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Rabbani B, Moghadam MA, Esmaeili S, Rabbani A, Akbari B, Mahdieh N. Pancreatitis as a Main Consequence of APOC2-Related Hypertriglyceridemia: The Role of Nonsense and Frameshift Variants. Int J Genomics 2024; 2024:6653857. [PMID: 38938447 PMCID: PMC11208794 DOI: 10.1155/2024/6653857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/13/2023] [Accepted: 05/17/2024] [Indexed: 06/29/2024] Open
Abstract
APOC2-related hypertriglyceridemia occurs due to biallelic variants of this gene. Here, genotype-phenotype architecture of all pathogenic APOC2 variants is investigated among heterozygous and homozygous individuals. Clinical heterogeneity of various types of the variants is also described, and pancreatitis in more than half of homozygotes carrying chain-termination variants is highlighted as well. For this study, patients were selected who had a plasma triglyceride level above 250 mg/dL. The coding and intronic regions of the APOC2 gene were amplified using the Sanger sequencing to investigate the presence of variants. The genotypes, lipid profiles, and detailed clinical features were documented for all APOC2-related patients and heterozygous individuals. Pathogenicity of the variants was predicted and categorized using available bioinformatics tools such as MutationTaster and PolyPhen-2 and ACMG criteria. MetaDome and Phyre2 were applied for structural and functional in silico analyses. 40% (12 out of 30) of APOC2 variants were chain-termination (nonsense and frameshift) variants. These types of variants were determined in 60.53% of patients. 55% of these patients showed pancreatitis followed by lipemia retinalis (29%), abdominal pain (24%), hepatosplenomegaly (24%), and xanthomas (18%). The mean age of onset was about 22 years old. In at least 50% of 38 homozygous individuals, the TG level was more than 2000 mg/dL. More than 25% of heterozygous individuals showed at least one symptom. Pancreatitis and a severe form of HTG were found in 5 and 2% of heterozygous individuals, respectively. The main clinical features of APOC2-related hypertriglyceridemia include pancreatitis, lipemia retinalis, abdominal pain, hepatosplenomegaly, and xanthomas. Nonsense and frameshift homozygous variants usually lead to a severe form of hypertriglyceridemia. Pancreatitis is one of the main consequences of these types of mutations; thus, it is important to consider this point when evaluating asymptomatic individuals. Heterozygous individuals may become symptomatic due to the role of unknown modifying agent including environmental genetic factors.
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Affiliation(s)
- Bahareh Rabbani
- Growth and Development Research CenterTehran University of Medical Sciences, Tehran, Iran
| | - Mohadeseh Aghli Moghadam
- Department of GeneticsFaculty of SciencesShahid Chamran University of Ahvaz, Ahvaz, Iran
- Cardiogenetic Research CenterRajaie Cardiovascular Medical and Research CenterIran University of Medical Sciences, Tehran, Iran
| | - Shiva Esmaeili
- Growth and Development Research CenterTehran University of Medical Sciences, Tehran, Iran
| | - Amirhassan Rabbani
- Taleghani HospitalDepartment of Transplant & Hepatobiliary SurgeryShahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahman Akbari
- Department of Medical BiotechnologySchool of MedicineKermanshah University of Medical Sciences, Kermanshah, Iran
| | - Nejat Mahdieh
- Growth and Development Research CenterTehran University of Medical Sciences, Tehran, Iran
- Cardiogenetic Research CenterRajaie Cardiovascular Medical and Research CenterIran University of Medical Sciences, Tehran, Iran
- Physiology Research CenterIran University of Medical Sciences, Tehran, Iran
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Mahdieh N, Heidari M, Rezaei Z, Tavasoli AR, Hosseinpour S, Rasulinejad M, Dehnavi AZ, Ghahvechi Akbari M, Badv RS, Vafaei E, Mohebbi A, Mohammadi P, Hosseiny SMM, Azizimalamiri R, Nikkhah A, Pourbakhtyaran E, Rohani M, Khanbanha N, Nikbakht S, Movahedinia M, Karimi P, Ghabeli H, Hosseini SA, Rashidi FS, Garshasbi M, Kashani MR, Ghiasvand NM, Zuchner S, Synofzik M, Ashrafi MR. The genetic basis of early-onset hereditary ataxia in Iran: results of a national registry of a heterogeneous population. Hum Genomics 2024; 18:35. [PMID: 38570878 PMCID: PMC10988936 DOI: 10.1186/s40246-024-00598-5] [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: 01/14/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND To investigate the genetics of early-onset progressive cerebellar ataxia in Iran, we conducted a study at the Children's Medical Center (CMC), the primary referral center for pediatric disorders in the country, over a three-year period from 2019 to 2022. In this report, we provide the initial findings from the national registry. METHODS We selected all early-onset patients with an autosomal recessive mode of inheritance to assess their phenotype, paraclinical tests, and genotypes. The clinical data encompassed clinical features, the Scale for the Assessment and Rating of Ataxia (SARA) scores, Magnetic Resonance Imaging (MRI) results, Electrodiagnostic exams (EDX), and biomarker features. Our genetic investigations included single-gene testing, Whole Exome Sequencing (WES), and Whole Genome Sequencing (WGS). RESULTS Our study enrolled 162 patients from various geographic regions of our country. Among our subpopulations, we identified known and novel pathogenic variants in 42 genes in 97 families. The overall genetic diagnostic rate was 59.9%. Notably, we observed PLA2G6, ATM, SACS, and SCA variants in 19, 14, 12, and 10 families, respectively. Remarkably, more than 59% of the cases were attributed to pathogenic variants in these genes. CONCLUSIONS Iran, being at the crossroad of the Middle East, exhibits a highly diverse genetic etiology for autosomal recessive hereditary ataxia. In light of this heterogeneity, the development of preventive strategies and targeted molecular therapeutics becomes crucial. A national guideline for the diagnosis and management of patients with these conditions could significantly aid in advancing healthcare approaches and improving patient outcomes.
