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Carrizosa C, Undlien DE, Vigeland MD. shinyseg: a web application for flexible cosegregation and sensitivity analysis. Bioinformatics 2024; 40:btae201. [PMID: 38598476 PMCID: PMC11069105 DOI: 10.1093/bioinformatics/btae201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/12/2024] [Accepted: 04/16/2024] [Indexed: 04/12/2024] Open
Abstract
MOTIVATION Cosegregation analysis is a powerful tool for identifying pathogenic genetic variants, but its implementation remains challenging. Existing software is either limited in scope or too demanding for many end users. Moreover, current solutions lack methods for assessing the robustness of cosegregation evidence, which is important due to its reliance on uncertain estimates. RESULTS We present shinyseg, a comprehensive web application for clinical cosegregation analysis. Our app streamlines penetrance specification based on either liability classes or epidemiological data such as risks, hazard ratios, and age of onset distribution. In addition, it incorporates sensitivity analyses to assess the robustness of cosegregation evidence, and offers support in clinical interpretation. AVAILABILITY AND IMPLEMENTATION The shinyseg app is freely available at https://chrcarrizosa.shinyapps.io/shinyseg, with documentation and complete R source code on https://chrcarrizosa.github.io/shinyseg and https://github.com/chrcarrizosa/shinyseg.
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Affiliation(s)
- Christian Carrizosa
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Dag E Undlien
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0424 Oslo, Norway
| | - Magnus D Vigeland
- Department of Forensic Sciences, Oslo University Hospital, 0424 Oslo, Norway
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2
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Yang Y, Luo H, Pan L, Feng C, Guo Z, Zou Y, Zeng B, Huang S, Yuan H, Wu P, Liu D, Dan Y, Xiao J, Li X, Chen Z, Zeng XN, Jiang X, Yang B, Liu Y, Liu Y. Reevaluating the splice-altering variant in TECTA as a cause of nonsyndromic hearing loss DFNA8/12 by functional analysis of RNA. Hum Mol Genet 2024:ddae071. [PMID: 38676628 DOI: 10.1093/hmg/ddae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/25/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
PURPOSE The aim of this study was to determine the genetic cause of early onset autosomal dominant hearing loss segregating in five-generation kindred of Chinese descent and provide preimplantation genetic testing (PGT)for them. METHODS Clinical examination, pedigree analysis and exome sequencing were carried out on the family. Minigene-based splicing analysis, in vivo RNA analysis and protein structure prediction by molecular modeling were conducted on the candidate variant. PGT for the causative variation and chromosome aneuploidis based on SNP analysis has been used for avoidance of hearing loss in this family. RESULTS All the affected individuals presented with moderate down-sloping hearing loss and whole-exome sequencing identified a novel splice-site variant c.5383+6T>A in the tested subjects within the TECTA locus. Genotyping of all the 32 family members confirmed segregation of this variant and the hearing loss phenotype in the extended family. Functional analysis of RNA and molecular modeling indicates that c.5383+6T>A is a pathogenic splice-site variant and should be considered as genetic cause of the hearing loss. Furthermore, a successful singleton pregnancy with no variation in TECTA c.5383+6 was established and a healthy male child was born by PGT. CONCLUSION We have identified a novel variant c.5383+6T>A in TECTA ZA-ZP inter-domain, which could be attributable to the early-onset autosomal dominant hearing loss. The implications of our study are valuable in elucidating the disrupted RNA splicing and uncovering the genetic cause of hearing loss with TECTA pathogenic variants, as well as providing reproductive approaches to healthy offspring.
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Affiliation(s)
- Yan Yang
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Haiyan Luo
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Lijuan Pan
- Department of Obstetrics, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Kaifu District, Changsha City, Hunan Province, 410083, China
| | - Chuanxin Feng
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Zhen Guo
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Yongyi Zou
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Baitao Zeng
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Shuhui Huang
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Huizhen Yuan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Ping Wu
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, No. 566, University Avenue Road, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Danping Liu
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Yi Dan
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Junfang Xiao
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - XinYu Li
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - ZhongFa Chen
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Xiao Ni Zeng
- Department of Neurology, The First Affiliated Hospital of Nanchang University, No. 17, Yongwai Zhengjie Road, Donghu District, Nanchang City, Jiangxi Province, 330006, China
| | - XiangLong Jiang
- Nan Chang Reproductive Hospital, No. 198, Jinggangshan Avenue Road, Qingyun Pu District, Nanchang City, Jiangxi Province Nanchang, 330006, China
| | - Bicheng Yang
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
| | - Yuhe Liu
- Department of Otolaryngology, Head and Neck Surgery, Beijing Friendship Hospital, Capital Medical University, No. 95 Yongan Road, Xicheng District, Beijing, 100050, China
| | - Yanqiu Liu
- Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, No. 508, Xizhan Street, Honggutan District, Nanchang City, Jiangxi Province, 330006, China
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Ha ZY, Chijiwa C, Lewis S. Clinical and Molecular Characterization of a Novel Homozygous Frameshift Variant in AEBP1-Related Classical-like Ehlers Danlos Syndrome Type 2 with Comparison to Previously Reported Rare Cases. Genes (Basel) 2024; 15:461. [PMID: 38674395 PMCID: PMC11049394 DOI: 10.3390/genes15040461] [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: 03/06/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Recently, an autosomal recessive subtype of connective tissue disorder within the spectrum of Ehlers-Danlos syndrome (EDS), named classical-like EDS type 2 (clEDS2), was identified. clEDS2 is associated with biallelic variants in the adipocyte enhancer binding protein 1 (AEBP1) gene, specifically, affecting its aortic carboxypeptidase-like protein (ACLP) isoform. We described the 15th patient (13th family) diagnosed with clEDS2. This patient presented with notable similarities in phenotype to the documented cases, along with additional characteristics such as significant prematurity and short stature. An EDS sequencing panel-based analysis revealed homozygous AEBP1: NM_001129.5:c.2923del, p.Ala975Profs*22 likely pathogenic variants, and maternally inherited heterozygous COL11A1: NM_001854.4:c.1160A>G, p.Lys387Arg variant of uncertain significance in our patient. Upon comprehensive review of all previously reported clEDS2 patients, our patient exhibited the following overlapping phenotypes, including cutaneous features: hyperextensibility, atrophic scars/delayed wound healing (100%), easy bruising (100%), excessive skin (93%); skeletal features: generalized joint hypermobility (93%), pes planus (93%), dislocation/subluxation (93%); and cardiovascular features (86%). Our patient did not display symptoms of the critical complications reported in a few individuals, including superior mesenteric artery aneurysms and ruptures, aortic root aneurysm/dissection, spontaneous pneumothoraxes, and bowel ruptures. Together, this case expands the genetic and clinical phenotypic spectrum of AEBP1-related clEDS2.
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Affiliation(s)
- Zong Yi Ha
- Department of Medical Genetics, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada (S.L.)
| | - Chieko Chijiwa
- Department of Medical Genetics, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada (S.L.)
- The BC Provincial Medical Genetics Program, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada (S.L.)
- The BC Provincial Medical Genetics Program, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- BC Children’s Hospital Research Institute, University of British Columbia, C234-4500 Oak Street, Vancouver, BC V6H 3N1, Canada
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Sun Y, You Y, Wu Q, Hu R, Dai K. Genetically inspired organoids prevent joint degeneration and alleviate chondrocyte senescence via Col11a1-HIF1α-mediated glycolysis-OXPHOS metabolism shift. Clin Transl Med 2024; 14:e1574. [PMID: 38314968 PMCID: PMC10840017 DOI: 10.1002/ctm2.1574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
INTRODUCTION Developmental dysplasia of hip (DDH) is a hip joint disorder leading to subsequent osteoarthritis. Previous studies suggested collagen XI alpha 1 (COL11A1) as a potential gene in hip dysplasia and chondrocyte degeneration. However, no genetic association has reported COL11A1-related cellular therapy as treatment of DDH and joint degeneration. METHODS AND RESULTS We report identified genetic association between COL11A1 locus and DDH with genome-wide association study (GWAS). Further exome sequencing for familial DDH patients was conducted in different populations to identify potential pathogenic Col11A1 variants for familiar DDH. Further studies demonstrated involvement of COL11A1 expression was down-regulated in femoral head cartilage of DDH patients and Col11a1-KO mice with induced DDH. Col11a1-KO mice demonstrated aggravated joint degeneration and severe OA phenotype. To explore the underlying mechanism of Col11a1 in cartilage and DDH development, we generated scRNA-seq profiles for DDH and Col11a1-KO cartilage, demonstrating disrupted chondrocyte homeostasis and cellular senescence caused by Col11a1-HIF1α-mediated glycolysis-OXPHOS shift in chondrocytes. Genetically and biologically inspired, we further fabricated an intra-articular injection therapy to preventing cartilage degeneration by generating a Col11a1-over-expressed (OE) SMSC mini-organoids. Col11a1-OE organoids demonstrated superior chondrogenesis and ameliorated cartilage degeneration in DDH mice via regulating cellular senescence by up-regulated Col11a1/HIF1α-mediated glycolysis in chondrocytes. CONCLUSION We reported association between COL11A1 loci and DDH with GWAS and exome sequencing. Further studies demonstrated involvement of COL11A1 in DDH patients and Col11a1-KO mice. ScRNA-seq for DDH and Col11a1-KO cartilage demonstrated disrupted chondrocyte homeostasis and cellular senescence caused by Col11a1-HIF1α-mediated glycolysis-OXPHOS shift in chondrocytes. Genetically and biologically inspired, an intra-articular injection therapy was fabricated to prevent cartilage degeneration with Col11a1-OE SMSC organoids. Col11a1-OE organoids ameliorated cartilage degeneration in DDH mice via regulating cellular senescence by up-regulated Col11a1/HIF1α-mediated glycolysis in chondrocytes.
