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Shadab M, Abbasi AA, Ejaz A, Ben-Mahmoud A, Gupta V, Kim HG, Vona B. Autosomal recessive non-syndromic hearing loss genes in Pakistan during the previous three decades. J Cell Mol Med 2024; 28:e18119. [PMID: 38534090 DOI: 10.1111/jcmm.18119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 11/29/2023] [Accepted: 01/02/2024] [Indexed: 03/28/2024] Open
Abstract
Hearing loss is a clinically and genetically heterogeneous disorder, with over 148 genes and 170 loci associated with its pathogenesis. The spectrum and frequency of causal variants vary across different genetic ancestries and are more prevalent in populations that practice consanguineous marriages. Pakistan has a rich history of autosomal recessive gene discovery related to non-syndromic hearing loss. Since the first linkage analysis with a Pakistani family that led to the mapping of the DFNB1 locus on chromosome 13, 51 genes associated with this disorder have been identified in this population. Among these, 13 of the most prevalent genes, namely CDH23, CIB2, CLDN14, GJB2, HGF, MARVELD2, MYO7A, MYO15A, MSRB3, OTOF, SLC26A4, TMC1 and TMPRSS3, account for more than half of all cases of profound hearing loss, while the prevalence of other genes is less than 2% individually. In this review, we discuss the most common autosomal recessive non-syndromic hearing loss genes in Pakistani individuals as well as the genetic mapping and sequencing approaches used to discover them. Furthermore, we identified enriched gene ontology terms and common pathways involved in these 51 autosomal recessive non-syndromic hearing loss genes to gain a better understanding of the underlying mechanisms. Establishing a molecular understanding of the disorder may aid in reducing its future prevalence by enabling timely diagnostics and genetic counselling, leading to more effective clinical management and treatments of hearing loss.
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Affiliation(s)
- Madiha Shadab
- Department of Zoology, Mirpur University of Science and Technology, Mirpur, Pakistan
| | - Ansar Ahmed Abbasi
- Department of Zoology, Mirpur University of Science and Technology, Mirpur, Pakistan
| | - Ahsan Ejaz
- Department of Physics, University of Kotli Azad Jammu and Kashmir, Kotli, Pakistan
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, China
| | - Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - 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
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Aliazami F, Gilani S, Farhud D, Naraghi M, Afshari M, Eslami M. Epidemiology, etiology, genetic variants in non- syndromic hearing loss in Iran: A systematic review and meta-analysis. Int J Pediatr Otorhinolaryngol 2023; 168:111512. [PMID: 37086676 DOI: 10.1016/j.ijporl.2023.111512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/27/2023] [Accepted: 03/11/2023] [Indexed: 04/24/2023]
Abstract
OBJECTIVES Hearing loss is one of the most common heterogeneous complicated disorders worldwide. We previously analyzed the results of published data on non-syndromic hearing loss in the Iranian population systematically. A broad range of genes is a challenge for molecular screening and clinical diagnosis in our populations on the ground of distinct genetics. The aim of this study was to analyze the role and frequency of the variants accountable for non-syndromic hearing loss (NSHL) in the Iranian population. These were identified with different methods including whole exome sequencing (WES), next-generation sequencing (NGS), targeted genomic enrichment and massively parallel sequencing (TGE + MPS), autozygosity mapping, STR markers, linkage analysis, and direct sequencing. This is the comprehensively study focusing on classifying 13 common NSHL genes according to their frequencies. Previous studies have not studied different regions and the Iranian population, and this is the definitive study on the topic. METHODS We searched Scopus, PubMed, Science Direct databases, and Google Scholar. After a systematic review of the evidence 95 studies