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Affiliation(s)
- Nejat Mahdieh
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Morteza Heidari
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Rezaei
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Reza Tavasoli
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Pediatric Headache Program, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Sareh Hosseinpour
- Department of Pediatrics, Division of Paediatric Neurology, Vali-E-Asr Hospital, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Rasulinejad
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Zare Dehnavi
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Ghahvechi Akbari
- Physical Medicine and Rehabilitation Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Shervin Badv
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Elahe Vafaei
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Mohebbi
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Pouria Mohammadi
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyyed Mohammad Mahdi Hosseiny
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Azizimalamiri
- Division of Pediatric Neurology, Department of Pediatrics, Golestan Medical, Educational and Research Center, Ahvaz Jundishapour University of Medical Sciences, Ahvaz, Iran
| | - Ali Nikkhah
- Department of Pediatrics, Division of Paediatric Neurology, Vali-E-Asr Hospital, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
- Department of Pediatrics, Division of Paediatric Neurology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elham Pourbakhtyaran
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Rohani
- Department of Neurology, School of Medicine, Hazrat Rasool-E Akram General Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Narges Khanbanha
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sedigheh Nikbakht
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mojtaba Movahedinia
- Children Growth Disorders Research Center, Department of Pediatric, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Parviz Karimi
- Department of Pediatric Diseases, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Homa Ghabeli
- Department of Pediatrics, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Seyed Ahmad Hosseini
- Department of Pediatrics, Taleghani Children's Hospital, Golestan University of Medical Sciences, Gorgan, Iran
| | - Fatemeh Sadat Rashidi
- Neuroscience Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Noor M Ghiasvand
- Department of Biology, Grand Valley State University, Allendale, MI, 49401, USA
| | - Stephan Zuchner
- Department of Human Genetics and John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany
- Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Mahmoud Reza Ashrafi
- Pediatric Neurology Division, Pediatrics Center of Excellence, Ataxia Clinic, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Pediatrics, Division of Paediatric Neurology, Growth and Development Research Center, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
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Vafaei N, Mohebbi A, Rezaei Z, Heidari M, Hosseinpour S, Dehnavi AZ, Ghamari A, Salehipour M, Rabbani A, Mahdieh N, Ashrafi MR. TPP1 Variants in Iranian patients: A Novel Pathogenic Homozygous Variant Causing Neuronal Ceroid Lipofuscinosis 2. Mol Syndromol 2024; 15:30-36. [PMID: 38357261 PMCID: PMC10862320 DOI: 10.1159/000534100] [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: 06/21/2023] [Accepted: 09/11/2023] [Indexed: 02/16/2024] Open
Abstract
Introduction TPP1 variants have been identified as a causative agent of neuronal ceroid lipofuscinosis 2 disease, that ataxia is one of its clinical features. Therefore, here, molecular study of TPP1 variants is presented in an Iranian cohort and a novel pathogenic variant is described. Methods This investigation was conducted as a cross-sectional study in a tertiary referral hospital, Children's Medical Center, Pediatrics Center of Excellence. Clinical presentations and pedigrees were documented. Patients with cerebellar ataxia were enrolled in this study. Next-generation sequencing was applied to confirm the diagnosis. Segregation and bioinformatics analyses were also done for the variants using Sanger sequencing. Results Forty-five patients were included in our study. The mean age of onset was 104 (+55.60) months (minimum = 31 months, maximum = 216 months). The majority of cases (73.3%) were born to consanguineous parents and only 1 patient (2.2%) had an affected sibling. Of the 45 patients, only 1 patient with a novel pathogenic variant (c.1425_1425+1delinsAT, p.A476Cfs*15) in the TPP1 gene was identified. Discussion The main strength of current study is the relatively large sample size. Besides, a novel pathogenic variant could be important toward the diagnosis and management of this condition. With significant advances in various therapies, early diagnosis could improve the treatments using personalized-based medicine.