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Affiliation(s)
- Ye Sun
- Department of OrthopaedicsThe First Affiliated Hospital of Nanjing Medical UniversityJiangsuChina
- Department of Orthopaedic SurgeryShanghai Key Laboratory of Orthopaedic ImplantsShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yongqing You
- Department of Renal DiseasesAffiliated Hospital of Nanjing University of Chinese MedicineNanjingChina
| | - Qiang Wu
- Department of Orthopaedic SurgeryShanghai Key Laboratory of Orthopaedic ImplantsShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Rui Hu
- Department of OrthopaedicsThe First Affiliated Hospital of Nanjing Medical UniversityJiangsuChina
| | - Kerong Dai
- Department of Orthopaedic SurgeryShanghai Key Laboratory of Orthopaedic ImplantsShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
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Clifford RE, Maihofer AX, Chatzinakos C, Coleman JRI, Daskalakis NP, Gasperi M, Hogan K, Mikita EA, Stein MB, Tcheandjieu C, Telese F, Zuo Y, Ryan AF, Nievergelt CM. Genetic architecture distinguishes tinnitus from hearing loss. Nat Commun 2024; 15:614. [PMID: 38242899 PMCID: PMC10799010 DOI: 10.1038/s41467-024-44842-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/04/2024] [Indexed: 01/21/2024] Open
Abstract
Tinnitus is a heritable, highly prevalent auditory disorder treated by multiple medical specialties. Previous GWAS indicated high genetic correlations between tinnitus and hearing loss, with little indication of differentiating signals. We present a GWAS meta-analysis, triple previous sample sizes, and expand to non-European ancestries. GWAS in 596,905 Million Veteran Program subjects identified 39 tinnitus loci, and identified genes related to neuronal synapses and cochlear structural support. Applying state-of-the-art analytic tools, we confirm a large number of shared variants, but also a distinct genetic architecture of tinnitus, with higher polygenicity and large proportion of variants not shared with hearing difficulty. Tissue-expression analysis for tinnitus infers broad enrichment across most brain tissues, in contrast to hearing difficulty. Finally, tinnitus is not only correlated with hearing loss, but also with a spectrum of psychiatric disorders, providing potential new avenues for treatment. This study establishes tinnitus as a distinct disorder separate from hearing difficulties.
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Affiliation(s)
- Royce E Clifford
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA.
- University of California San Diego, Division of Otolaryngology - Head and Neck Surgery, La Jolla, CA, USA.
| | - Adam X Maihofer
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
| | - Chris Chatzinakos
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- McLean Hospital, Center of Excellence in Depression and Anxiety Disorders, Belmont, MA, USA
| | - Jonathan R I Coleman
- King's College London, NIHR Maudsley BRC, London, UK
- King's College London, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Nikolaos P Daskalakis
- Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- McLean Hospital, Center of Excellence in Depression and Anxiety Disorders, Belmont, MA, USA
| | - Marianna Gasperi
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
| | - Kelleigh Hogan
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
| | - Elizabeth A Mikita
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
| | - Murray B Stein
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Psychiatry Service, San Diego, CA, USA
- University of California San Diego, School of Public Health, La Jolla, CA, USA
| | | | - Francesca Telese
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
| | - Yanning Zuo
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA
| | - Allen F Ryan
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
- University of California San Diego, Division of Otolaryngology - Head and Neck Surgery, La Jolla, CA, USA
| | - Caroline M Nievergelt
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA.
- University of California San Diego, Department of Psychiatry, La Jolla, CA, USA.
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Pressé MT, Malgrange B, Delacroix L. The cochlear matrisome: Importance in hearing and deafness. Matrix Biol 2024; 125:40-58. [PMID: 38070832 DOI: 10.1016/j.matbio.2023.12.002] [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: 08/25/2023] [Revised: 11/20/2023] [Accepted: 12/06/2023] [Indexed: 02/12/2024]
Abstract
The extracellular matrix (ECM) consists in a complex meshwork of collagens, glycoproteins, and proteoglycans, which serves a scaffolding function and provides viscoelastic properties to the tissues. ECM acts as a biomechanical support, and actively participates in cell signaling to induce tissular changes in response to environmental forces and soluble cues. Given the remarkable complexity of the inner ear architecture, its exquisite structure-function relationship, and the importance of vibration-induced stimulation of its sensory cells, ECM is instrumental to hearing. Many factors of the matrisome are involved in cochlea development, function and maintenance, as evidenced by the variety of ECM proteins associated with hereditary deafness. This review describes the structural and functional ECM components in the auditory organ and how they are modulated over time and following injury.
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Affiliation(s)
- Mary T Pressé
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, 15 avenue Hippocrate - CHU - B36 (1st floor), Liège B-4000, Belgium
| | - Brigitte Malgrange
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, 15 avenue Hippocrate - CHU - B36 (1st floor), Liège B-4000, Belgium
| | - Laurence Delacroix
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, 15 avenue Hippocrate - CHU - B36 (1st floor), Liège B-4000, Belgium.
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7
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Aldè M, Cantarella G, Zanetti D, Pignataro L, La Mantia I, Maiolino L, Ferlito S, Di Mauro P, Cocuzza S, Lechien JR, Iannella G, Simon F, Maniaci A. Autosomal Dominant Non-Syndromic Hearing Loss (DFNA): A Comprehensive Narrative Review. Biomedicines 2023; 11:1616. [PMID: 37371710 DOI: 10.3390/biomedicines11061616] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Autosomal dominant non-syndromic hearing loss (HL) typically occurs when only one dominant allele within the disease gene is sufficient to express the phenotype. Therefore, most patients diagnosed with autosomal dominant non-syndromic HL have a hearing-impaired parent, although de novo mutations should be considered in all cases of negative family history. To date, more than 50 genes and 80 loci have been identified for autosomal dominant non-syndromic HL. DFNA22 (MYO6 gene), DFNA8/12 (TECTA gene), DFNA20/26 (ACTG1 gene), DFNA6/14/38 (WFS1 gene), DFNA15 (POU4F3 gene), DFNA2A (KCNQ4 gene), and DFNA10 (EYA4 gene) are some of the most common forms of autosomal dominant non-syndromic HL. The characteristics of autosomal dominant non-syndromic HL are heterogenous. However, in most cases, HL tends to be bilateral, post-lingual in onset (childhood to early adulthood), high-frequency (sloping audiometric configuration), progressive, and variable in severity (mild to profound degree). DFNA1 (DIAPH1 gene) and DFNA6/14/38 (WFS1 gene) are the most common forms of autosomal dominant non-syndromic HL affecting low frequencies, while DFNA16 (unknown gene) is characterized by fluctuating HL. A long audiological follow-up is of paramount importance to identify hearing threshold deteriorations early and ensure prompt treatment with hearing aids or cochlear implants.
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Affiliation(s)
- Mirko Aldè
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Giovanna Cantarella
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Diego Zanetti
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Lorenzo Pignataro
- Department of Clinical Sciences and Community Health, University of Milan, 20090 Milan, Italy
- Department of Specialist Surgical Sciences, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy
| | - Ignazio La Mantia
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Luigi Maiolino
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Salvatore Ferlito
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Paola Di Mauro
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Salvatore Cocuzza
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
| | - Jérôme René Lechien
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Giannicola Iannella
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Francois Simon
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
| | - Antonino Maniaci
- Otology Study Group of the Young-Otolaryngologists of the International Federations of Oto-Rhino-Laryngological Societies (YO-IFOS), 75000 Paris, France
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia, University of Catania, 95123 Catania, Italy
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8
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Xu L, Wang X, Li J, Chen L, Wang H, Xu S, Zhang Y, Li W, Yao P, Tan M, Zhou S, Chen M, Pan Y, Chen X, Chen X, Liu Y, Lin N, Huang H, Cao H. A novel PLS1 c.981+1G>A variant causes autosomal-dominant hereditary hearing loss in a family. Clin Genet 2023; 103:413-423. [PMID: 36537221 DOI: 10.1111/cge.14283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/03/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
The fimbrin protein family contains a variety of proteins, among which Plastin1 (PLS1) is an important member. According to recent studies, variations in the coding region of the PLS1 gene are associated with the development of deafness. However, the molecular mechanism of deafness caused by PLS1 gene variants remains unknown. Whole-exome sequencing was performed on hearing-impaired family members and hearing family members to identify pathogenic variants, followed by Sanger sequencing. A minigene assay was conducted to investigate the effect of the variant on PLS1 mRNA splicing. The pathogenicity of the variant was further investigated in zebrafish. RNA-sequencing (RNA-seq) was performed to analyze the dysregulation of downstream signaling pathways caused by knockdown of PLS1 expression. We identified a novel variant, PLS1 c.981+1G>A, in a large Chinese family with hearing loss and showed that the variant is responsible for the occurrence of hearing loss by inducing exon 8 skipping. The variant caused abnormal inner ear phenotypes, characterized by decreases in the mean otolith distance, anterior otolith diameter, posterior otolith diameter, cochlear diameter, and swimming speed and distance in zebrafish. Furthermore, silencing PLS1 expression significantly upregulated the expression of genes in the PI3K-Akt signaling pathway, including Col6a3, Spp1, Itgb3 and hepatocyte growth factor (Hgf). PLS1 c.981+1G>A is a novel pathogenic variant causing hearing loss by inducing exon 8 skipping. Upregulation of the expression of genes in the PI3K-Akt signaling pathway plays an important role in the pathogenesis caused by variants in the PLS1 gene.