were considered then 31 studies were eligible for meta-analysis. In total, 6995 families, 358 variants, and 117 novel variants were included. Statistical analyses were conducted using Stata SE version 11 software. The inverse variance method enjoyed combining data. Heterogeneity of the preliminary results was assessed using Q (Cochrane test), and I square index. Random effects or fixed models were applied to combine the results, relying on the degree of heterogeneity. Point and pooled prevalence of variants acting on different regions were illustrated by forest plots. RESULTS The total prevalence of at least one variant of GJB2 and SLC26A genes was estimated at 26% and 5%, respectively. Variant c.35delG accounted for 18% of the GJB2 variants while 1% of these variants were novel ones. The next most common variants in the GJB2 gene were c.109G>A at 3.5% and c.-23+1G>A at 2.3%. Moreover, the prevalence of GJB2 gene variants varied on average 0.002% from one region to another in Iran (p=0.849). Our meta-analysis also showed that the frequency of at least one variant of MYO15A varied between 1.2% and 12.5%. Corresponding prevalences for the other variants were as follows: ILDR1 (3.5%-3.7%), CDH23 (2%-10%), PJVK (1.4%-33%), TECTA (1.3%-6.7%), MYO6 (2%-4.8%), TMC1 (1.8%-2%), MYO7A (0.7%-5%), MARVELD2 (0.7-5%), OTOF (0.7%-4%), LRTOMT (0.7%-2.5%). Finally, we did not find any relationship between geographic area and the presence of these variants. CONCLUSION GJB2 gene variants were the most common cause of NSHL in Iran. Understanding the prevalence of NSHL gene frequency in Iran may be the foundation for future studies in an Iranian population which may lead to future NSHL therapy.
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Affiliation(s)
- Farnoush Aliazami
- Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Applied Biotechnology Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Sapideh Gilani
- Department of Surgery, Division of Otolaryngology, University of California, San Diego, 200 West Arbor Drive, MC 8654, San Diego, CA, 92103, United States.
| | - Dariush Farhud
- School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Department of Basic Sciences, Iranian Academy of Medical Sciences, Valiasr Sq., 22 Keshavarz Blvd, Tehran, 14, Iran.
| | - Mohsen Naraghi
- Department of Otorhinolaryngology-Head and Neck Surgery, TUMS School of Medicine, Rhinology Research Society, Orphans World Wide, 4411 Sunbeam Rd., Jacksonville, FL, 32257, United States.
| | - Mahdi Afshari
- Department of Community Medicine, School of Medicine, Zabol University of Medical Sciences, Rajaee Street, Zabol, Iran.
| | - Maryam Eslami
- Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Applied Biotechnology Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Sugawara T, Furuse K, Otani T, Wakayama T, Furuse M. Angulin-1 seals tricellular contacts independently of tricellulin and claudins. J Cell Biol 2021; 220:e202005062. [PMID: 34269802 PMCID: PMC8289698 DOI: 10.1083/jcb.202005062] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 04/24/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
Tricellular tight junctions (tTJs) are specialized tight junctions (TJs) that seal the intercellular space at tricellular contacts (TCs), where the vertices of three epithelial cells meet. Tricellulin and angulin family membrane proteins are known constituents of tTJs, but the molecular mechanism of tTJ formation remains elusive. Here, we investigated the roles of angulin-1 and tricellulin in tTJ formation in MDCK II cells by genome editing. Angulin-1-deficient cells lost the plasma membrane contact at TCs with impaired epithelial barrier function. The C terminus of angulin-1 bound to the TJ scaffold protein ZO-1, and disruption of their interaction influenced the localization of claudins at TCs, but not the tricellular sealing. Strikingly, the plasma membrane contact at TCs was formed in tricellulin- or claudin-deficient cells. These findings demonstrate that angulin-1 is responsible for the plasma membrane seal at TCs independently of tricellulin and claudins.