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Affiliation(s)
- Nahid Vafaei
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Mohebbi
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Rezaei
- Pediatrics Center of Excellence, Department of Pediatric Neurology, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Morteza Heidari
- Pediatric Neurology Division, Children’s Medical Center, Pediatrics Center of Excellence, Myelin Disorders Clinic, Tehran University of Medical Sciences, Tehran, Iran
| | - Sareh Hosseinpour
- Pediatrics Center of Excellence, Department of Pediatric Neurology, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Zare Dehnavi
- Pediatrics Center of Excellence, Department of Pediatric Neurology, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Azin Ghamari
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Salehipour
- Department of Biology, Parand Branch, Islamic Azad University, Parand, Iran
| | - Ali Rabbani
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nejat Mahdieh
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Cardiogenetic Research Center, Rajaie Cardiovascular, Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Reza Ashrafi
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Pediatrics Center of Excellence, Department of Pediatric Neurology, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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Eshaghian T, Rabbani B, Badv RS, Mikaeeli S, Gharib B, Iyadurai S, Mahdieh N. COLQ-related congenital myasthenic syndrome: An integrative view. Neurogenetics 2023; 24:189-200. [PMID: 37231228 DOI: 10.1007/s10048-023-00719-7] [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: 03/14/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
Congenital myasthenic syndromes are inherited disorders caused by mutation in components of the neuromuscular junction and manifest early in life. Mutations in COLQ gene result in congenital myasthenic syndrome. Here, we present the analysis of data from 209 patients from 195 unrelated families highlighting genotype-phenotype correlation. In addition, we describe a COLQ homozygous variant a new patient and discuss it utilizing the Phyre2 and I-TASSER programs. Clinical, molecular genetics, imaging (MRI), and electrodiagnostic (EEG, EMG/NCS) evaluations were performed. Our data showed 89 pathogenic/likely pathogenic variants including 35 missenses, 21 indels, 14 nonsense, 14 splicing, and 5 large deletions variants. Eight common variants were responsible for 48.46% of those. Weakness in proximal muscles, hypotonia, and generalized weakness were detected in all individuals tested. Apart from the weakness, extensive clinical heterogeneity was noted among patients with COLQ-related patients based on their genotypes-those with variants affecting the splice site exhibited more severe clinical features while those with missense variants displayed milder phenotypes, suggesting the role of differential splice variants in multiple functions within the muscle. Analyses and descriptions of these COLQ variants may be helpful in clinical trial readiness and potential development of novel therapies in the setting of established structure-function relationships.
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Affiliation(s)
- Tina Eshaghian
- Growth and Development Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahareh Rabbani
- Growth and Development Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Shervin Badv
- Growth and Development Research, Tehran University of Medical Sciences, Tehran, Iran
- Children's Hospital Center, Pediatric Center of Excellence, Tehran University of Medical Center, Tehran, Iran
| | - Sahar Mikaeeli
- Growth and Development Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Behdad Gharib
- Children's Hospital Center, Pediatric Center of Excellence, Tehran University of Medical Center, Tehran, Iran
| | - Stanley Iyadurai
- Johns Hopkins All Children's Hospital, Division of Neurology, 601 5th Street S, St. Petersburg, FL, 33701, USA
| | - Nejat Mahdieh
- Growth and Development Research, Tehran University of Medical Sciences, Tehran, Iran.
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Niayesh-Vali asr Intersection, Tehran, Iran.
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Aboagye ET, Adadey SM, Wonkam-Tingang E, Amenga-Etego L, Awandare GA, Wonkam A. Global Distribution of Founder Variants Associated with Non-Syndromic Hearing Impairment. Genes (Basel) 2023; 14:399. [PMID: 36833326 PMCID: PMC9957346 DOI: 10.3390/genes14020399] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The genetic etiology of non-syndromic hearing impairment (NSHI) is highly heterogeneous with over 124 distinct genes identified. The wide spectrum of implicated genes has challenged the implementation of molecular diagnosis with equal clinical validity in all settings. Differential frequencies of allelic variants in the most common NSHI causal gene, gap junction beta 2 (GJB2), has been described as stemming from the segregation of a founder variant and/or spontaneous germline variant hot spots. We aimed to systematically review the global distribution and provenance of founder variants associated with NSHI. The study protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews, with the registration number "CRD42020198573". Data from 52 reports, involving 27,959 study participants from 24 countries, reporting 56 founder pathogenic or likely pathogenic (P/LP) variants in 14 genes (GJB2, GJB6, GSDME, TMC1, TMIE, TMPRSS3, KCNQ4, PJVK, OTOF, EYA4, MYO15A, PDZD7, CLDN14, and CDH23), were reviewed. Varied number short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) were used for haplotype analysis to identify the shared ancestral informative markers in a linkage disequilibrium and variants' origins, age estimates, and common ancestry computations in the reviewed reports. Asia recorded the highest number of NSHI founder variants (85.7%; 48/56), with variants in all 14 genes, followed by Europe (16.1%; 9/56). GJB2 had the highest number of ethnic-specific P/LP founder variants. This review reports on the global distribution of NSHI founder variants and relates their evolution to population migration history, bottleneck events, and demographic changes in populations linked with the early evolution of deleterious founder alleles. International migration and regional and cultural intermarriage, coupled to rapid population growth, may have contributed to re-shaping the genetic architecture and structural dynamics of populations segregating these pathogenic founder variants. We have highlighted and showed the paucity of data on hearing impairment (HI) variants in Africa, establishing unexplored opportunities in genetic traits.