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Affiliation(s)
- Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xinrui Wang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primates, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Jia Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co., Ltd., Shijiazhuang, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Haiwei Wang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Shiyi Xu
- The First Clinical Medical College, Guangxi Medical University, Nanning, China
| | - Yanhong Zhang
- Department of Laboratory Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Meihua Tan
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Si Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co., Ltd., Shijiazhuang, China
- College of Life Sciences, University of Chinese Academy of Sciences, China
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yali Pan
- Department of Laboratory Medicine, Medical Technology and Engineering College of Fujian Medical University, Fuzhou, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaolan Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yunliang Liu
- Otolaryngological Department of Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hua Cao
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primates, Fujian Maternity and Child Health Hospital, Fuzhou, China
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9
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Shi M, Cao L, Ding D, Shi L, Hu Y, Qi G, Zhan L, Zhu Y, Yu W, Lv P, Yu N. Acute Noise Causes Down-Regulation of ECM Protein Expression in Guinea Pig Cochlea. Mol Biotechnol 2022; 65:774-785. [PMID: 36209333 DOI: 10.1007/s12033-022-00557-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 09/05/2022] [Indexed: 11/24/2022]
Abstract
Proteomics technology reveals the marker proteins, potential pathogenesis, and intervention targets after noise-induced hearing loss. To study the differences in cochlea protein expression before and after noise exposure using proteomics to reveal the pathological mechanism of noise-induced hearing loss (NIHL). A guinea pig NIHL model was established to test the ABR thresholds before and after noise exposure. The proteomics technology was used to study the mechanism of differential protein expression in the cochlea by noise stimulation. The average hearing threshold of guinea pigs on the first day after noise exposure was 57.00 ± 6.78 dB Sound pressure level (SPL); the average hearing threshold on the seventh day after noise exposure was 45.83 ± 6.07 dB SPL. The proteomics technology identified 3122 different inner ear proteins, of which six proteins related to the hearing were down-regulation: Tenascin C, Collagen Type XI alpha two chains, Collagen Type II alpha one chain, Thrombospondin 2, Collagen Type XI alpha one chain and Ribosomal protein L38, and are enriched in protein absorption, focal adhesion, and extracellular matrix receptor pathways. Impulse noise can affect the expression of differential proteins through focal adhesion pathways. This data can provide an experimental basis for the research on the prevention and treatment of NIHL.
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Affiliation(s)
- Min Shi
- Senior Department of Otolaryngology Head and Neck Surgery, The Sixth Medical Center of PLA General Hospital, Beijing, 100853, China.,Suining Central Hospital, Suining, 629000, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| | - Lei Cao
- The First Clinical Medical College of Gansu University of Traditional Chinese Medicine, Lanzhou, 730000, China
| | - Daxiong Ding
- Department of Otorhinolaryngology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Lei Shi
- Senior Department of Otolaryngology Head and Neck Surgery, The Sixth Medical Center of PLA General Hospital, Beijing, 100853, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| | - Yiyong Hu
- Senior Department of Otolaryngology Head and Neck Surgery, The Sixth Medical Center of PLA General Hospital, Beijing, 100853, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| | - Guowei Qi
- Senior Department of Otolaryngology Head and Neck Surgery, The Sixth Medical Center of PLA General Hospital, Beijing, 100853, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| | - Li Zhan
- Senior Department of Otolaryngology Head and Neck Surgery, The Sixth Medical Center of PLA General Hospital, Beijing, 100853, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| | - Yuhua Zhu
- Senior Department of Otolaryngology Head and Neck Surgery, The Sixth Medical Center of PLA General Hospital, Beijing, 100853, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China
| | - Wenxing Yu
- Suining Central Hospital, Suining, 629000, China
| | - Ping Lv
- Department of Otorhinolaryngology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Ning Yu
- Senior Department of Otolaryngology Head and Neck Surgery, The Sixth Medical Center of PLA General Hospital, Beijing, 100853, China. .,National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China.
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10
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Zhang D, Wu J, Yuan Y, Li X, Gao X, Han M, Gao S, Huang S, Dai P. A novel missense variant in CEACAM16 gene causes autosomal dominant nonsyndromic hearing loss. Ann Hum Genet 2022; 86:207-217. [PMID: 35292975 PMCID: PMC9314904 DOI: 10.1111/ahg.12463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 11/27/2022]
Abstract
AbstractAimAutosomal dominant non‐syndromic hearing loss is a common sensorineural disorder with extremely high genetic heterogeneity. CEA antigen‐related cell adhesion molecule 16(CEACAM16)is a secreted glycoprotein encoded by the CEACAM16 gene. Mutations in CEACAM16 lead to autosomal dominant non‐syndromic hearing loss in humans, due defects in the tectorial membrane of the inner ear. Here we reported a novel missense variant in CEACAM16 gene causes autosomal dominant non‐syndromic hearing loss.Material and methodsA four‐generation Chinese family affected by late‐onset and progressive hearing loss was enrolled in this study. The proband was analyzed by targeted next‐generation sequencing and bioinformatic analysis. And in vitro experiments were performed in overexpressed transfected HEK293T cells to investigate the pathogenesis of the mutant protein.ResultsWe identified a novel missense variant in the CEACAM16 gene c.763A>G; (p.Arg255Gly) as causing autosomal dominant non‐syndromic hearing loss in the Chinese family. Using Western blot analysis, ELISA, and immunofluorescence we found increased expression level of the secreted mutant CEACAM16 protein, both intracellularly and extracellularly, compared with wild type CEACAM16 protein.ConclusionOur study showed that the p.Arg255Gly variant leads to increased secretion of mutant CEACAM16 protein, with potential deleterious effect to the function of the protein. Our findings expand the mutation spectrum of CEACAM16, and further the understanding CEACAM16 function and implications in disease.
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Affiliation(s)
- Dejun Zhang
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- Department of Otolaryngology Head and Neck SurgeryThe Second Hospital of Jilin UniversityChangchunChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
| | - Jie Wu
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
| | - Yongyi Yuan
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
| | - Xiaohong Li
- Department of Otolaryngology, Head and Neck Surgery, National Children's Medical Center/Beijing Children's HospitalCapital Medical UniversityBeijingPR China
| | - Xue Gao
- Department of OtolaryngologyPLA Rocket Force Characteristic Medical CenterBeijingChina
| | - Mingyu Han
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
| | - Song Gao
- Department of OtolaryngologySouth‐East Hospital Affiliated to Xiamen UniversityZhangzhouChina
| | - Shasha Huang
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
| | - Pu Dai
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
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11
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Berry V, Fujinami K, Mochizuki K, Iwata T, Pontikos N, Quinlan RA, Michaelides M. A recurrent variant in LIM2 causes an isolated congenital sutural/lamellar cataract in a Japanese family. Ophthalmic Genet 2022; 43:622-626. [PMID: 35736209 PMCID: PMC9612932 DOI: 10.1080/13816810.2022.2090010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Genetically determined cataract is both clinically and molecularly highly heterogeneous. Here, we have identified a heterozygous variant in the lens integral membrane protein LIM2, the second most abundant protein in the lens, responsible for congenital sutural/lamellar cataract in a three-generation Japanese family. Methods Whole exome sequencing (WES) was undertaken in one affected and one unaffected individual from a family with autosomal dominant congenital cataract to establish the underlying genetic basis. Results A recurrent missense variant LIM2: c.388C>T; p.R130C was identified and found to co-segregate with disease. In addition, one variant COL11A1:c.3788C>T of unknown significance (VUS) was also identified. Conclusions We report a variant in LIM2 causing an isolated autosomal-dominant congenital sutural/lamellar cataract in a Japanese family. This is the first report of a LIM2 variant in the Japanese population. Hence, we expand the mutation spectrum of LIM2 variants in different ethnic groups.
