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Shearer AE. Genetic testing for pediatric sensorineural hearing loss in the era of gene therapy. Curr Opin Otolaryngol Head Neck Surg 2024; 32:352-356. [PMID: 39146193 DOI: 10.1097/moo.0000000000001005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
PURPOSE OF REVIEW To summarize indications, methods, and diagnostic yields for genetic testing for pediatric hearing loss. RECENT FINDINGS Genetic testing has become a cornerstone of clinical care for children with sensorineural hearing loss. Recent studies have shown the efficacy of gene panels and exome sequencing for any child with sensorineural hearing loss. Recent findings have underscored the importance of a diagnosis in clinical care. Clinical trials for gene therapy for hearing loss have begun. SUMMARY Genetic testing has become critical for personalized care for children with hearing loss. Recent studies have shown a 43% overall diagnostic yield for genetic testing for pediatric hearing loss, though the diagnostic yield may range from 10 to 60% depending on clinical features. Syndromic diagnoses comprise 25% of positive genetic tests for pediatric sensorineural hearing loss. While diagnostic yield is lower for children with unilateral or asymmetric sensorineural hearing loss, the likelihood of syndromic hearing loss finding is higher. An early and accurate genetic diagnosis is required for participating in clinical trials for gene therapy for hearing loss.
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Affiliation(s)
- A Eliot Shearer
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School
- Boston Children's Hospital, Department of Otolaryngology & Communication Enhancement, Boston, Massachusetts, USA
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2
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Scheetz TE, Tollefson MR, Roos BR, Boese EA, Pouw AE, Stone EM, Schnieders MJ, Fingert JH. METTL23 Variants and Patients With Normal-Tension Glaucoma. JAMA Ophthalmol 2024:2824091. [PMID: 39325437 PMCID: PMC11428026 DOI: 10.1001/jamaophthalmol.2024.3829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Importance This research confirms and further establishes that pathogenic variants in a fourth gene, METTL23, are associated with autosomal dominant normal-tension glaucoma (NTG). Objective To determine the frequency of glaucoma-causing pathogenic variants in the METTL23 gene in a cohort of patients with NTG from Iowa. Design, Setting, and Participants This case-control study took place at a single tertiary care center in Iowa from January 1997 to January 2024, with analysis occurring between January 2023 and January 2024. Two groups of participants were enrolled from the University of Iowa clinics: 331 patients with NTG and 362 control individuals without glaucoma. Patients with a history of trauma; steroid use; stigmata of pigment dispersion syndrome; exfoliation syndrome; or pathogenic variants in MYOC, TBK1, or OPTN were also excluded. Main Outcomes and Measures Detection of an enrichment of METTL23 pathogenic variants in individuals with NTG compared with control individuals without glaucoma. Results The study included 331 patients with NTG (mean [SD] age, 68.0 [11.7] years; 228 [68.9%] female and 103 [31.1%] male) and 362 control individuals without glaucoma (mean [SD] age, 64.5 [12.6] years; 207 [57.2%] female and 155 [42.8%] male). There were 5 detected instances of 4 unique METTL23 pathogenic variants in patients with NTG. Three METTL23 variants-p.Ala7Val, p.Pro22Arg, and p.Arg63Trp-were judged to be likely pathogenic and were detected in 3 patients (0.91%) with NTG. However, when all detected variants were evaluated with either mutation burden analysis or logistic regression, their frequency was not statistically higher in individuals with NTG than in control individuals without glaucoma (1.5% vs 2.5%; P = .27). Conclusion and Relevance This investigation provides evidence that pathogenic variants in METTL23 are associated with NTG. Within an NTG cohort at a tertiary care center, pathogenic variants were associated with approximately 1% of NTG cases, a frequency similar to that of other known normal-tension glaucoma genes, including optineurin (OPTN), TANK-binding kinase 1 (TBK1), and myocilin (MYOC). The findings suggest that METTL23 pathogenic variants are likely involved in a biologic pathway that is associated with glaucoma that occurs at lower intraocular pressures.