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Affiliation(s)
- Taichi Sugawara
- Division of Cell Structure, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki, Aichi, Japan
- Department of Physiological Sciences, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Aichi, Japan
- Department of Histology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kyoko Furuse
- Division of Cell Structure, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki, Aichi, Japan
| | - Tetsuhisa Otani
- Division of Cell Structure, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki, Aichi, Japan
- Department of Physiological Sciences, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Aichi, Japan
| | - Tomohiko Wakayama
- Department of Histology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mikio Furuse
- Division of Cell Structure, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki, Aichi, Japan
- Department of Physiological Sciences, The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Aichi, Japan
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Van Heurck R, Carminho-Rodrigues MT, Ranza E, Stafuzza C, Quteineh L, Gehrig C, Hammar E, Guipponi M, Abramowicz M, Senn P, Guinand N, Cao-Van H, Paoloni-Giacobino A. Benefits of Exome Sequencing in Children with Suspected Isolated Hearing Loss. Genes (Basel) 2021; 12:genes12081277. [PMID: 34440452 PMCID: PMC8391342 DOI: 10.3390/genes12081277] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/03/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022] Open
Abstract
Purpose: Hearing loss is characterized by an extensive genetic heterogeneity and remains a common disorder in children. Molecular diagnosis is of particular benefit in children, and permits the early identification of clinically-unrecognized hearing loss syndromes, which permits effective clinical management and follow-up, including genetic counselling. Methods: We performed whole-exome sequencing with the analysis of a panel of 189 genes associated with hearing loss in a prospective cohort of 61 children and 9 adults presenting mainly with isolated hearing loss. Results: The overall diagnostic rate using exome sequencing was 47.2% (52.5% in children; 22% in adults). In children with confirmed molecular results, 17/32 (53.2%) showed autosomal recessive inheritance patterns, 14/32 (43.75%) showed an autosomal dominant condition, and one case had X-linked hearing loss. In adults, the two patients showed an autosomal dominant inheritance pattern. Among the 32 children, 17 (53.1%) had nonsyndromic hearing loss and 15 (46.7%) had syndromic hearing loss. One adult was diagnosed with syndromic hearing loss and one with nonsyndromic hearing loss. The most common causative genes were STRC (5 cases), GJB2 (3 cases), COL11A1 (3 cases), and ACTG1 (3 cases). Conclusions: Exome sequencing has a high diagnostic yield in children with hearing loss and can reveal a syndromic hearing loss form before other organs/systems become involved, allowing the surveillance of unrecognized present and/or future complications associated with these syndromes.
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Affiliation(s)
- Roxane Van Heurck
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Maria Teresa Carminho-Rodrigues
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Emmanuelle Ranza
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Caterina Stafuzza
- Ear-Nose-Throat/Head and Neck Surgery Division, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.S.); (P.S.); (N.G.); (H.C.-V.)
| | - Lina Quteineh
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Corinne Gehrig
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Eva Hammar
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Michel Guipponi
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Marc Abramowicz
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
| | - Pascal Senn
- Ear-Nose-Throat/Head and Neck Surgery Division, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.S.); (P.S.); (N.G.); (H.C.-V.)
| | - Nils Guinand
- Ear-Nose-Throat/Head and Neck Surgery Division, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.S.); (P.S.); (N.G.); (H.C.-V.)
| | - Helene Cao-Van
- Ear-Nose-Throat/Head and Neck Surgery Division, Geneva University Hospitals, 1205 Geneva, Switzerland; (C.S.); (P.S.); (N.G.); (H.C.-V.)
| | - Ariane Paoloni-Giacobino
- Division of Genetic Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (R.V.H.); (M.T.C.-R.); (E.R.); (L.Q.); (C.G.); (E.H.); (M.G.); (M.A.)
- Correspondence:
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Naz S. Molecular genetic landscape of hereditary hearing loss in Pakistan. Hum Genet 2021; 141:633-648. [PMID: 34308486 DOI: 10.1007/s00439-021-02320-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/17/2021] [Indexed: 01/13/2023]
Abstract
Approximately 14.5 million Pakistani individuals have a hearing loss and half of these cases may be due to genetic causes. Though significant progress has been made in uncovering genetic variants for recessively inherited nonsyndromic deafness, Pendred syndrome, and Usher syndromes, the same is not true for dominantly inherited hearing loss, most syndromic cases and deafness with complex inheritance patterns. Variants of 57 genes have been reported to cause nonsyndromic recessive deafness in Pakistan, though most are rare. Variants of just five genes GJB2, HGF, MYO7A, SLC26A4, and TMC1 together explain 57% of profound deafness while those of GJB2, MYO15A, OTOF, SLC26A4, TMC1, and TMPRSS3 account for 47% of moderate to severe hearing loss. In contrast, although variants of at least 39 genes have been implicated in different deafness syndromes, their prevalence in the population and the spectrum of mutations have not been explored. Furthermore, research on genetics of deafness has mostly focused on individuals from the Punjab province and needs to be extended to other regions of Pakistan. Identifying the genes and their variants causing deafness in all ethnic groups is important as it will pinpoint rare as well as recurrent mutations. This information may ultimately help in offering genetic counseling and future treatments.