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Affiliation(s)
- Vanita Berry
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Kaoru Fujinami
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization, Tokyo Medical Centre, Tokyo, Japan
| | - Kiyofumi Mochizuki
- Department of Ophthalmology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Nikolas Pontikos
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Roy A Quinlan
- Department of Biosciences, University of Durham, Durham, UK
| | - Michel Michaelides
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
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12
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Bjornsdottir G, Stefansdottir L, Thorleifsson G, Sulem P, Norland K, Ferkingstad E, Oddsson A, Zink F, Lund SH, Nawaz MS, Bragi Walters G, Skuladottir AT, Gudjonsson SA, Einarsson G, Halldorsson GH, Bjarnadottir V, Sveinbjornsson G, Helgadottir A, Styrkarsdottir U, Gudmundsson LJ, Pedersen OB, Hansen TF, Werge T, Banasik K, Troelsen A, Skou ST, Thørner LW, Erikstrup C, Nielsen KR, Mikkelsen S, Jonsdottir I, Bjornsson A, Olafsson IH, Ulfarsson E, Blondal J, Vikingsson A, Brunak S, Ostrowski SR, Ullum H, Thorsteinsdottir U, Stefansson H, Gudbjartsson DF, Thorgeirsson TE, Stefansson K. Rare SLC13A1 variants associate with intervertebral disc disorder highlighting role of sulfate in disc pathology. Nat Commun 2022; 13:634. [PMID: 35110524 PMCID: PMC8810832 DOI: 10.1038/s41467-022-28167-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 01/12/2022] [Indexed: 12/12/2022] Open
Abstract
Back pain is a common and debilitating disorder with largely unknown underlying biology. Here we report a genome-wide association study of back pain using diagnoses assigned in clinical practice; dorsalgia (119,100 cases, 909,847 controls) and intervertebral disc disorder (IDD) (58,854 cases, 922,958 controls). We identify 41 variants at 33 loci. The most significant association (ORIDD = 0.92, P = 1.6 × 10−39; ORdorsalgia = 0.92, P = 7.2 × 10−15) is with a 3’UTR variant (rs1871452-T) in CHST3, encoding a sulfotransferase enzyme expressed in intervertebral discs. The largest effects on IDD are conferred by rare (MAF = 0.07 − 0.32%) loss-of-function (LoF) variants in SLC13A1, encoding a sodium-sulfate co-transporter (LoF burden OR = 1.44, P = 3.1 × 10−11); variants that also associate with reduced serum sulfate. Genes implicated by this study are involved in cartilage and bone biology, as well as neurological and inflammatory processes. Little is known about the biology of back pain, a leading cause of disability. Here the authors report 30 new back pain loci, implicating genes involved in cartilage/bone biology, as well as neurological and inflammatory processes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Muhammad S Nawaz
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - G Bragi Walters
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Gisli H Halldorsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Ole B Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Folkmann Hansen
- Danish Headache Center, Dept. Neurology, Rigshospitalet-Glostrup, Glostrup, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark.,Lundbeck Foundation for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Troelsen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Orthopaedic Surgery, CAG ROAD-Research OsteoArthritis Denmark, Copenhagen University Hospital, Hvidovre, Denmark
| | - Soren T Skou
- Research Unit for Musculoskeletal Function and Physiotherapy, Department of Sports Science and Clinical Biomechanics, University of Southern Denmark, Odense, Denmark.,The Research Unit PROgrez, Department of Physiotherapy and Occupational Therapy, Næstved-Slagelse-Ringsted Hospitals, Næstved, Denmark
| | - Lise Wegner Thørner
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Kaspar Rene Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Susan Mikkelsen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Aron Bjornsson
- Department of Neurosurgery, Landspitali University Hospital, Reykjavik, Iceland
| | - Ingvar H Olafsson
- Department of Neurosurgery, Landspitali University Hospital, Reykjavik, Iceland
| | - Elfar Ulfarsson
- Department of Neurosurgery, Landspitali University Hospital, Reykjavik, Iceland
| | - Josep Blondal
- Health Care Institution of West Iceland, Stykkisholmur, Iceland
| | | | - Soren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sisse R Ostrowski
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Henrik Ullum
- Statens Serum Institut, Copenhagen, Copenhagen, Denmark
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. .,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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13
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Adeyemo A, Faridi R, Chattaraj P, Yousaf R, Tona R, Okorie S, Bharadwaj T, Nouel-Saied LM, Acharya A, Schrauwen I, Morell RJ, Leal SM, Friedman TB, Griffith AJ, Roux I. Genomic analysis of childhood hearing loss in the Yoruba population of Nigeria. Eur J Hum Genet 2021; 30:42-52. [PMID: 34837038 PMCID: PMC8738750 DOI: 10.1038/s41431-021-00984-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/02/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Although variant alleles of hundreds of genes are associated with sensorineural deafness in children, the genes and alleles involved remain largely unknown in the Sub-Saharan regions of Africa. We ascertained 56 small families mainly of Yoruba ethno-lingual ancestry in or near Ibadan, Nigeria, that had at least one individual with nonsyndromic, severe-to-profound, prelingual-onset, bilateral hearing loss not attributed to nongenetic factors. We performed a combination of exome and Sanger sequencing analyses to evaluate both nuclear and mitochondrial genomes. No biallelic pathogenic variants were identified in GJB2, a common cause of deafness in many populations. Potential causative variants were identified in genes associated with nonsyndromic hearing loss (CIB2, COL11A1, ILDR1, MYO15A, TMPRSS3, and WFS1), nonsyndromic hearing loss or Usher syndrome (CDH23, MYO7A, PCDH15, and USH2A), and other syndromic forms of hearing loss (CHD7, OPA1, and SPTLC1). Several rare mitochondrial variants, including m.1555A>G, were detected in the gene MT-RNR1 but not in control Yoruba samples. Overall, 20 (33%) of 60 independent cases of hearing loss in this cohort of families were associated with likely causal variants in genes reported to underlie deafness in other populations. None of these likely causal variants were present in more than one family, most were detected as compound heterozygotes, and 77% had not been previously associated with hearing loss. These results indicate an unusually high level of genetic heterogeneity of hearing loss in Ibadan, Nigeria and point to challenges for molecular genetic screening, counseling, and early intervention in this population.
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Affiliation(s)
- Adebolajo Adeyemo
- Institute of Child Health, College of Medicine, University of Ibadan, Ibadan, Nigeria.
| | - Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Parna Chattaraj
- Otolaryngology Branch, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rizwan Yousaf
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Risa Tona
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel Okorie
- Institute of Child Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Liz M Nouel-Saied
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Robert J Morell
- Genomics and Computational Biology Core, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew J Griffith
- Otolaryngology Branch, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Otolaryngology, College of Medicine, University of Tennessee Health Science Center, 910 Madison Avenue, Memphis, TN, 38163, USA
| | - Isabelle Roux
- Otolaryngology Branch, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA.
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14
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Pavlenkova Z, Varga L, Borecka S, Karhanek M, Huckova M, Skopkova M, Profant M, Gasperikova D. Comprehensive molecular-genetic analysis of mid-frequency sensorineural hearing loss. Sci Rep 2021; 11:22488. [PMID: 34795337 PMCID: PMC8602250 DOI: 10.1038/s41598-021-01876-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
The genetic heterogeneity of sensorineural hearing loss (SNHL) is a major hurdle to the detection of disease-causing variants. We aimed to identify underlying causal genes associated with mid-frequency hearing loss (HL), which contributes to less than about 1% of SNHL cases, by whole exome sequencing (WES). Thirty families segregating mid-frequency SNHL, in whom biallelic GJB2 mutations had been previously excluded, were selected from among 851 families in our DNA repository of SNHL. DNA samples from the probands were subjected to WES analysis and searched for candidate variants associated with SNHL. We were able to identify the genetic aetiology in six probands (20%). In total, we found three pathogenic and three likely pathogenic variants in four genes (COL4A5, OTOGL, TECTA, TMPRSS3). One more proband was a compound heterozygote for a pathogenic variant and a variant of uncertain significance (VUS) in MYO15A gene. To date, MYO15A and TMPRSS3 have not yet been described in association with mid-frequency SNHL. In eight additional probands, eight candidate VUS variants were detected in five genes (DIAPH1, MYO7A, TECTA, TMC1, TSPEAR). Seven of these 16 variants have not yet been published or mentioned in the available databases. The most prevalent gene was TECTA, identified in 23% of all tested families. Furthermore, we confirmed the hypothesis that a substantive portion of cases with this conspicuous audiogram shape is a consequence of a genetic disorder.
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Affiliation(s)
- Zuzana Pavlenkova
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia.,DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lukas Varga
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia. .,DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.
| | - Silvia Borecka
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miloslav Karhanek
- Laboratory of Bioinformatics, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miloslava Huckova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Skopkova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Milan Profant
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia
| | - Daniela Gasperikova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
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15
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Diagnostic Yield of Targeted Hearing Loss Gene Panel Sequencing in a Large German Cohort With a Balanced Age Distribution from a Single Diagnostic Center: An Eight-year Study. Ear Hear 2021; 43:1049-1066. [PMID: 34753855 PMCID: PMC9007094 DOI: 10.1097/aud.0000000000001159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Objectives: Hereditary hearing loss exhibits high degrees of genetic and clinical heterogeneity. To elucidate the population-specific and age-related genetic and clinical spectra of hereditary hearing loss, we investigated the sequencing data of causally associated hearing loss genes in a large cohort of hearing-impaired probands with a balanced age distribution from a single center in Southwest Germany. Design: Genetic testing was applied to 305 hearing-impaired probands/families with a suspected genetic hearing loss etiology and a balanced age distribution over a period of 8 years (2011–2018). These individuals were representative of the regional population according to age and sex distributions. The genetic testing workflow consisted of single-gene screening (n = 21) and custom-designed hearing loss gene panel sequencing (n = 284) targeting known nonsyndromic and syndromic hearing loss genes in a diagnostic setup. Retrospective reanalysis of sequencing data was conducted by applying the current American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines. Results: A genetic diagnosis was established for 75 (25%) of the probands that involved 75 causal variants in 35 genes, including 16 novel causal variants and 9 medically significant variant reclassifications. Nearly half of the solved cases (47%; n = 35) were related to variants in the five most frequently affected genes: GJB2 (25%), MYO15A, WFS1, SLC26A4, and COL11A1 (all 5%). Nearly one-quarter of the cases (23%; n = 17) were associated with variants in seven additional genes (TMPRSS3, COL4A3, LOXHD1, EDNRB, MYO6, TECTA, and USH2A). The remaining one-third of single cases (33%; n = 25) were linked to variants in 25 distinct genes. Diagnostic rates and gene distribution were highly dependent on phenotypic characteristics. A positive family history of autosomal-recessive inheritance in combination with early onset and higher grades of hearing loss significantly increased the solve rate up to 60%, while late onset and lower grades of hearing loss yielded significantly fewer diagnoses. Regarding genetic diagnoses, autosomal-dominant genes accounted for 37%, autosomal-recessive genes for 60%, and X-linked genes for 3% of the solved cases. Syndromic/nonsyndromic hearing loss mimic genes were affected in 27% of the genetic diagnoses. Conclusions: The genetic epidemiology of the largest German cohort subjected to comprehensive targeted sequencing for hereditary hearing loss to date revealed broad causal gene and variant spectra in this population. Targeted hearing loss gene panel analysis proved to be an effective tool for ensuring an appropriate diagnostic yield in a routine clinical setting including the identification of novel variants and medically significant reclassifications. Solve rates were highly sensitive to phenotypic characteristics. The unique population-adapted and balanced age distribution of the cohort favoring late hearing loss onset uncovered a markedly large contribution of autosomal-dominant genes to the diagnoses which may be a representative for other age balanced cohorts in other populations.
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Booth KT, Hirsch Y, Vardaro AC, Ekstein J, Yefet D, Quint A, Weiden T, Corey DP. Identification of Novel and Recurrent Variants in MYO15A in Ashkenazi Jewish Patients With Autosomal Recessive Nonsyndromic Hearing Loss. Front Genet 2021; 12:737782. [PMID: 34733312 PMCID: PMC8558392 DOI: 10.3389/fgene.2021.737782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/21/2021] [Indexed: 12/02/2022] Open
Abstract
Hearing loss is a genetically and phenotypically heterogeneous disorder. The purpose of this study was to determine the genetic cause underlying hearing loss in four Ashkenazi Jewish families. We screened probands from each family using a combination of targeted mutation screening and exome sequencing to identifiy the genetic cause of hearing loss in each family. We identified four variants in MYO15A, two novel variants never previously linked to deafness (c.7212+5G>A and p.Leu2532ArgfsTer37) and two recurrent variants (p.Tyr2684His and p.Gly3287Gly). One family showed locus heterogeneity, segregrating two genetic forms of hearing loss. Mini-gene assays revealed the c.7212+5G>A variant results in abnormal splicing and is most likely a null allele. We show that families segregrating the p.Gly3287Gly variant show both inter and intra-familial phenotypic differences. These results add to the list of MYO15A deafness-causing variants, further confirm the pathogenicity of the p.Gly3287Gly variant and shed further light on the genetic etiology of hearing loss in the Ashkenazi Jewish population.
