trisomy 21 pregnancy. Translocation breakpoints in the t(16;17) involve ANKRD11 and WNT3 and disruption of ANKRD11 resulted in KBG syndrome confirmed in postnatal follow-up. Breakpoints in the t(2;19) are within ATP6V1B1 and the 3' UTR of CEP89, and are not interpreted to cause disease. Genotype-phenotype correlation confirms the causative role of WDR26 in the Skraban-Deardorff and 1q41q42 microdeletion phenocopy syndromes, and that disruption of ANKS1B causes ANKS1B haploinsufficiency syndrome. In sum, we show that an liGS-based approach can be realized in PND care providing additional information concerning clinical outcomes of dnBCAs in patients with such rearrangements.
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Affiliation(s)
- Dezső David
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
| | - João P Freixo
- Department of Medical Genetics, Central Lisbon Hospital Center (CHLC), Lisbon, Portugal
| | - Joana Fino
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Inês Carvalho
- Department of Medical Genetics, Central Lisbon Hospital Center (CHLC), Lisbon, Portugal
| | - Mariana Marques
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Manuela Cardoso
- Department of Human Genetics, National Health Institute Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
| | - Raul E Piña-Aguilar
- Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Cynthia C Morton
- Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Manchester Academic Health Science Center, University of Manchester, Manchester, UK
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24
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Small fish, big prospects: using zebrafish to unravel the mechanisms of hereditary hearing loss. Hear Res 2020; 397:107906. [PMID: 32063424 DOI: 10.1016/j.heares.2020.107906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/13/2020] [Accepted: 01/29/2020] [Indexed: 12/16/2022]
Abstract
Over the past decade, advancements in high-throughput sequencing have greatly enhanced our knowledge of the mutational signatures responsible for hereditary hearing loss. In its present state, the field has a largely uncensored view of protein coding changes in a growing number of genes that have been associated with hereditary hearing loss, and many more that have been proposed as candidate genes. Sequencing data can now be generated using methods that have become widespread and affordable. The greatest hurdles facing the field concern functional validation of uncharacterized genes and rapid application to human diseases, including hearing and balance disorders. To date, over 30 hearing-related disease models exist in zebrafish. New genome editing technologies, including CRISPR/Cas9 will accelerate the functional validation of hearing loss genes and variants in zebrafish. Here, we discuss current progress in the field and recent advances in genome editing approaches.
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