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Affiliation(s)
- Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Samuel Mawuli Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG Box 54, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- McKusick-Nathans Institute and Department of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Sharma N, Kumari D, Panigrahi I, Khetarpal P. A systematic review of the monogenic causes of Non-Syndromic Hearing Loss (NSHL) and discussion of Current Diagnosis and Treatment options. Clin Genet 2023; 103:16-34. [PMID: 36089522 DOI: 10.1111/cge.14228] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/13/2022]
Abstract
Hearing impairment is one of the most widespread inheritable sensory disorder affecting at least 1 in every 1000 born. About two-third of hereditary hearing loss (HHL) disorders are non-syndromic. To provide comprehensive update of monogenic causes of non-syndromic hearing loss (NSHL), literature search has been carried out with appropriate keywords in the following databases-PubMed, Google Scholar, Cochrane library, and Science Direct. Out of 2214 papers, 271 papers were shortlisted after applying inclusion and exclusion criterion. Data extracted from selected papers include information about gene name, identified pathogenic variants, ethnicity of the patient, age of onset, gender, title, authors' name, and year of publication. Overall, pathogenic variants in 98 different genes have been associated with NSHL. These genes have important role to play during early embryonic development in ear structure formation and hearing development. Here, we also review briefly the recent information about diagnosis and treatment approaches. Understanding pathogenic genetic variants are helpful in the management of affected and may offer targeted therapies in future.
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Affiliation(s)
- Nandita Sharma
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Divya Kumari
- Department of Pediatrics Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Inusha Panigrahi
- Department of Pediatrics Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Preeti Khetarpal
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
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Avraham KB, Khalaily L, Noy Y, Kamal L, Koffler-Brill T, Taiber S. The noncoding genome and hearing loss. Hum Genet 2022; 141:323-333. [PMID: 34491412 DOI: 10.1007/s00439-021-02359-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/29/2021] [Indexed: 12/16/2022]
Abstract
The age of sequencing has provided unprecedented insights into the human genome. The coding region of the genome comprises nearly 20,000 genes, of which approximately 4000 are associated with human disease. Beyond the protein-coding genome, which accounts for only 3% of the genome, lies a vast pool of regulatory elements in the form of promoters, enhancers, RNA species, and other intricate elements. These features undoubtably influence human health and disease, and as a result, a great deal of effort is currently being invested in deciphering their identity and mechanism. While a paucity of material has caused a lag in identifying these elements in the inner ear, the emergence of technologies for dealing with a minimal number of cells now has the field working overtime to catch up. Studies on microRNAs (miRNAs), long non-coding RNAs (lncRNAs), methylation, histone modifications, and more are ongoing. A number of microRNAs and other noncoding elements are known to be associated with hearing impairment and there is promise that regulatory elements will serve as future tools and targets of therapeutics and diagnostics. This review covers the current state of the field and considers future directions for the noncoding genome and implications for hearing loss.
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Affiliation(s)
- Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel.
| | - Lama Khalaily
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Yael Noy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Lara Kamal
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Shahar Taiber
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel
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8
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Ghasemnejad T, Shekari Khaniani M, Nouri Nojadeh J, Mansoori Derakhshan S. A novel missense variant in ESRRB gene causing autosomal recessive non-syndromic hearing loss: in silico analysis of a case. BMC Med Genomics 2022; 15:18. [PMID: 35101039 PMCID: PMC8805370 DOI: 10.1186/s12920-022-01165-4] [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: 07/08/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022] Open
Abstract
Background Hereditary hearing loss (HHL) is a common heterogeneous disorder affecting all ages, ethnicities, and genders. The most common form of HHL is autosomal recessive non-syndromic hearing loss (ARNSHL), in which there is no genotype–phenotype correlation in the majority of cases. This study aimed to identify the genetic causes of hearing loss (HL) in a family with Iranian Azeri Turkish ethnicity negative for gap junction beta-2 (GJB2), gap junction beta-6 (GJB6), and mitochondrially encoded 12S rRNA (MT-RNR1) deleterious mutations.
Methods Targeted genome sequencing method was applied to detect genetic causes of HL in the family. Sanger sequencing was employed to verify the segregation of the variant. Finally, we used bioinformatics tools and American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines to determine whether the detected variant might affect the corresponding protein or not. Results A novel homozygous missense mutation, c.499G>A (p.G167R), was identified in exon 5 of the ESRRB (estrogen-related receptor beta) gene. Healthy and affected family members confirmed the co-segregation of the variant with ARNSHL. Eventually, the variant's pathogenicity was confirmed by the in silico analysis and the ACMG/AMP guidelines. Conclusion The study suggests that the detected variant, c.499G>A, plays a crucial role in the development of ARNSHL, emphasizing the clinical significance of the ESRRB gene in ARNSHL patients. Additionally, it would be helpful for genetic counseling and clinical management of ARNSHL patients and providing preventive opportunities. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01165-4.