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Affiliation(s)
- Kevin T. Booth
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Yoel Hirsch
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, United States
| | - Anna C. Vardaro
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Josef Ekstein
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, United States
| | - Devorah Yefet
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, Israel
| | - Adina Quint
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, Israel
| | - Tzvi Weiden
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, Israel
| | - David P. Corey
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
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Ciorba A, Corazzi V, Melegatti M, Morgan A, Pelliccione G, Girotto G, Bigoni S. Non-Syndromic Sensorineural Prelingual and Postlingual Hearing Loss due to COL11A1 Gene Mutation. J Int Adv Otol 2021; 17:81-83. [PMID: 33605226 DOI: 10.5152/iao.2020.8179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This paper aims to present a third world case of Non-Syndromic sensorineural hearing loss (NSHL) due to a novel missense variant in COL11A1 gene, defined as DFNA37 non-syndromic hearing loss. The clinical features of a 6-year-old boy affected by a bilateral moderate to severe down-sloping sensorineural hearing loss are presented, as well as the genetic analysis, the latter identifying a heterozygous missense variation in the COL11A1 gene. In addition, in families with autosomal dominant transmission, COL11A1 gene should be considered in the genetic workup of the NSHL with prelingual onset.
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Affiliation(s)
- Andrea Ciorba
- Department of ENT - Audiology, University Hospital of Ferrara, Ferrara, Italy
| | - Virginia Corazzi
- Department of ENT - Audiology, University Hospital of Ferrara, Ferrara, Italy
| | - Michela Melegatti
- Department of ENT - Audiology, University Hospital of Ferrara, Ferrara, Italy
| | - Anna Morgan
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy
| | - Giulia Pelliccione
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy;Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Giorgia Girotto
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy;Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Stefania Bigoni
- Medical Genetic Unit, Ferrara University Hospital, Ferrara, Italy
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18
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Hirsch Y, Tangshewinsirikul C, Booth KT, Azaiez H, Yefet D, Quint A, Weiden T, Brownstein Z, Macarov M, Davidov B, Pappas J, Rabin R, Kenna MA, Oza AM, Lafferty K, Amr SS, Rehm HL, Kolbe DL, Frees K, Nishimura C, Luo M, Farra C, Morton CC, Scher SY, Ekstein J, Avraham KB, Smith RJH, Shen J. A synonymous variant in MYO15A enriched in the Ashkenazi Jewish population causes autosomal recessive hearing loss due to abnormal splicing. Eur J Hum Genet 2021; 29:988-997. [PMID: 33398081 PMCID: PMC8187401 DOI: 10.1038/s41431-020-00790-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 11/04/2020] [Accepted: 11/25/2020] [Indexed: 11/09/2022] Open
Abstract
Nonsyndromic hearing loss is genetically heterogeneous. Despite comprehensive genetic testing, many cases remain unsolved because the clinical significance of identified variants is uncertain or because biallelic pathogenic variants are not identified for presumed autosomal recessive cases. Common synonymous variants are often disregarded. Determining the pathogenicity of synonymous variants may improve genetic diagnosis. We report a synonymous variant c.9861 C > T/p.(Gly3287=) in MYO15A in homozygosity or compound heterozygosity with another pathogenic or likely pathogenic MYO15A variant in 10 unrelated families with nonsyndromic sensorineural hearing loss. Biallelic variants in MYO15A were identified in 21 affected and were absent in 22 unaffected siblings. A mini-gene assay confirms that the synonymous variant leads to abnormal splicing. The variant is enriched in the Ashkenazi Jewish population. Individuals carrying biallelic variants involving c.9861 C > T often exhibit progressive post-lingual hearing loss distinct from the congenital profound deafness typically associated with biallelic loss-of-function MYO15A variants. This study establishes the pathogenicity of the c.9861 C > T variant in MYO15A and expands the phenotypic spectrum of MYO15A-related hearing loss. Our work also highlights the importance of multicenter collaboration and data sharing to establish the pathogenicity of a relatively common synonymous variant for improved diagnosis and management of hearing loss.
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Affiliation(s)
- Yoel Hirsch
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, 11211, USA
| | - Chayada Tangshewinsirikul
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02215, USA
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Devorah Yefet
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, 91506, Israel
| | - Adina Quint
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, 91506, Israel
| | - Tzvi Weiden
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, 91506, Israel
| | - Zippora Brownstein
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Michal Macarov
- Department of Genetics and Metabolic Diseases, Hadassah Medical Center, Jerusalem, 91120, Israel
| | - Bella Davidov
- Department of Medical Genetics, Rabin Medical Center, Petah Tikva, 49100, Israel
| | - John Pappas
- Department of Pediatrics, New York University School of Medicine, New York, NY, 10016, USA
| | - Rachel Rabin
- Department of Pediatrics, New York University School of Medicine, New York, NY, 10016, USA
| | - Margaret A Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
| | - Andrea M Oza
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
| | - Katherine Lafferty
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
- Maine Medical Center, Scarborough, ME, 04074, USA
| | - Sami S Amr
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Heidi L Rehm
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Diana L Kolbe
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Kathy Frees
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Carla Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA
| | - Minjie Luo
- The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Chantal Farra
- Medical Genetics Unit, American University of Beirut Medical Center, AUBMC, 1107 2020, Beirut, Lebanon
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Manchester Centre for Audiology and Deafness, School of Health Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Sholem Y Scher
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, 11211, USA
| | - Josef Ekstein
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, 11211, USA
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Jun Shen
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, 02115, USA.
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA.
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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Chen S, Gao C, Yu T, Qu Y, Xiao GG, Huang Z. Bioinformatics Analysis of a Prognostic miRNA Signature and Potential Key Genes in Pancreatic Cancer. Front Oncol 2021; 11:641289. [PMID: 34094925 PMCID: PMC8174116 DOI: 10.3389/fonc.2021.641289] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/31/2021] [Indexed: 12/11/2022] Open
Abstract
Background In this study, miRNAs and their critical target genes related to the prognosis of pancreatic cancer were screened based on bioinformatics analysis to provide targets for the prognosis and treatment of pancreatic cancer. Methods R software was used to screen differentially expressed miRNAs (DEMs) and genes (DEGs) downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, respectively. A miRNA Cox proportional hazards regression model was constructed based on the miRNAs, and a miRNA prognostic model was generated. The target genes of the prognostic miRNAs were predicted using TargetScan and miRDB and then intersected with the DEGs to obtain common genes. The functions of the common genes were subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses. A protein-protein interaction (PPI) network of the common genes was constructed with the STRING database and visualized with Cytoscape software. Key genes were also screened with the MCODE and cytoHubba plug-ins of Cytoscape. Finally, a prognostic model formed by the key gene was also established to help evaluate the reliability of this screening process. Results A prognostic model containing four downregulated miRNAs (hsa-mir-424, hsa-mir-3613, hsa-mir-4772 and hsa-mir-126) related to the prognosis of pancreatic cancer was constructed. A total of 118 common genes were enriched in two KEGG pathways and 33 GO functional annotations, including extracellular matrix (ECM)-receptor interaction and cell adhesion. Nine key genes related to pancreatic cancer were also obtained: MMP14, ITGA2, THBS2, COL1A1, COL3A1, COL11A1, COL6A3, COL12A1 and COL5A2. The prognostic model formed by nine key genes also possessed good prognostic ability. Conclusions The prognostic model consisting of four miRNAs can reliably predict the prognosis of patients with pancreatic cancer. In addition, the screened nine key genes, which can also form a reliable prognostic model, are significantly related to the occurrence and development of pancreatic cancer. Among them, one novel miRNA (hsa-mir-4772) and two novel genes (COL12A1 and COL5A2) associated with pancreatic cancer have great potential to be used as prognostic factors and therapeutic targets for this tumor.
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Affiliation(s)
- Shuoling Chen
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,The Second School of Clinical Medicine, Guangdong Medical University, Dongguan, China
| | - Chang Gao
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Tianyang Yu
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Yueyang Qu
- School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian, China
| | - Gary Guishan Xiao
- School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian, China
| | - Zunnan Huang
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
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20
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Tang S, Yonezawa T, Maeda Y, Ono M, Maeba T, Miyoshi T, Momota R, Tomono Y, Oohashi T. Lack of collagen α6(IV) chain in mice does not cause severe-to-profound hearing loss or cochlear malformation, a distinct phenotype from nonsyndromic hearing loss with COL4A6 missense mutation. PLoS One 2021; 16:e0249909. [PMID: 33848312 PMCID: PMC8043391 DOI: 10.1371/journal.pone.0249909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/26/2021] [Indexed: 11/18/2022] Open
Abstract
Congenital hearing loss affects 1 in every 1000 births, with genetic mutations contributing to more than 50% of all cases. X-linked nonsyndromic hereditary hearing loss is associated with six loci (DFNX1-6) and five genes. Recently, the missense mutation (c.1771G>A, p.Gly591Ser) in COL4A6, encoding the basement membrane (BM) collagen α6(IV) chain, was shown to be associated with X-linked congenital nonsyndromic hearing loss with cochlear malformation. However, the mechanism by which the COL4A6 mutation impacts hereditary hearing loss has not yet been elucidated. Herein, we investigated Col4a6 knockout (KO) effects on hearing function and cochlear formation in mice. Immunohistochemistry showed that the collagen α6(IV) chain was distributed throughout the mouse cochlea within subepithelial BMs underlying the interdental cells, inner sulcus cells, basilar membrane, outer sulcus cells, root cells, Reissner's membrane, and perivascular BMs in the spiral limbus, spiral ligament, and stria vascularis. However, the click-evoked auditory brainstem response analysis did not show significant changes in the hearing threshold of Col4a6 KO mice compared with wild-type (WT) mice with the same genetic background. In addition, the cochlear structures of Col4a6 KO mice did not exhibit morphological alterations, according to the results of high-resolution micro-computed tomography and histology. Hence, loss of Col4a6 gene expression in mice showed normal click ABR thresholds and normal cochlear formation, which differs from humans with the COL4A6 missense mutation c.1771G>A, p.Gly591Ser. Therefore, the deleterious effects in the auditory system caused by the missense mutation in COL4A6 are likely due to the dominant-negative effects of the α6(IV) chain and/or α5α6α5(IV) heterotrimer with an aberrant structure that would not occur in cases with loss of gene expression.