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Affiliation(s)
- Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
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6
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Panigrahi I, Kumari D, Kumar BNA. Single gene variants causing deafness in Asian Indians. J Genet 2021. [DOI: 10.1007/s12041-021-01288-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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He Y, Li DZ. Co-occurrence of two rare genetic diseases: A potential pitfall for prenatal diagnosis in successive pregnancies. Prenat Diagn 2020; 40:1606-1609. [PMID: 33015857 DOI: 10.1002/pd.5839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 11/12/2022]
Affiliation(s)
- Yi He
- Prenatal Diagnosis Unit, Dongguan Women and Children Healthcare Hospital, Guangzhou, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
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Sadeghi Z, Chavoshi Tarzjani SP, Miri Moosavi RS, Saber S, Ebrahimi A. A Rare Mutation in the MARVELD2 Gene Can Cause Nonsyndromic Hearing Loss. Int Med Case Rep J 2020; 13:291-296. [PMID: 32884365 PMCID: PMC7434373 DOI: 10.2147/imcrj.s257654] [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: 04/18/2020] [Accepted: 07/10/2020] [Indexed: 11/23/2022] Open
Abstract
The MARVELD2 gene which is located on the 5q13.2 may cause nonsyndromic hearing loss (NSHL) with autosomal recessive inherited pattern. So far c.1331+1G>A (IVS4+1G>A); NM_001038603.3, variant in deafness, has only reported previously in one Pakistani family in 2008 and it is reported for the first time in Iran and second time in the world. The case is a 21-year-old Iranian woman who has NSHL referred for genetic consultation, and her parents had a consanguineous marriage. To study the responsible genes for the mentioned disorder, whole exome sequencing (WES) was performed for the case. The result of WES analysis revealed a transition at the splice donor variant site of the MARVELD2 gene. The NGS result was confirmed by Sanger sequencing.
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Affiliation(s)
- Zahra Sadeghi
- Department of Genetics, Tehran-North Branch, Islamic Azad University, Tehran, Iran.,Jordan Medical and Genetic Laboratory, Tehran, Iran
| | | | | | - Siamak Saber
- Jordan Medical and Genetic Laboratory, Tehran, Iran
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Angulin-2/ILDR1, a tricellular tight junction protein, does not affect water transport in the mouse large intestine. Sci Rep 2020; 10:10374. [PMID: 32587380 PMCID: PMC7316798 DOI: 10.1038/s41598-020-67319-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 04/23/2020] [Indexed: 11/09/2022] Open
Abstract
Angulin-2/ILDR1 is a member of the angulin protein family, which is exclusively expressed at tricellular tight junctions in epithelia. Tricellular tight junctions are found where three cells meet and where three bicellular tight junction strands converge. Tricellular tight junctions are thought to be important for paracellular permeability of ions and water in epithelial tissues. It was recently reported that angulin-2/ILDR1 knockout mice have water transport abnormalities in the kidney. Since angulin-2/ILDR1 is the main tricellular tight junction protein in the large intestine, the goal of this research was to examine the effect of angulin-2/ILDR1 knockout on large intestinal paracellular water transport. We found that Ildr1 knockout mice showed no detectable phenotype other than deafness. In addition, paracellular transport as assessed by Ussing chamber was unchanged in Ildr1 knockout mice. However, we found that in the colon and the kidney of Ildr1 knockout mice, another tricellular tight junction protein, angulin-1/LSR, changes its expression pattern. We propose that with this replacement in tissue localization, angulin-1/LSR compensates for the loss of angulin-2/ILDR1 and maintains the barrier and function of the epithelia in the large intestine as well as the kidney.