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Affiliation(s)
- Todd E Scheetz
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Mallory R Tollefson
- Deparment of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City
| | - Ben R Roos
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Erin A Boese
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Andrew E Pouw
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Edwin M Stone
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Michael J Schnieders
- Institute for Vision Research, University of Iowa, Iowa City
- Deparment of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City
| | - John H Fingert
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
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3
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Rhim JW, Kim DK, Han JY, Park J. A sensorineural hearing loss harboring novel compound heterozygous variant in the TRIOBP gene: A case report. Heliyon 2024; 10:e36717. [PMID: 39296067 PMCID: PMC11408809 DOI: 10.1016/j.heliyon.2024.e36717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/21/2024] Open
Abstract
Background Autosomal recessive non-syndromic deafness-28 (DFNB28; OMIM #609823) specifically refers to prelingual sensorineural hearing loss (SNHL) resulting from homozygous or compound heterozygous mutations in the TRIO- and F-actin-binding protein, TRIOBP gene. In this report, we present a pediatric patient exhibiting novel compound heterozygous deleterious variants in the TRIOBP gene. Methods The auditory brainstem response result revealed both left- and right-sided deafness with a threshold of 20 dB normal hearing level in the proband. A comprehensive trio whole exome sequencing (WES) using the Celemics G-Mendeliome Whole Exome Sequencing Panel was employed. Results The WES analysis revealed compound heterozygous TRIOBP variants in the proband, namely c.1192_1195delCAACinsT/p.Gln398* classified as pathogenic and c.3661C > T/p.Arg1221Trp categorized as a variant of uncertain significance according to American College of Medical Genetics and Genomics guidelines. These variants are considered the most probable cause of the proband's SNHL. Conclusion TRIOBP isoforms are predominantly expressed in the inner ear, contributing to the formation of stereocilia rootlets. Further investigations are required to fully understand the phenotypic variability and establish the pathogenicity of the identified variant in relation to the TRIOBP gene and SNHL.
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Affiliation(s)
- Jung Woo Rhim
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Dong-Kee Kim
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea, Seoul, 06591, Republic of Korea
| | - Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, 54907, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, 54907, Republic of Korea
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Tsai CY, Hsu JSJ, Chen PL, Wu CC. Implementing next-generation sequencing for diagnosis and management of hereditary hearing impairment: a comprehensive review. Expert Rev Mol Diagn 2024; 24:753-765. [PMID: 39194060 DOI: 10.1080/14737159.2024.2396866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
INTRODUCTION Sensorineural hearing impairment (SNHI), a common childhood disorder with heterogeneous genetic causes, can lead to delayed language development and psychosocial problems. Next-generation sequencing (NGS) offers high-throughput screening and high-sensitivity detection of genetic etiologies of SNHI, enabling clinicians to make informed medical decisions, provide tailored treatments, and improve prognostic outcomes. AREAS COVERED This review covers the diverse etiologies of HHI and the utility of different NGS modalities (targeted sequencing and whole exome/genome sequencing), and includes HHI-related studies on newborn screening, genetic counseling, prognostic prediction, and personalized treatment. Challenges such as the trade-off between cost and diagnostic yield, detection of structural variants, and exploration of the non-coding genome are also highlighted. EXPERT OPINION In the current landscape of NGS-based diagnostics for HHI, there are both challenges (e.g. detection of structural variants and non-coding genome variants) and opportunities (e.g. the emergence of medical artificial intelligence tools). The authors advocate the use of technological advances such as long-read sequencing for structural variant detection, multi-omics analysis for non-coding variant exploration, and medical artificial intelligence for pathogenicity assessment and outcome prediction. By integrating these innovations into clinical practice, precision medicine in the diagnosis and management of HHI can be further improved.
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Affiliation(s)
- Cheng-Yu Tsai
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Jacob Shu-Jui Hsu
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
- Department of Otolaryngology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
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Gogal RA, Nessler AJ, Thiel AC, Bernabe HV, Corrigan Grove RA, Cousineau LM, Litman JM, Miller JM, Qi G, Speranza MJ, Tollefson MR, Fenn TD, Michaelson JJ, Okada O, Piquemal JP, Ponder JW, Shen J, Smith RJH, Yang W, Ren P, Schnieders MJ. Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. J Chem Phys 2024; 161:012501. [PMID: 38958156 PMCID: PMC11223778 DOI: 10.1063/5.0214652] [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: 04/18/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid-base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.