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Affiliation(s)
- Shaoying Tang
- Department of Molecular Biology and Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Tomoko Yonezawa
- Department of Molecular Biology and Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- * E-mail:
| | - Yukihide Maeda
- Department of Otolaryngology-Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Mitsuaki Ono
- Department of Molecular Biology and Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Takahiro Maeba
- Department of Molecular Biology and Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toru Miyoshi
- Department of Cardiovascular Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Ryusuke Momota
- Department of Human Morphology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yasuko Tomono
- Division of Molecular and Cell Biology, Shigei Medical Research Institute, Okayama, Japan
| | - Toshitaka Oohashi
- Department of Molecular Biology and Biochemistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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Salazar-Silva R, Dantas VLG, Alves LU, Batissoco AC, Oiticica J, Lawrence EA, Kawafi A, Yang Y, Nicastro FS, Novaes BC, Hammond C, Kague E, Mingroni-Netto RC. NCOA3 identified as a new candidate to explain autosomal dominant progressive hearing loss. Hum Mol Genet 2021; 29:3691-3705. [PMID: 33326993 PMCID: PMC7823111 DOI: 10.1093/hmg/ddaa240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/21/2020] [Accepted: 10/15/2020] [Indexed: 12/27/2022] Open
Abstract
Hearing loss is a frequent sensory impairment in humans and genetic factors account for an elevated fraction of the cases. We have investigated a large family of five generations, with 15 reported individuals presenting non-syndromic, sensorineural, bilateral and progressive hearing loss, segregating as an autosomal dominant condition. Linkage analysis, using SNP-array and selected microsatellites, identified a region of near 13 cM in chromosome 20 as the best candidate to harbour the causative mutation. After exome sequencing and filtering of variants, only one predicted deleterious variant in the NCOA3 gene (NM_181659, c.2810C > G; p.Ser937Cys) fit in with our linkage data. RT-PCR, immunostaining and in situ hybridization showed expression of ncoa3 in the inner ear of mice and zebrafish. We generated a stable homozygous zebrafish mutant line using the CRISPR/Cas9 system. ncoa3-/- did not display any major morphological abnormalities in the ear, however, anterior macular hair cells showed altered orientation. Surprisingly, chondrocytes forming the ear cartilage showed abnormal behaviour in ncoa3-/-, detaching from their location, invading the ear canal and blocking the cristae. Adult mutants displayed accumulation of denser material wrapping the otoliths of ncoa3-/- and increased bone mineral density. Altered zebrafish swimming behaviour corroborates a potential role of ncoa3 in hearing loss. In conclusion, we identified a potential candidate gene to explain hereditary hearing loss, and our functional analyses suggest subtle and abnormal skeletal behaviour as mechanisms involved in the pathogenesis of progressive sensory function impairment.
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Affiliation(s)
- R Salazar-Silva
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Vitor Lima Goes Dantas
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Leandro Ucela Alves
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Ana Carla Batissoco
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
- Laboratório de Otorrinolaringologia/LIM32 –Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo , 01246-903, São Paulo, Brazil
| | - Jeanne Oiticica
- Laboratório de Otorrinolaringologia/LIM32 –Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo , 01246-903, São Paulo, Brazil
| | - Elizabeth A Lawrence
- School of Pharmacology, Physiology and Neuroscience, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Abdelwahab Kawafi
- School of Pharmacology, Physiology and Neuroscience, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Yushi Yang
- School of Physics, University of Bristol, Bristol, BS8 1TL, United Kingdom
- Centre for Nanoscience and Quantum Information, University of Bristol, Bristol, BS8 1FD, United Kingdom
- Bristol Centre for Functional Nanomaterials, University of Bristol, Bristol, BS8 1FD, United Kingdom
| | - Fernanda Stávale Nicastro
- Divisão de Educação e Reabilitação dos Distúrbios da Comunicação da Pontifícia Universidade Católica de São Paulo, 04022-040, São Paulo, Brazil
| | - Beatriz Caiuby Novaes
- Divisão de Educação e Reabilitação dos Distúrbios da Comunicação da Pontifícia Universidade Católica de São Paulo, 04022-040, São Paulo, Brazil
| | - Chrissy Hammond
- School of Pharmacology, Physiology and Neuroscience, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Erika Kague
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
- School of Pharmacology, Physiology and Neuroscience, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - R C Mingroni-Netto
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
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22
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Gorski JP, Franz NT, Pernoud D, Keightley A, Eyre DR, Oxford JT. A repeated triple lysine motif anchors complexes containing bone sialoprotein and the type XI collagen A1 chain involved in bone mineralization. J Biol Chem 2021; 296:100436. [PMID: 33610546 PMCID: PMC8008188 DOI: 10.1016/j.jbc.2021.100436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/05/2021] [Accepted: 02/16/2021] [Indexed: 01/16/2023] Open
Abstract
While details remain unclear, initiation of woven bone mineralization is believed to be mediated by collagen and potentially nucleated by bone sialoprotein (BSP). Interestingly, our recent publication showed that BSP and type XI collagen form complexes in mineralizing osteoblastic cultures. To learn more, we examined the protein composition of extracellular sites of de novo hydroxyapatite deposition which were enriched in BSP and Col11a1 containing an alternatively spliced "6b" exonal sequence. An alternate splice variant "6a" sequence was not similarly co-localized. BSP and Col11a1 co-purify upon ion-exchange chromatography or immunoprecipitation. Binding of the Col11a1 "6b" exonal sequence to bone sialoprotein was demonstrated with overlapping peptides. Peptide 3, containing three unique lysine-triplet sequences, displayed the greatest binding to osteoblastic cultures; peptides containing fewer lysine triplet motifs or derived from the "6a" exon yielded dramatically lower binding. Similar results were obtained with 6-carboxyfluorescein (FAM)-conjugated peptides and western blots containing extracts from osteoblastic cultures. Mass spectroscopic mapping demonstrated that FAM-peptide 3 bound to 90 kDa BSP and its 18 to 60 kDa fragments, as well as to 110 kDa nucleolin. In osteoblastic cultures, FAM-peptide 3 localized to biomineralization foci (site of BSP) and to nucleoli (site of nucleolin). In bone sections, biotin-labeled peptide 3 bound to sites of new bone formation which were co-labeled with anti-BSP antibodies. These results establish the fluorescent peptide 3 conjugate as the first nonantibody-based method to identify BSP on western blots and in/on cells. Further examination of the "6b" splice variant interactions will likely reveal new insights into bone mineralization during development.
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Affiliation(s)
- Jeff P Gorski
- Center of Excellence in Mineralized Tissue Research, School of Dentistry, University of Missouri-Kansas City, Kansas City, Missouri, USA; Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri-Kansas City, Kansas City, Missouri, USA.
| | - Nichole T Franz
- Center of Excellence in Mineralized Tissue Research, School of Dentistry, University of Missouri-Kansas City, Kansas City, Missouri, USA; Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Daniel Pernoud
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Andrew Keightley
- Department of Ophthalmology and Proteomics Core Facility, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - David R Eyre
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington, USA
| | - Julia Thom Oxford
- Department of Biological Sciences, Center of Biomedical Research Excellence in Matrix Biology, Boise State University, Boise, Idaho, USA
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23
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Exon-Trapping Assay Improves Clinical Interpretation of COL11A1 and COL11A2 Intronic Variants in Stickler Syndrome Type 2 and Otospondylomegaepiphyseal Dysplasia. Genes (Basel) 2020; 11:genes11121513. [PMID: 33348901 PMCID: PMC7766184 DOI: 10.3390/genes11121513] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 11/17/2022] Open
Abstract
Stickler syndrome (SS) is a hereditary connective tissue disorder affecting bones, eyes, and hearing. Type 2 SS and the SS variant otospondylomegaepiphyseal dysplasia (OSMED) are caused by deleterious variants in COL11A1 and COL11A2, respectively. In both genes, available database information indicates a high rate of potentially deleterious intronic variants, but published evidence of their biological effect is usually insufficient for a definite clinical interpretation. We report four previously unpublished intronic variants in COL11A1 (c.2241 + 5G>T, c.2809 − 2A>G, c.3168 + 5G>C) and COL11A2 (c.4392 + 1G>A) identified in type 2 SS/OSMED individuals. The pathogenic effect of these variants was first predicted in silico and then investigated by an exon-trapping assay. We demonstrated that all variants can induce exon in-frame deletions, which lead to the synthesis of shorter collagen XI α1 or 2 chains. Lacking residues are located in the α-triple helical region, which has a crucial role in regulating collagen fibrillogenesis. In conclusion, this study suggests that these alternative COL11A1 and COL11A2 transcripts might result in aberrant triple helix collagen. Our approach may help to improve the diagnostic molecular pathway of COL11-related disorders.