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Affiliation(s)
- Tohid Ghasemnejad
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahmoud Shekari Khaniani
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Nouri Nojadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sima Mansoori Derakhshan
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Vaché C, Baux D, Bianchi J, Baudoin C, Faugère V, Francannet C, Koenig M, Kalatzis V, Roux AF. Reclassification of a TMC1 synonymous substitution as a variant disrupting splicing regulatory elements associated with recessive hearing loss. Eur J Hum Genet 2022; 30:34-41. [PMID: 34857896 PMCID: PMC8738754 DOI: 10.1038/s41431-021-01010-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 01/03/2023] Open
Abstract
Alterations of the transmembrane channel-like 1 gene (TMC1) are involved in autosomal recessive and dominant nonsyndromic hearing loss (NSHL). To date, up to 117 causal variants including substitutions, insertions and splice variants have been reported in families from different populations. In a patient suffering from severe prelingual NSHL, we identified, in the homozygous state, the previously considered likely benign synonymous c.627C>T; p.(Leu209=) substitution. We used in silico tools predicting variant-induced alterations of splicing regulatory elements (SREs) and pinpointed this transition as a candidate splice-altering variation. Functional splicing analysis, using a minigene assay, confirmed that the variant altered a critical regulatory sequence which is essential for the exon 11 inclusion in the TMC1 transcripts. This result was reinforced by the analysis of orthologous TMC1 mammalian sequences for which the deleterious effect on the mRNA processing of a native thymidine was always counteracted by the presence of a stronger donor splice site or additional enhancer motifs. This study demonstrates, for the first time, the pathogenicity of the c.627C>T alteration leading to its reclassification as a causal variant impacting SREs and highlights the major importance of exhaustive studies to accurately evaluate the pathogenicity of a variant, regardless of the variation type.
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Affiliation(s)
- Christel Vaché
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France ,grid.121334.60000 0001 2097 0141Institute for Neurosciences of Montpellier, Univ Montpellier, Inserm, Montpellier, France
| | - David Baux
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France ,grid.121334.60000 0001 2097 0141Institute for Neurosciences of Montpellier, Univ Montpellier, Inserm, Montpellier, France
| | - Julie Bianchi
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Corinne Baudoin
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Valérie Faugère
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Christine Francannet
- grid.411163.00000 0004 0639 4151Department of Medical Genetics, Estaing Hospital, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Michel Koenig
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Vasiliki Kalatzis
- grid.121334.60000 0001 2097 0141Institute for Neurosciences of Montpellier, Univ Montpellier, Inserm, Montpellier, France
| | - Anne-Françoise Roux
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France ,grid.121334.60000 0001 2097 0141Institute for Neurosciences of Montpellier, Univ Montpellier, Inserm, Montpellier, France
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10
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Zardadi S, Razmara E, Asgaritarghi G, Jafarinia E, Bitarafan F, Rayat S, Almadani N, Morovvati S, Garshasbi M. Novel homozygous variants in the TMC1 and CDH23 genes cause autosomal recessive nonsyndromic hearing loss. Mol Genet Genomic Med 2020; 8:e1550. [PMID: 33205915 PMCID: PMC7767568 DOI: 10.1002/mgg3.1550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/22/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Background Hereditary hearing loss (HL) is a heterogeneous and most common sensory neural disorder. At least, 76 genes have been reported in association with autosomal recessive nonsyndromic HL (ARNSHL). Herein, we subjected two patients with bilateral sensorineural HL in two distinct consanguineous Iranian families to figure out the underlying genetic factors. Methods Physical and sensorineural examinations were performed on the patients. Imaging also was applied to unveil any abnormalities in anatomical structures of the middle and inner ear. In order to decipher the possible genetic causes of the verified GJB2‐negative samples, the probands were subjected to whole‐exome sequencing and, subsequently, Sanger sequencing was applied for variant confirmation. Results Clinical examinations showed ARNSHL in the patients. After doing whole exome sequencing, two novel variants were identified that were co‐segregating with HL that were absent in 100 ethnically matched controls. In the first family, a novel homozygous variant, NM_138691.2: c.530T>C; p.(lle177Thr), in TMC1 gene co‐segregated with prelingual ARNSHL. In the second family, NM_022124.6: c.2334G>A; p.(Trp778*) was reported as a nonsense variant causing prelingual ARNSHL. Conclusion These findings can, in turn, endorse how TMC1 and CDH23 screening is critical to detecting HL in Iranian patients. Identifying TMC1 and CDH23 pathogenic variants doubtlessly help in the detailed genotypic characterization of HL.