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Affiliation(s)
- Rose A. Gogal
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Aaron J. Nessler
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Andrew C. Thiel
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Hernan V. Bernabe
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Rae A. Corrigan Grove
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Leah M. Cousineau
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jacob M. Litman
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jacob M. Miller
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Guowei Qi
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Matthew J. Speranza
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Mallory R. Tollefson
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Timothy D. Fenn
- Analytical Development, LEXEO Therapeutics, New York, New York 10010, USA
| | - Jacob J. Michaelson
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | - Okimasa Okada
- Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | | | - Jay W. Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Richard J. H. Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | | | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas, Austin, Texas 78712, USA
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Zafeer MF, Ramzan M, Duman D, Mutlu A, Seyhan S, Kalcioglu T, Fitoz S, DeRosa BA, Guo S, Dykxhoorn DM, Tekin M. Human Organoids for Rapid Validation of Gene Variants Linked to Cochlear Malformations. RESEARCH SQUARE 2024:rs.3.rs-4474071. [PMID: 38947059 PMCID: PMC11213182 DOI: 10.21203/rs.3.rs-4474071/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Developmental anomalies of the hearing organ, the cochlea, are diagnosed in approximately one-fourth of individuals with congenital deafness. Most patients with cochlear malformations remain etiologically undiagnosed due to insufficient knowledge about underlying genes or the inability to make conclusive interpretations of identified genetic variants. We used exome sequencing for genetic evaluation of hearing loss associated with cochlear malformations in three probands from unrelated families. We subsequently generated monoclonal induced pluripotent stem cell (iPSC) lines, bearing patient-specific knockins and knockouts using CRISPR/Cas9 to assess pathogenicity of candidate variants. We detected FGF3 (p.Arg165Gly) and GREB1L (p.Cys186Arg), variants of uncertain significance in two recognized genes for deafness, and PBXIP1(p.Trp574*) in a candidate gene. Upon differentiation of iPSCs towards inner ear organoids, we observed significant developmental aberrations in knockout lines compared to their isogenic controls. Patient-specific single nucleotide variants (SNVs) showed similar abnormalities as the knockout lines, functionally supporting their causality in the observed phenotype. Therefore, we present human inner ear organoids as a tool to rapidly validate the pathogenicity of DNA variants associated with cochlear malformations.
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Affiliation(s)
| | | | - Duygu Duman
- Ankara University Faculty of Health Sciences
| | | | | | | | | | | | - Shengru Guo
- University of Miami Miller School of Medicine
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Ramzan M, Zafeer MF, Abad C, Guo S, Owrang D, Alper O, Mutlu A, Atik T, Duman D, Bademci G, Vona B, Kalcioglu MT, Walz K, Tekin M. Genetic heterogeneity in hereditary hearing loss: Potential role of kinociliary protein TOGARAM2. Eur J Hum Genet 2024; 32:639-646. [PMID: 38374469 PMCID: PMC11153511 DOI: 10.1038/s41431-024-01562-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 01/25/2024] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
Hearing loss (HL) is a heterogenous trait with pathogenic variants in more than 200 genes that have been discovered in studies involving small and large HL families. Over one-third of families with hereditary HL remain etiologically undiagnosed after screening for mutations in the recognized genes. Genetic heterogeneity complicates the analysis in multiplex families where variants in more than one gene can be causal in different individuals even in the same sibship. We employed exome or genome sequencing in at least two affected individuals with congenital or prelingual-onset, severe to profound, non-syndromic, bilateral sensorineural HL from four multiplex families. Bioinformatic analysis was performed to identify variants in known and candidate deafness genes. Our results show that in these four families, variants in a single HL gene do not explain HL in all affected family members, and variants in another known or candidate HL gene were detected to clarify HL in the entire family. We also present a variant in TOGARAM2 as a potential cause underlying autosomal recessive non-syndromic HL by showing its presence in a family with HL, its expression in the cochlea and the localization of the protein to cochlear hair cells. Conclusively, analyzing all affected family members separately can serve as a good source for the identification of variants in known and novel candidate genes for HL.