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24
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Rad A, Schade-Mann T, Gamerdinger P, Yanus GA, Schulte B, Müller M, Imyanitov EN, Biskup S, Löwenheim H, Tropitzsch A, Vona B. Aberrant COL11A1 splicing causes prelingual autosomal dominant nonsyndromic hearing loss in the DFNA37 locus. Hum Mutat 2020; 42:25-30. [PMID: 33169910 DOI: 10.1002/humu.24136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/18/2020] [Accepted: 10/28/2020] [Indexed: 12/27/2022]
Abstract
Alpha-chain collagen molecules encoded by genes that include COL11A1 are essential for skeletal, ocular, and auditory function. COL11A1 variants have been reported in syndromes involving these organ systems. However, a description of the complete clinical spectrum is lacking, as evidenced by a recent association of autosomal dominant nonsyndromic hearing loss due to a splice-altering variant in COL11A1, mapping the DFNA37 locus. Here, we describe two German families presenting prelingual autosomal dominant nonsyndromic hearing loss with novel COL11A1 heterozygous splice-altering variants (c.652-1G>C and c.4338+2T>C) that were molecularly characterized. Interestingly, the c.652-1G>C variant affects the same intron 4 canonical splice site originally reported in the DFNA37 family (c.652-2A>C) but elicits a different splicing outcome. Furthermore, the c.4338+2T>C variant originated de novo. We provide clinical and molecular genetic evidence to unambiguously confirm that COL11A1 splice-altering variants cause DFNA37 hearing loss and affirm that COL11A1 be included in the genetic testing of patients with nonsyndromic deafness.
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Affiliation(s)
- Aboulfazl Rad
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Thore Schade-Mann
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Philipp Gamerdinger
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Grigoriy A Yanus
- Department of Medical Genetics, Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russia.,Department of Tumor Growth Biology, N. N. Petrov Institute of Oncology, Saint Petersburg, Russia
| | - Björn Schulte
- CeGaT GmbH and Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Marcus Müller
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Evgeny N Imyanitov
- Department of Medical Genetics, Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russia.,Department of Tumor Growth Biology, N. N. Petrov Institute of Oncology, Saint Petersburg, Russia.,Department of Oncology, I. I. Mechnikov North-Western Medical University, Saint Petersburg, Russia
| | - Saskia Biskup
- CeGaT GmbH and Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Hubert Löwenheim
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Anke Tropitzsch
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Barbara Vona
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
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25
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Clifford RE, Maihofer AX, Stein MB, Ryan AF, Nievergelt CM. Novel Risk Loci in Tinnitus and Causal Inference With Neuropsychiatric Disorders Among Adults of European Ancestry. JAMA Otolaryngol Head Neck Surg 2020; 146:1015-1025. [PMID: 32970095 PMCID: PMC7516809 DOI: 10.1001/jamaoto.2020.2920] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023]
Abstract
Importance Tinnitus affects at least 16 million US adults, but its pathophysiology is complicated, and treatment options remain limited. A heritable component has been identified in family and twin studies; however, no large-scale genome-wide association studies (GWAS) have been accomplished. Objective To identify genetic risk loci associated with tinnitus, determine genetic correlations, and infer possible relationships of tinnitus with hearing loss and neuropsychiatric disorders and traits. Design, Setting, and Participants A GWAS of self-reported tinnitus was performed in the UK Biobank (UKB) cohort using a linear mixed-model method implemented in BOLT-LMM (linear mixed model). Replication of significant findings was sought in the nonoverlapping US Million Veteran Program (MVP) cohort. A total of 172 995 UKB (discovery) and 260 832 MVP (replication) participants of European ancestry with self-report regarding tinnitus and hearing loss underwent genomic analysis. Linkage-disequilibrium score regression and mendelian randomization were performed between tinnitus and hearing loss and neuropsychiatric disorders. Data from the UKB were acquired and analyzed from September 24, 2018, to December 13, 2019. Data acquisition for the MVP cohort was completed July 22, 2019. Data analysis for both cohorts was completed on February 11, 2020. Main Outcomes and Measures Estimates of single nucleotide variation (SNV)-based heritability for tinnitus, identification of genetic risk loci and genes, functional mapping, and replication were performed. Genetic association and inferred causality of tinnitus compared with hearing loss and neuropsychiatric disorders and traits were analyzed. Results Of 172 995 UKB participants (53.7% female; mean [SD], 58.0 [8.2] years), 155 395 unrelated participants underwent SNV-based heritability analyses across a range of tinnitus phenotype definitions that explained approximately 6% of the heritability. The GWAS based on the most heritable model in the full UKB cohort identified 6 genome-wide significant loci and 27 genes in gene-based analyses, with replication of 3 of 6 loci and 8 of 27 genes in 260 832 MVP cohort participants (92.8% men; mean [SD] age, 63.8 [13.2] years). Mendelian randomization indicated that major depressive disorder had a permissive effect (β = 0.133; P = .003) and years of education had a protective effect (β = -0.322, P = <.001) on tinnitus, whereas tinnitus and hearing loss inferred a bidirectional association (β = 0.072, P = .001 and β = 1.546, P = <.001, respectively). Conclusions and Relevance This large GWAS characterizes the genetic architecture of tinnitus, demonstrating modest but significant heritability and a polygenic profile with multiple significant risk loci and genes. Genetic correlation and inferred causation between tinnitus and major depressive disorder, educational level, and hearing impairment were identified, consistent with clinical and neuroimaging evidence. These findings may guide gene-based diagnostic and therapeutic approaches to this pervasive disorder.
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Affiliation(s)
- Royce E Clifford
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, La Jolla
- Harvard School of Public Health, Boston, Massachusetts
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Adam X Maihofer
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
- Department of Psychiatry, University of California, San Diego, La Jolla
| | - Murray B Stein
- Department of Psychiatry, University of California, San Diego, La Jolla
- Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Allen F Ryan
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, La Jolla
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Caroline M Nievergelt
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
- Department of Psychiatry, University of California, San Diego, La Jolla
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, California
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26
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Akil O. Dual and triple AAV delivery of large therapeutic gene sequences into the inner ear. Hear Res 2020; 394:107912. [DOI: 10.1016/j.heares.2020.107912] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/17/2022]
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27
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Nixon T, Richards AJ, Lomas A, Abbs S, Vasudevan P, McNinch A, Alexander P, Snead MP. Inherited and de novo biallelic pathogenic variants in COL11A1 result in type 2 Stickler syndrome with severe hearing loss. Mol Genet Genomic Med 2020; 8:e1354. [PMID: 32578940 PMCID: PMC7507023 DOI: 10.1002/mgg3.1354] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
Background Type 2 Stickler syndrome is usually a dominant disorder resulting from pathogenic variants in COL11A1 encoding the alpha 1 chain of type XI collagen. Typical molecular changes result in either substitution of an obligate glycine within the Gly‐Xaa‐Yaa amino acid sequence repeat region of the molecule, mRNA missplicing or deletions/duplications that typically leaves the message in‐frame. Clinical features include myopia, retinal detachment, craniofacial, joint, and hearing problems. Fibrochondrogenesis is also a COL11A1 related disorder, but here disease‐associated variants are recessive and may be either null alleles or substitutions of glycine, and the condition is usually lethal in infancy. Methods The patient was assessed in the NHS England Stickler syndrome diagnostic service. DNA from the patient and family were analyzed with Next Generation Sequencing on a panel of genes known to cause Stickler Syndrome. The effect of sequence variants was assessed using minigene analysis. Allele‐specific RT‐PCR was performed. Results This patient had clinical type 2 Stickler syndrome but with severe hearing loss and severe ocular features including retinal atrophy and retinal tears in childhood. We identified a de novo in frame deletion of COL11A1 (c.4109_4126del) consistent with dominantly inherited Stickler syndrome but also a second inherited variant (c.1245+2T>C), on the other allele, affecting normal splicing of COL11A1 exon 9. Conclusion Exon 9 of COL11A1 is alternatively expressed and disease causing changes affecting only this exon modify the phenotype resulting from biallelic COL11A1 disease‐associated variants and, instead of fibrochondrogenesis, produce a form of Stickler syndrome with severe hearing loss. Disease phenotypes from de novo pathogenic variants can be modified by inherited recessive variants on the other allele. This highlights the need for functional and family analysis to confirm the mode of inheritance in COL11A1‐related disorders, particularly for those variants that may alter normal pre‐mRNA splicing.
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Affiliation(s)
- Thomas Nixon
- School of Clinical Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Vitreoretinal Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Allan J Richards
- Department of Pathology, University of Cambridge, Cambridge, UK.,East Midlands and East of England NHS Genomic Laboratory Hub, Addenbrooke's Treatment Centre, Cambridge, UK
| | - Adrian Lomas
- East Midlands and East of England NHS Genomic Laboratory Hub, Addenbrooke's Treatment Centre, Cambridge, UK
| | - Stephen Abbs
- East Midlands and East of England NHS Genomic Laboratory Hub, Addenbrooke's Treatment Centre, Cambridge, UK
| | - Pradeep Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Annie McNinch
- Vitreoretinal Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Pathology, University of Cambridge, Cambridge, UK
| | - Philip Alexander
- School of Clinical Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Vitreoretinal Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Martin P Snead
- School of Clinical Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Vitreoretinal Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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28
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Novel loss-of-function mutations in COCH cause autosomal recessive nonsyndromic hearing loss. Hum Genet 2020; 139:1565-1574. [PMID: 32562050 DOI: 10.1007/s00439-020-02197-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022]
Abstract
COCH is the most abundantly expressed gene in the cochlea. Unsurprisingly, mutations in COCH underly hearing loss in mice and humans. Two forms of hearing loss are linked to mutations in COCH, the well-established autosomal dominant nonsyndromic hearing loss, with or without vestibular dysfunction (DFNA9) via a gain-of-function/dominant-negative mechanism, and more recently autosomal recessive nonsyndromic hearing loss (DFNB110) via nonsense variants. Using a combination of targeted gene panels, exome sequencing, and functional studies, we identified four novel pathogenic variants (two nonsense variants, one missense, and one inframe deletion) in COCH as the cause of autosomal recessive hearing loss in a multi-ethnic cohort. To investigate whether the non-truncating variants exert their effect via a loss-of-function mechanism, we used minigene splicing assays. Our data showed both the missense and inframe deletion variants altered RNA splicing by creating an exon splicing silencer and abolishing an exon splicing enhancer, respectively. Both variants create frameshifts and are predicted to result in a null allele. This study confirms the involvement of loss-of-function mutations in COCH in autosomal recessive nonsyndromic hearing loss, expands the mutational landscape of DFNB110 to include coding variants that alter RNA splicing, and highlights the need to investigate the effect of coding variants on RNA splicing.