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Affiliation(s)
- Safoura Zardadi
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Golareh Asgaritarghi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Jafarinia
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Bitarafan
- Department of Cellular and Molecular Biology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Sima Rayat
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Navid Almadani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Saeid Morovvati
- Department of Genetics, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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11
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Sadeghian L, Tabatabaiefar MA, Fattahi N, Pourreza MR, Tahmasebi P, Alavi Z, Hashemzadeh Chaleshtori M. Next-generation sequencing reveals a novel pathological mutation in the TMC1 gene causing autosomal recessive non-syndromic hearing loss in an Iranian kindred. Int J Pediatr Otorhinolaryngol 2019; 124:99-105. [PMID: 31176026 DOI: 10.1016/j.ijporl.2019.05.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/18/2019] [Accepted: 05/19/2019] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Hearing loss (HL) is the most common sensory-neural disorder with excessive clinical and genetic heterogeneity, which negatively affects life quality. Autosomal recessive non-syndromic hearing loss (ARNSHL) is the most common form of the disease with no specific genotype-phenotype correlation in most of the cases. Whole exome sequencing (WES) is a powerful tool to overcome the problem of finding mutations in heterogeneous disorders. METHODS A comprehensive clinical and pedigree examination was performed on a multiplex family from Khuzestan province suffering from hereditary HL. Direct sequencing of GJB2 and genetic linkage analysis of DFNB1A/B was accomplished. WES was utilized to find possible genetic etiology of the disease. Co-segregation analysis of the candidate variant was done. High resolution melting analysis was applied to detect variant status in 50 healthy matched controls. RESULTS Clinical investigations suggested ARNSHL in the pedigree. The family was negative for DFNB1A/B. WES revealed a novel nonsense mutation, c.256G > T (p.Glu86*), in TMC1 segregating with the phenotype in the pedigree. The variant was absent in the controls. CONCLUSION Here, we report successful application of WES to identify the molecular pathogenesis of ARNSHL in a large family. The novel nonsense TMC1 variant meets the criteria of being pathogenic according to the ACMG-AMP variant interpretation guideline.
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Affiliation(s)
- Ladan Sadeghian
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran; Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Najmeh Fattahi
- Cilinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammad Reza Pourreza
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Parisa Tahmasebi
- Department of Biology, Faculty of Sciences, Ilam University, Ilam, Iran
| | - Zahra Alavi
- Department of Genetics, Islamic Azad University, Shahrekord Branch, Shahrekord, Iran
| | - Morteza Hashemzadeh Chaleshtori
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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12
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Ghasemnejad T, Shekari Khaniani M, Zarei F, Farbodnia M, Mansoori Derakhshan S. An update of common autosomal recessive non-syndromic hearing loss genes in Iranian population. Int J Pediatr Otorhinolaryngol 2017; 97:113-126. [PMID: 28483220 DOI: 10.1016/j.ijporl.2017.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 11/16/2022]
Abstract
Autosomal-recessive genes are responsible for about 80% of the hereditary non-syndromic hearing loss (NSHL) cases. In Iran, due to consanguineous marriages, NSHL is the second most frequent disability after intellectual disability, occurring one in 16 individuals. Enormous heterogeneity in the genetic pathology of hearing loss causes a major challenge in identification of responsible genes. In Iran, GJB2 is responsible for the most cases of pre-lingual and non-syndromic hearing loss (with frequency of 16.7%) which followed by other genes with lower frequency. Although several studies have indicated that a large proportion of both syndromic and non-syndromic hearing loss in Iranian populations are caused by defects in just a few genes, new detection strategies such as NGS (Next-generation sequencing) have increased the spectrum of responsible mutations. However, by applying this technique in Iran patients screening, the role of lots of novel related genes have been reported. In this review, we aim to describe function of these genes and their contribution to non-syndromic genetic hearing loss in Iranian population and we classify the genes by their functions.
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Affiliation(s)
- Tohid Ghasemnejad
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Genetic, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Fatemeh Zarei
- Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mina Farbodnia
- Department of Cellular and Molecular Biology, Faculty of Sciences, Saba University, Urmia, Iran
| | - Sima Mansoori Derakhshan
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Genetic, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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13
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Motavaf M, Soveizi M, Maleki M, Mahdieh N. MYO15A splicing mutations in hearing loss: A review literature and report of a novel mutation. Int J Pediatr Otorhinolaryngol 2017; 96:35-38. [PMID: 28390610 DOI: 10.1016/j.ijporl.2017.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/27/2017] [Accepted: 03/02/2017] [Indexed: 10/20/2022]
Abstract
Sensorineural hearing loss (SNHL) is the most prevalent genetic sensory defect in humans, affecting about 1 in 1000 newborns around the world. Non-syndromic SNHL accounts for nearly 70% of hereditary hearing loss and 80% of SNHL cases show an autosomal recessive mode of inheritance (ARNSHL). In the present study, we applied targeted-exome sequencing to a family with a single proband affected by congenital sensorineural hearing loss. 127 known genes were sequenced to find the causative mutation. One novel homozygous donor splice site mutation, c.4596 + 1G > A (IVS12 + 1G > A) was found in MYO15A gene. Analysis of this mutation within the family showed that the mutation segregates with hearing loss. New DNA sequencing technologies could lead to identification of the disease causing variants especially in highly heterogeneous disorders such as hearing loss.
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Affiliation(s)
- Mahsa Motavaf
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahdieh Soveizi
- Genetics Research Laboratory, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Genetics Research Laboratory, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Nejat Mahdieh
- Genetics Research Laboratory, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.