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Affiliation(s)
- Memoona Ramzan
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mohammad Faraz Zafeer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Clemer Abad
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Daniel Owrang
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and Inner Ear Lab, University Medical Center Göttingen, Göttingen, Germany
| | - Ozgul Alper
- Department of Medical Genetics, Antalya University Medical School, Antalya, Turkey
| | - Ahmet Mutlu
- Departmet of Otolaryngology, Istanbul Medeniyet University School of Medicine, Istanbul, Turkey
- Otorhinolaryngology Clinic of Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
| | - Tahir Atik
- Division of Pediatric Genetics, Ege University School of Medicine, Izmir, Turkey
| | - Duygu Duman
- Department of Audiology, Ankara University Faculty of Health Sciences, Ankara, Turkey
| | - Guney Bademci
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and Inner Ear Lab, University Medical Center Göttingen, Göttingen, Germany
| | - Mahmut Tayyar Kalcioglu
- Departmet of Otolaryngology, Istanbul Medeniyet University School of Medicine, Istanbul, Turkey
- Otorhinolaryngology Clinic of Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
| | - Katherina Walz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- IQUIBICEN CONICET, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, Argentina
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
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Gwack J, Kim N, Park J. Improving the Yield of Genetic Diagnosis through Additional Genetic Panel Testing in Hereditary Ophthalmic Diseases. Curr Issues Mol Biol 2024; 46:5010-5022. [PMID: 38785568 PMCID: PMC11119902 DOI: 10.3390/cimb46050300] [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: 04/07/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024] Open
Abstract
Numerous hereditary ophthalmic diseases display significant genetic diversity. Consequently, the utilization of gene panel sequencing allows a greater number of patients to receive a genetic diagnosis for their clinical manifestations. We investigated how to improve the yield of genetic diagnosis through additional gene panel sequencing in hereditary ophthalmic diseases. A gene panel sequencing consisting of a customized hereditary retinopathy panel or hereditary retinitis pigmentosa (RP) panel was prescribed and referred to a CAP-accredited clinical laboratory. If no significant mutations associated with hereditary retinopathy and RP were detected in either panel, additional gene panel sequencing was requested for research use, utilizing the remaining panel. After additional gene panel sequencing, a total of 16 heterozygous or homozygous variants were identified in 15 different genes associated with hereditary ophthalmic diseases. Of 15 patients carrying any candidate variants, the clinical symptoms could be tentatively accounted for by genetic mutations in seven patients. However, in the remaining eight patients, given the in silico mutation predictive analysis, variant allele frequency in gnomAD, inheritance pattern, and genotype-phenotype correlation, fully elucidating the clinical manifestations with the identified rare variant was challenging. Our study highlights the utility of gene panel sequencing in achieving accurate diagnoses for hereditary ophthalmic diseases and enhancing the diagnostic yield through additional gene panel sequencing. Thus, gene panel sequencing can serve as a primary tool for the genetic diagnosis of hereditary ophthalmic diseases, even in cases where a single genetic cause is suspected. With a deeper comprehension of the genetic mechanisms underlying these diseases, it becomes feasible.