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10
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Matsubara A, Miyashita T, Inamoto R, Sakaguchi H, Kamitani T, Mori N, Hoshikawa H. Tricellulin Expression and its Deletion Effects in the Endolymphatic Sac. J Int Adv Otol 2019; 14:312-316. [PMID: 30100545 DOI: 10.5152/iao.2018.5473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVES Tricellulin is a tight junction (TJ)-forming protein that participates in the sealing function of tricellular TJs. Tricellulin-knockout (Tric-/-) mice show progressive hearing loss with degeneration of hair cells in the cochlea without physiological or physical disorders. In the present study, we investigated the tricellulin expression and its deletion effects in the endolymphatic sac (ES) using Tric-/- mice. MATERIALS AND METHODS The ES epithelia from wild-type (WT) mice were laser-microdissected, and RT-PCR was performed. The ES sections from Tric-/- and WT mice were immunostained with an anti-tricellulin antibody. Hematoxylin and eosin staining was performed for morphological examination. The inner ear of Tric-/- mice was perfused with biotinylation reagents, and the ES sections were observed for tracer permeability assay after applying streptavidin-Alexa Fluor 488 conjugate. RESULTS The tricellulin expression was confirmed by RT-PCR and by immunohistochemistry in the WT ES. The ES in Tric-/- mice showed normal morphology and revealed no biotin leakage from the lumen. CONCLUSION The ES in Tric-/- mice showed no changes in morphology or disruption in macromolecular barrier function. The effects of solute leakages in the ES of Tric-/- mice may be very limited and compensatable, or that the ES epithelia may have other sealing system covering the lack of tricellulin.
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Affiliation(s)
- Ai Matsubara
- Department of Otolaryngology, Kagawa University, School of Medicine, Kagawa, Japan
| | - Takenori Miyashita
- Department of Otolaryngology, Kagawa University, School of Medicine, Kagawa, Japan
| | - Ryuhei Inamoto
- Department of Otolaryngology, Kagawa University, School of Medicine, Kagawa, Japan
| | - Hirofumi Sakaguchi
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectual University of Medicine, Kyoto, Japan
| | - Toru Kamitani
- Department of Otolaryngology, Kagawa University, School of Medicine, Kagawa, Japan
| | - Nozomu Mori
- Department of Otolaryngology, Kagawa University, School of Medicine, Kagawa, Japan
| | - Hiroshi Hoshikawa
- Department of Otolaryngology, Kagawa University, School of Medicine, Kagawa, Japan
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Zheng J, Meng WF, Zhang CF, Liu HQ, Yao J, Wang H, Chen Y, Guan MX. New SNP variants of MARVELD2 (DFNB49) associated with non-syndromic hearing loss in Chinese population. J Zhejiang Univ Sci B 2018; 20:164-169. [PMID: 30406641 DOI: 10.1631/jzus.b1700185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Non-syndromic hearing loss (NSHL) is a common defect in humans. Variants of MARVELD2 at the DFNB49 locus have been shown to cause bilateral, moderate to profound NSHL. However, the role of MARVELD2 in NSHL susceptibility in the Chinese population has not been studied. Here we conducted a case-control study in an eastern Chinese population to profile the spectrum and frequency of MARVELD2 variants, as well as the association of MARVELD2 gene variants with NSHL. Our results showed that variants identified in the Chinese population are significantly different from those reported in Slovak, Hungarian, and Czech Roma, as well as Pakistani families. We identified 11 variants in a cohort of 283 NSHL cases. Through Sanger sequencing and bioinformatics analysis, we found that c.730G>A variant has detrimental effects in the eastern Chinese population, and may have relatively high correlation with NSHL pathogenicity.