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14
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Beheshtian M, Babanejad M, Azaiez H, Bazazzadegan N, Kolbe D, Sloan-Heggen C, Arzhangi S, Booth K, Mohseni M, Frees K, Azizi MH, Daneshi A, Farhadi M, Kahrizi K, Smith RJ, Najmabadi H. Heterogeneity of Hereditary Hearing Loss in Iran: a Comprehensive Review. ARCHIVES OF IRANIAN MEDICINE 2017; 19:720-728. [PMID: 27743438 DOI: 0161910/aim.0010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A significant contribution to the causes of hereditary hearing impairment comes from genetic factors. More than 120 genes and 160 loci have been identified to be involved in hearing impairment. Given that consanguine populations are more vulnerable to most inherited diseases, such as hereditary hearing loss (HHL), the genetic picture of HHL among the Iranian population, which consists of at least eight ethnic subgroups with a high rate of intermarriage, is expected to be highly heterogeneous. Using an electronic literature review through various databases such as PubMed, MEDLINE, and Scopus, we review the current picture of HHL in Iran. In this review, we present more than 39 deafness genes reported to cause non-syndromic HHL in Iran, of which the most prevalent causative genes include GJB2, SLC26A4, MYO15A, and MYO7A. In addition, we highlight some of the more common genetic causes of syndromic HHL in Iran. These results are of importance for further investigation and elucidation of the molecular basis of HHL in Iran and also for developing a national diagnostic tool tailored to the Iranian context enabling early and efficient diagnosis of hereditary hearing impairment.
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Affiliation(s)
- Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hela Azaiez
- Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Niloofar Bazazzadegan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Diana Kolbe
- Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Christina Sloan-Heggen
- Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kevin Booth
- Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kathy Frees
- Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | | | - Ahmad Daneshi
- Head and Neck Surgery Department and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhadi
- Head and Neck Surgery Department and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Richard Jh Smith
- Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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15
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Gao X, Huang SS, Yuan YY, Wang GJ, Xu JC, Ji YB, Han MY, Yu F, Kang DY, Lin X, Dai P. Targeted gene capture and massively parallel sequencing identify TMC1 as the causative gene in a six-generation Chinese family with autosomal dominant hearing loss. Am J Med Genet A 2015; 167A:2357-65. [PMID: 26079994 DOI: 10.1002/ajmg.a.37206] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 05/25/2015] [Indexed: 12/26/2022]
Abstract
Hereditary nonsyndromic hearing loss is extremely heterogeneous. Mutations in the transmembrane channel-like gene1 (TMC1) are known to cause autosomal dominant and recessive forms of nonsyndromic hearing loss linked to the loci of DFNA36 and DFNB7/11, respectively. We characterized a six-generation Chinese family (5315) with progressive, postlingual autosomal dominant nonsyndromic hearing loss (ADNSHL). By combining targeted capture of 82 known deafness genes, next-generation sequencing and bioinformatic analysis, we identified TMC1 c.1714G>A (p. D572N) as the disease-causing mutation. This mutation co-segregated with hearing loss in other family members and was not detected in 308 normal controls. In order to determine the prevalence of TMC1 c.1714G>A in Chinese ADNSHL families, we used DNA samples from 67 ADNSHL families with sloping audiogram and identified two families carry this mutation. To determine whether it arose from a common ancestor, we analyzed nine STR markers. Our results indicated that TMC1 c.1714G>A (p.D572N) account for about 4.4% (3/68) of ADNSHL in the Chinese population.
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Affiliation(s)
- Xue Gao
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China.,Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China.,Department of Otorhinolaryngology, Second Artillery General Hospital, Beijing, P. R. China
| | - Sha-Sha Huang
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Yong-Yi Yuan
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Guo-Jian Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China.,Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
| | - Jin-Cao Xu
- Department of Otorhinolaryngology, Second Artillery General Hospital, Beijing, P. R. China
| | - Yu-Bin Ji
- Department of Otorhinolaryngology, Second Artillery General Hospital, Beijing, P. R. China
| | - Ming-Yu Han
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China.,Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
| | - Fei Yu
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Dong-Yang Kang
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Xi Lin
- Department of Otolaryngology, Emory University School of Medicine, Atlanta, GA
| | - Pu Dai
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China.,Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
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16
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Davoudi-Dehaghani E, Fallah MS, Tavakkoly-Bazzaz J, Bagherian H, Zeinali S. Allelic heterogeneity among Iranian DFNB7/11 families: report of a new Iranian deaf family with TMC1 mutation identified by next-generation sequencing. Acta Otolaryngol 2015; 135:125-9. [PMID: 25423259 DOI: 10.3109/00016489.2014.969383] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
CONCLUSION Co-segregation of c.2030T>C mutation with hearing loss in an Iranian family and absence of this mutation in 100 Iranian controls confirms the pathogenicity of this mutation. Allelic heterogeneity among Iranian DFNB7/11 families has been shown by the identification of six different mutations in eight families. OBJECTIVES Transmembrane channel-like 1 (TMC1) gene encodes an integral membrane protein such that its mutations can cause DFNB7/11 hearing loss. To date, several TMC1 mutations have been reported from Iran. Here we report a new DFNB7/11 Iranian family with an unreported TMC1 mutation in Iran. METHODS A total of 66 genes related to hearing loss were analyzed using the OtoSCOPE platform in an affected member of an Iranian deaf family (Irn-Deaf-6866). Sanger sequencing was performed to confirm next-generation sequencing findings. RESULTS A mutation, c.2030T>C, was identified in exon 21 of the TMC1 gene in the investigated member of the family. Sequencing results in all members of the family confirmed association of this mutation with hearing loss. None of 100 ethnically matched healthy controls had this mutation.