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Affiliation(s)
- Jin Gwack
- Department of Preventive Medicine, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea;
| | - Namsu Kim
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
| | - Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
- Department of Laboratory Medicine, Daejeon St. Mary’s Hospital, Daejeon 34943, Republic of Korea
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Singh J, Randle MR, Walters BJ, Cox BC. The transcription factor Pou4f3 is essential for the survival of postnatal and adult mouse cochlear hair cells and normal hearing. Front Cell Neurosci 2024; 18:1369282. [PMID: 38566840 PMCID: PMC10985149 DOI: 10.3389/fncel.2024.1369282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Hair cells (HCs) of the cochlea are responsible for sound transduction and hearing perception in mammals. Genetic mutations in the transcription factor Pou4f3 cause non-syndromic autosomal dominant hearing loss in humans (DFNA15) which varies in the age of onset depending on the individual mutation. Mouse models with germline deletion or mutations in Pou4f3 have previously demonstrated its critical role in the maturation and survival of cochlear HCs during embryonic development. However, the role of Pou4f3 in auditory function and in the survival or maintenance of cochlear HCs after birth and during adulthood has not been studied. Methods Therefore, using the inducible CreER-loxP system, we deleted Pou4f3 from mouse cochlear HCs at different postnatal ages, relevant to specific stages of HC maturation and hearing function. Results and discussion Elevated auditory brainstem response thresholds and significant HC loss were detected in mice with Pou4f3 deletion compared to their control littermates, regardless of the age when Pou4f3 was deleted. However, HC loss occurred more rapidly when Pou4f3 was deleted from immature HCs. Additionally, HC loss caused by Pou4f3 deletion did not affect the number of cochlear supporting cells, but caused a delayed loss of spiral ganglion neurons at 4 months after the deletion. In conclusion, Pou4f3 is necessary for the survival of cochlear HCs and normal hearing at all postnatal ages regardless of their maturation state. Our data also suggest that Pou4f3 indirectly regulates the survival of spiral ganglion neurons.
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Affiliation(s)
- Jarnail Singh
- Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, United States
| | - Michelle R. Randle
- Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, United States
| | - Bradley J. Walters
- Department of Otolaryngology-Head and Neck Surgery, University of Mississippi Medical Center, Jackson, MS, United States
| | - Brandon C. Cox
- Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, United States
- Department of Otolaryngology, Southern Illinois University School of Medicine, Springfield, IL, United States
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Takahashi S, Kojima T, Wasano K, Homma K. Functional Studies of Deafness-Associated Pendrin and Prestin Variants. Int J Mol Sci 2024; 25:2759. [PMID: 38474007 PMCID: PMC10931795 DOI: 10.3390/ijms25052759] [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: 01/30/2024] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Pendrin and prestin are evolutionary-conserved membrane proteins that are essential for normal hearing. Dysfunction of these proteins results in hearing loss in humans, and numerous deafness-associated pendrin and prestin variants have been identified in patients. However, the pathogenic impacts of many of these variants are ambiguous. Here, we report results from our ongoing efforts to experimentally characterize pendrin and prestin variants using in vitro functional assays. With previously established fluorometric anion transport assays, we determined that many of the pendrin variants identified on transmembrane (TM) 10, which contains the essential anion binding site, and on the neighboring TM9 within the core domain resulted in impaired anion transport activity. We also determined the range of functional impairment in three deafness-associated prestin variants by measuring nonlinear capacitance (NLC), a proxy for motor function. Using the results from our functional analyses, we also evaluated the performance of AlphaMissense (AM), a computational tool for predicting the pathogenicity of missense variants. AM prediction scores correlated well with our experimental results; however, some variants were misclassified, underscoring the necessity of experimentally assessing the effects of variants. Together, our experimental efforts provide invaluable information regarding the pathogenicity of deafness-associated pendrin and prestin variants.
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Affiliation(s)
- Satoe Takahashi
- Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Takashi Kojima
- Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Otolaryngology, Head and Neck Surgery, National Hospital Organization Tochigi Medical Center, Tochigi 320-0057, Japan
| | - Koichiro Wasano
- Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Otolaryngology, Head and Neck Surgery, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Kazuaki Homma
- Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, IL 60208, USA
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Takahashi S, Kojima T, Wasano K, Homma K. Functional studies of deafness-associated pendrin and prestin variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576877. [PMID: 38328051 PMCID: PMC10849616 DOI: 10.1101/2024.01.23.576877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Pendrin and prestin are evolutionary conserved membrane proteins that are essential for normal hearing. Pendrin is an anion transporter required for normal development and maintenance of ion homeostasis in the inner ear, while prestin is a voltage-dependent motor responsible for cochlear amplification essential for high sensitivity and frequency selectivity of mammalian hearing. Dysfunction of these proteins result in hearing loss in humans, and numerous deafness-associated pendrin and prestin variants have been identified in patients. However, the pathogenic impacts of many of these variants are ambiguous. Here we report results from our ongoing efforts in experimentally characterizing pendrin and prestin variants using in vitro functional assays, providing invaluable information regarding their pathogenicity.
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