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Affiliation(s)
- Jing Zheng
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Institute of Genetics, Zhejiang University, Hangzhou 310058, China
| | - Wen-Fang Meng
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Institute of Genetics, Zhejiang University, Hangzhou 310058, China
| | - Chao-Fan Zhang
- Institute of Genetics, Zhejiang University, Hangzhou 310058, China
| | - Han-Qing Liu
- Institute of Genetics, Zhejiang University, Hangzhou 310058, China
| | - Juan Yao
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Hui Wang
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Ye Chen
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Institute of Genetics, Zhejiang University, Hangzhou 310058, China
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Institute of Genetics, Zhejiang University, Hangzhou 310058, China
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Taghipour-Sheshdeh A, Nemati-Zargaran F, Zarepour N, Tahmasebi P, Saki N, Tabatabaiefar MA, Mohammadi-Asl J, Hashemzadeh-Chaleshtori M. A novel pathogenic variant in the MARVELD2 gene causes autosomal recessive non-syndromic hearing loss in an Iranian family. Genomics 2018; 111:840-848. [PMID: 29752989 DOI: 10.1016/j.ygeno.2018.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 04/28/2018] [Accepted: 05/08/2018] [Indexed: 10/16/2022]
Abstract
BACKGROUND AND AIMS Hearing loss (HL) is the most common sensorineural disorder and one of the most common human defects. HL can be classified according to main criteria, including: the site (conductive, sensorineural and mixed), onset (pre-lingual and post-lingual), accompanying signs and symptoms (syndromic and non-syndromic), severity (mild, moderate, severe and profound) and mode of inheritance (Autosomal recessive, autosomal dominant, X-linked and mitochondrial). Autosomal recessive non-syndromic HL (ARNSHL) forms constitute a major share of the HL cases. In the present study, next-generation sequencing (NGS) was applied to investigate the underlying etiology of HL in a multiplex ARNSHL family from Khuzestan province, southwest Iran. METHODS In this descriptive study, 20 multiplex ARNSHL families from Khuzestan province, southwest of Iran were recruited. After DNA extraction, genetic linkage analysis (GLA) was applied to screen for a panel of more prevalent loci. One family, which was not linked to these loci, was subjected to Otogenetics deafness Next Generation Sequencing (NGS) panel. RESULTS NGS results showed a novel deletion-insertion variant (c.1555delinsAA) in the MARVELD2 gene. The variant which is a frameshift in the seventh exon of the MARVELD2 gene fulfills the criteria of being categorized as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guideline. CONCLUSION NGS is very promising to identify the molecular etiology of highly heterogeneous diseases such as HL. MARVELD2 might be important in the etiology of HL in this region of Iran.
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Affiliation(s)
- Afsaneh Taghipour-Sheshdeh
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Fatemeh Nemati-Zargaran
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Narges Zarepour
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Parisa Tahmasebi
- Department of Biology, Faculty of Sciences, Ilam University, Ilam, Iran
| | - Nader Saki
- Hearing Research Center, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, 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 Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Javad Mohammadi-Asl
- Department of Medical Genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Morteza Hashemzadeh-Chaleshtori
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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Yousaf R, Gu C, Ahmed ZM, Khan SN, Friedman TB, Riazuddin S, Shears SB, Riazuddin S. Mutations in Diphosphoinositol-Pentakisphosphate Kinase PPIP5K2 are associated with hearing loss in human and mouse. PLoS Genet 2018; 14:e1007297. [PMID: 29590114 PMCID: PMC5891075 DOI: 10.1371/journal.pgen.1007297] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 04/09/2018] [Accepted: 03/06/2018] [Indexed: 01/07/2023] Open
Abstract
Autosomal recessive nonsyndromic hearing loss is a genetically heterogeneous disorder. Here, we report a severe-to-profound sensorineural hearing loss locus, DFNB100 on chromosome 5q13.2-q23.2. Exome enrichment followed by massive parallel sequencing revealed a c.2510G>A transition variant in PPIP5K2 that segregated with DFNB100-associated hearing loss in two large apparently unrelated Pakistani families. PPIP5Ks enzymes interconvert 5-IP7 and IP8, two key members of the inositol pyrophosphate (PP-IP) cell-signaling family. Their actions at the interface of cell signaling and bioenergetic homeostasis can impact many biological processes. The c.2510G>A transition variant is predicted to substitute a highly invariant arginine residue with histidine (p.Arg837His) in the phosphatase domain of PPIP5K2. Biochemical studies revealed that the p.Arg837His variant reduces the phosphatase activity of PPIP5K2 and elevates its kinase activity. We found that in mouse inner ear, PPIP5K2 is expressed in the cochlear and vestibular sensory hair cells, supporting cells and spiral ganglion neurons. Mice homozygous for a targeted deletion of the Ppip5k2 phosphatase domain exhibit degeneration of cochlear outer hair cells and elevated hearing thresholds. Our demonstration that PPIP5K2 has a role in hearing in humans indicates that PP-IP signaling is important to hair cell maintenance and function within inner ear. Exome sequencing coupled with homozygosity mapping was used to identify a missense variant [c.2510G>A; p.