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17
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Lin F, Li D, Wang P, Fan D, De J, Zhu W. Autosomal recessive non-syndromic hearing loss is caused by novel compound heterozygous mutations in TMC1 from a Tibetan Chinese family. Int J Pediatr Otorhinolaryngol 2014; 78:2216-21. [PMID: 25458163 DOI: 10.1016/j.ijporl.2014.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/07/2014] [Accepted: 10/10/2014] [Indexed: 10/24/2022]
Abstract
OBJECTIVES Hearing loss is the most common sensory disorder worldwide. Biallelic mutations in 42 different genes have been identified as associated with autosomal recessive non-syndromic hearing loss (ARNSHL). One of the common genes responsible for ARNSHL is TMC1. TMC1 mutations have been reported to cause non-syndromic hearing loss in a variety of populations. The current study is designed to investigate mutations prevalent among Chinese ethnic groups with ARNSHL. METHODS Targeted exome sequencing (TES) was employed to study the genetic causes of two siblings with ARNSHL in a Tibetan Chinese family. Variants identified by TES were further confirmed by Sanger sequencing. RESULTS We identified two distinct variants in the TMC1 gene in two deaf siblings of one Tibetan Chinese family using TES. Both siblings inherited a paternal allele containing a deletion of c.1396_1398AAC (p.Asn466del) and a maternal allele containing an insertion of c.2210_2211insCT (p.Glu737HisfsX2). The former disrupts a highly conserved residue in the large intracellular loop domain adjacent to the fourth transmembrane domain, and the latter causes a truncation of a portion of the C-terminal domain. These variants were compound heterzygous and segregated with the hearing impairment in this family. CONCLUSION The novel compound heterozygous mutant alleles of TMC1 identified in this study were responsible for the ARNSHL in this Tibetan Chinese family. Although compound heterozygous mutations in TMC1 occurring in different TMC1 domains have been previously described in Han Chinese; this result suggests that the TMC1 variants contributing to hereditary deafness in Chinese populations may be more complex than initially assumed and that sequence-based diagnostics will be required for a comprehensive evaluation of ARNSHL.
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Affiliation(s)
- Fangzhu Lin
- Department of Otolaryngology-Head and Neck Surgery, First Hospital of Jilin University, Changchun 130021, China
| | - Dejun Li
- Center for Prenatal Diagnosis, First Hospital of Jilin University, Changchun 130021, China
| | - Ping Wang
- Department of Otolaryngology-Head and Neck Surgery, First Hospital of Jilin University, Changchun 130021, China
| | - Dongyan Fan
- School of Medicine, Tibet University, Lhasa 850000, China
| | - Ji De
- School of Medicine, Tibet University, Lhasa 850000, China
| | - Wei Zhu
- Department of Otolaryngology-Head and Neck Surgery, First Hospital of Jilin University, Changchun 130021, China.
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18
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Ganapathy A, Pandey N, Srisailapathy CRS, Jalvi R, Malhotra V, Venkatappa M, Chatterjee A, Sharma M, Santhanam R, Chadha S, Ramesh A, Agarwal AK, Rangasayee RR, Anand A. Non-syndromic hearing impairment in India: high allelic heterogeneity among mutations in TMPRSS3, TMC1, USHIC, CDH23 and TMIE. PLoS One 2014; 9:e84773. [PMID: 24416283 PMCID: PMC3885616 DOI: 10.1371/journal.pone.0084773] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 11/19/2013] [Indexed: 11/29/2022] Open
Abstract
Mutations in the autosomal genes TMPRSS3, TMC1, USHIC, CDH23 and TMIE are known to cause hereditary hearing loss. To study the contribution of these genes to autosomal recessive, non-syndromic hearing loss (ARNSHL) in India, we examined 374 families with the disorder to identify potential mutations. We found four mutations in TMPRSS3, eight in TMC1, ten in USHIC, eight in CDH23 and three in TMIE. Of the 33 potentially pathogenic variants identified in these genes, 23 were new and the remaining have been previously reported. Collectively, mutations in these five genes contribute to about one-tenth of ARNSHL among the families examined. New mutations detected in this study extend the allelic heterogeneity of the genes and provide several additional variants for structure-function correlation studies. These findings have implications for early DNA-based detection of deafness and genetic counseling of affected families in the Indian subcontinent.
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Affiliation(s)
- Aparna Ganapathy
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Nishtha Pandey
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | - Rajeev Jalvi
- Department of Audiology, Ali Yavar Jung National Institute for the Hearing Handicapped, Mumbai, India
| | - Vikas Malhotra
- Department of ENT, Maulana Azad Medical College, New Delhi, India
| | - Mohan Venkatappa
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Arunima Chatterjee
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Meenakshi Sharma
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Rekha Santhanam
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Shelly Chadha
- Department of ENT, Maulana Azad Medical College, New Delhi, India
| | - Arabandi Ramesh
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, Chennai, India
| | - Arun K. Agarwal
- Department of ENT, Maulana Azad Medical College, New Delhi, India
| | - Raghunath R. Rangasayee
- Department of Audiology, Ali Yavar Jung National Institute for the Hearing Handicapped, Mumbai, India
| | - Anuranjan Anand
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- * E-mail:
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