(Arg837His)] in PPIP5K2 at the DFNB100 locus that is associated with nonsyndromic, prelingual sensorineural deafness in two large consanguineous Pakistani families. PPIP5Ks are pivotal enzymes for regulating inositol pyrophosphate (PP-IP) turnover. Biochemical analyses revealed that, compared to wild type human PPIP5K2, the PPIP5K2R837H variant exhibited lower phosphatase activity and higher kinase activity, indicating that it promotes increased metabolic flux from 5-IP7 to IP8 in vivo. In rodent inner ears, PPIP5K2 immunoreactivity was observed in the cochlear and vestibular hair cells, supporting cells, and spiral ganglion neurons. Mouse mutants homozygous for the targeted deletion of Ppip5k2 phosphatase domain exhibit degeneration of cochlear outer hair cells and progressive hearing loss. Our work provides the first description of any amino acid variant of PPIP5K2 that is both functionally-significant and associates with a human disorder. The ‘futile cycling’ of the kinase/phosphatase activity of PPIP5K2 makes inner ear function particularly susceptible to even minor changes in the phosphatase activity of PPIP5K2. We have shown that a pathogenic variant in PPIP5K2 is associated with hearing loss in humans. Thus, PPIP5K2 is given new clinical significance by our observations.
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Affiliation(s)
- Rizwan Yousaf
- Laboratory of Molecular Genetics, Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, United States of America
| | - Chunfang Gu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States of America
| | - Zubair M. Ahmed
- Laboratory of Neurogenetics and Regenerative Medicine, Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, United States of America
| | - Shaheen N. Khan
- National Center for Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Thomas B. Friedman
- Section on Human Genetics, Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, United States of America
| | - Sheikh Riazuddin
- Shaheed Zulfiqar Ali Bhutto Medical University, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Stephen B. Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, United States of America
| | - Saima Riazuddin
- Laboratory of Molecular Genetics, Department of Otorhinolaryngology-Head & Neck Surgery, School of Medicine University of Maryland, Baltimore, MD, United States of America
- * E-mail:
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14
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Pater JA, Benteau T, Griffin A, Penney C, Stanton SG, Predham S, Kielley B, Squires J, Zhou J, Li Q, Abdelfatah N, O'Rielly DD, Young TL. A common variant in CLDN14 causes precipitous, prelingual sensorineural hearing loss in multiple families due to founder effect. Hum Genet 2016; 136:107-118. [PMID: 27838790 PMCID: PMC5215284 DOI: 10.1007/s00439-016-1746-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/07/2016] [Indexed: 12/16/2022]
Abstract
Genetic isolates provide unprecedented opportunities to identify pathogenic mutations and explore the full natural history of clinically heterogeneous phenotypes such as hearing loss. We noticed a unique audioprofile, characterized by prelingual and rapid deterioration of hearing thresholds at frequencies >0.5 kHz in several adults from unrelated families from the island population of Newfoundland. Targeted serial Sanger sequencing of probands for deafness alleles (n = 23) that we previously identified in this founder population was negative. Whole exome sequencing in four members of the largest family (R2010) identified a CLDN14 (DFNB29) variant [c.488C>T; p. (Ala163Val)], likely pathogenic, sensorineural hearing loss, autosomal recessive. Although not associated with deafness or disease, CLDN14 p.(Ala163Val) has been previously reported as a variant of uncertain significance (VUS). Targeted sequencing of 169 deafness probands identified one homozygote and one heterozygous carrier. Genealogical studies, cascade sequencing and haplotype analysis across four unrelated families showed all subjects with the unique audioprofile (n = 12) were also homozygous for p.(Ala163Val) and shared a 1.4 Mb DFNB29-associated haplotype on chromosome 21. Most significantly, sequencing 175 population controls revealed 1% of the population are heterozygous for CLDN14 p.(Ala163Val), consistent with a major founder effect in Newfoundland. The youngest CLDN14 [c.488C>T; p.(Ala163Val)] homozygote passed newborn screening and had normal hearing thresholds up to 3 years of age, which then deteriorated to a precipitous loss >1 kHz during the first decade. Our study suggests that genetic testing may be necessary to identify at-risk children in time to prevent speech, language and developmental delay.
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Affiliation(s)
- Justin A Pater
- Craig L. Dobbin Genetics Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada
| | - Tammy Benteau
- Craig L. Dobbin Genetics Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada
| | - Anne Griffin
- Craig L. Dobbin Genetics Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada
| | - Cindy Penney
- Craig L. Dobbin Genetics Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada
| | - Susan G Stanton
- Communication Sciences and Disorders, Western University, Elborn College, 1201 Western Road, London, ON, N6G 1H1, Canada
| | - Sarah Predham
- Craig L. Dobbin Genetics Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada
| | - Bernadine Kielley
- Department of Education and Early Childhood Development, Government of Newfoundland and Labrador, St. John's, NL, A1B 4J6, Canada
| | - Jessica Squires
- Craig L. Dobbin Genetics Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada
| | - Jiayi Zhou
- Craig L. Dobbin Genetics Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada
| | - Quan Li
- Craig L. Dobbin Genetics Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada
| | - Nelly Abdelfatah
- Craig L. Dobbin Genetics Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada
| | - Darren D O'Rielly
- Craig L. Dobbin Genetics Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada.,Molecular Diagnostic Laboratory, Eastern Health, Craig L. Dobbin Genetics Research Centre, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada
| | - Terry-Lynn Young
- Craig L. Dobbin Genetics Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada. .,Communication Sciences and Disorders, Western University, Elborn College, 1201 Western Road, London, ON, N6G 1H1, Canada. .,Molecular Diagnostic Laboratory, Eastern Health, Craig L. Dobbin Genetics Research Centre, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, NL, A1B 3V6, Canada.
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15
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Comprehensive Analysis of Deafness Genes in Families with Autosomal Recessive Nonsyndromic Hearing Loss. PLoS One 2015; 10:e0142154. [PMID: 26561413 PMCID: PMC4641619 DOI: 10.1371/journal.pone.0142154] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/19/2015] [Indexed: 11/25/2022] Open
Abstract
Comprehensive genetic testing has the potential to become the standard of care for individuals with hearing loss. In this study, we investigated the genetic etiology of autosomal recessive nonsyndromic hearing loss (ARNSHL) in a Turkish cohort including individuals with cochlear implant, who had a pedigree suggestive of an autosomal recessive inheritance. A workflow including prescreening of GJB2 and a targeted next generation sequencing panel (Illumına TruSightTM Exome) covering 2761 genes that we briefly called as mendelian exome sequencing was used. This panel includes 102 deafness genes and a number of genes causing Mendelian disorders. Using this approach, we identified causative variants in 21 of 29 families. Three different GJB2 variants were present in seven families. Remaining 14 families had 15 different variants in other known NSHL genes (MYO7A, MYO15A, MARVELD2, TMIE, DFNB31, LOXHD1, GPSM2, TMC1, USH1G, CDH23). Of these variants, eight are novel. Mutation detection rate of our workflow is 72.4%, confirming the usefulness of targeted sequencing approach in NSHL.
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