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29
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Čopíková J, Paděrová J, Románková V, Havlovicová M, Balaščáková M, Zelinová M, Vejvalková Š, Simandlová M, Štěpánková J, Hořínová V, Kantorová E, Křečková G, Pospíšilová J, Boday A, Meszarosová AU, Turnovec M, Votýpka P, Lišková P, Kremlíková Pourová R. Expanding the phenotype spectrum associated with pathogenic variants in the COL2A1 and COL11A1 genes. Ann Hum Genet 2020; 84:380-392. [PMID: 32427345 DOI: 10.1111/ahg.12386] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 01/15/2023]
Abstract
We report the clinical findings of 26 individuals from 16 unrelated families carrying variants in the COL2A1 or COL11A1 genes. Using Sanger and next-generation sequencing, 11 different COL2A1 variants (seven novel), were identified in 13 families (19 affected individuals), all diagnosed with Stickler syndrome (STL) type 1. In nine families, the COL2A1 disease-causing variant arose de novo. Phenotypically, we observed myopia (95%) and retinal detachment (47%), joint hyperflexibility (92%), midface retrusion (84%), cleft palate (53%), and various degrees of hearing impairment (50%). One patient had a splenic artery aneurysm. One affected individual carrying pathogenic variant in COL2A1 showed no ocular signs including no evidence of membranous vitreous anomaly. In three families (seven affected individuals), three novel COL11A1 variants were found. The propositus with a de novo variant showed an ultrarare Marshall/STL overlap. In the second family, the only common clinical sign was postlingual progressive sensorineural hearing impairment (DFNA37). Affected individuals from the third family had typical STL2 signs. The spectrum of disease phenotypes associated with COL2A1 or COL11A1 variants continues to expand and includes typical STL and various bone dysplasias, but also nonsyndromic hearing impairment, isolated myopia with or without retinal detachment, and STL phenotype without clinically detectable ocular pathology.
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Affiliation(s)
- Jana Čopíková
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jana Paděrová
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Věra Románková
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Miroslava Balaščáková
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Michaela Zelinová
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Šárka Vejvalková
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Martina Simandlová
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Jana Štěpánková
- Department of Ophthalmology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | | | - Eva Kantorová
- Department of Medical Genetics, Nemocnice České Budějovice, České Budějovice, Czech Republic
| | | | - Jana Pospíšilová
- Molecular Biology, AGEL Laboratories, Nový Jičín, Czech Republic
| | - Arpád Boday
- Molecular Biology, AGEL Laboratories, Nový Jičín, Czech Republic
| | - Anna Uhrová Meszarosová
- DNA Laboratory, Department of Child Neurology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Marek Turnovec
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Pavel Votýpka
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Petra Lišková
- Research Unit for Rare Diseases, Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Radka Kremlíková Pourová
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
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30
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Kim SY, Lee DH, Han JH, Choi BY. Novel Splice Site Pathogenic Variant of EFTUD2 Is Associated with Mandibulofacial Dysostosis with Microcephaly and Extracranial Symptoms in Korea. Diagnostics (Basel) 2020; 10:diagnostics10050296. [PMID: 32408545 PMCID: PMC7277841 DOI: 10.3390/diagnostics10050296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Elongation factor Tu guanosine-5'-triphosphate (GTP) binding domain containing 2 (EFTUD2) encodes a major component of the spliceosomal GTPase and, if mutated, causes mandibulofacial dysostosis with microcephaly (MFDM; MIM#610536). Despite the increasing number of potentially pathogenic variants reported in the literature, most previous studies have relied solely on in silico prediction of the pathogenic potential of EFTUD2 variants, which may result in misclassification of the variant's pathogenicity. Given the importance of the functional verification of EFTUD2 variants, we identified a novel splice donor site variant, c.271+1G>A of EFTUD2, whose pathogenicity was clearly verified at the RNA level using a minigene assay. A child with MFDM, mixed hearing loss, microcephaly, and a congenital cardiac defect was identified with this variant, which arose in a de novo fashion. The minigene assay showed erroneous integration of the 118 bp IVS3 of EFTUD2 exclusively among the c.271+1G>A variant clone. We first applied the minigene assay to identify the splice function of a splice site variant of EFTUD2, thereby allowing for in vitro functional verification of splice site variants in EFTUD2.
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Affiliation(s)
- So Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam 13496, Korea; (S.Y.K.); (D.-h.L.)
| | - Da-hye Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam 13496, Korea; (S.Y.K.); (D.-h.L.)
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam 13496, Korea;
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam 13496, Korea;
- Correspondence: ; Tel.: +82-31-787-7406; Fax: +82-31-787-4057
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31
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Ahmadmehrabi S, Brant J, Epstein DJ, Ruckenstein MJ, Rader DJ. Genetics of Postlingual Sensorineural Hearing Loss. Laryngoscope 2020; 131:401-409. [PMID: 32243624 DOI: 10.1002/lary.28646] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/19/2020] [Accepted: 02/28/2020] [Indexed: 12/11/2022]
Abstract
Literature and clinical practice around adult-onset hearing loss (HL) has traditionally focused on environmental risk factors, including noise exposure, ototoxic drug exposure, and cardiovascular disease. The most common diagnosis in adult-onset HL is presbycusis. However, the age of onset of presbycusis varies, and patients often describe family history of HL as well as individual variation in progression and severity. In recent years, there has been accumulating evidence of gene-environment interactions underlying adult cases of HL. Susceptibility loci for age-related HL have been identified, and genes related to postlingual nonsyndromic HL continue to be discovered through individual reports and genome-wide association studies. This review will outline main concepts in genetics as related to HL, identify implicated genes, and discuss clinical implications. Laryngoscope, 131:401-409, 2021.
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Affiliation(s)
- Shadi Ahmadmehrabi
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason Brant
- Department of Otorhinolaryngology Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas J Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael J Ruckenstein
- Department of Otorhinolaryngology Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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32
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When transcripts matter: delineating between non-syndromic hearing loss DFNB32 and hearing impairment infertile male syndrome (HIIMS). J Hum Genet 2020; 65:609-617. [PMID: 32231217 DOI: 10.1038/s10038-020-0740-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 01/24/2020] [Accepted: 03/02/2020] [Indexed: 12/30/2022]
Abstract
Mutations in the CDC14A (Cell Division-Cycle 14A) gene, which encodes a conserved dual-specificity protein tyrosine phosphatase, have been identified as a cause of autosomal recessive non-syndromic hearing loss (DFNB32) and hearing impairment infertility male syndrome (HIIMS). We used next-generation sequencing to screen six deaf probands from six families segregating sensorineural moderate-to-profound hearing loss. Data analysis and variant prioritization were completed using a custom bioinformatics pipeline. We identified three homozygous loss of function variants (p.Arg345Ter, p.Arg376Ter, and p.Ala451Thrfs*43) in the CDC14A gene, segregating with deafness in each family. Of the six families, four segregated the p.Arg376Ter mutation, one family segregated the p.Arg345Ter mutation and one family segregated a novel frameshift (p.Ala451Thrfs*43) mutation. In-depth phenotyping of affected individuals ruled out secondary syndromic findings. This study implicates the p.Arg376Ter mutation might be as a founder mutation in the Iranian population. It also provides the first semen analysis for deaf males carrying mutations in exon 11 of CDC14A and reveals a genotype-phenotype correlation that delineates between DFNB32 and HIIMS. The clinical results from affected males suggest the NM_033313.2 transcript alone is sufficient for proper male fertility, but not for proper auditory function. We conclude that DFNB32 is a distinct phenotypic entity in males.
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Small fish, big prospects: using zebrafish to unravel the mechanisms of hereditary hearing loss. Hear Res 2020; 397:107906. [PMID: 32063424 DOI: 10.1016/j.heares.2020.107906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/13/2020] [Accepted: 01/29/2020] [Indexed: 12/16/2022]
Abstract
Over the past decade, advancements in high-throughput sequencing have greatly enhanced our knowledge of the mutational signatures responsible for hereditary hearing loss. In its present state, the field has a largely uncensored view of protein coding changes in a growing number of genes that have been associated with hereditary hearing loss, and many more that have been proposed as candidate genes. Sequencing data can now be generated using methods that have become widespread and affordable. The greatest hurdles facing the field concern functional validation of uncharacterized genes and rapid application to human diseases, including hearing and balance disorders. To date, over 30 hearing-related disease models exist in zebrafish. New genome editing technologies, including CRISPR/Cas9 will accelerate the functional validation of hearing loss genes and variants in zebrafish. Here, we discuss current progress in the field and recent advances in genome editing approaches.
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Shi H, Wang H, Yao J, Lin C, Wei Q, Lu Y, Cao X. Comparative transcriptome analysis of auditory OC-1 cells and zebrafish inner ear tissues in the absence of human OSBPL2 orthologues. Biochem Biophys Res Commun 2019; 521:42-49. [PMID: 31629475 DOI: 10.1016/j.bbrc.2019.10.061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 10/05/2019] [Indexed: 12/16/2022]
Abstract
In our previous study, Oxysterol-binding protein-related protein 2 (OSBPL2) was first identified as a new deafness-causative gene contribute to non-syndromic hearing loss. However, the underlying mechanism of OSBPL2-induced hearing loss remains unknown. Here, we used hearing-specific cells and tissues OC-1 cells and zebrafish inner ear tissues as models to identify common transcriptome changes in genes and pathways in the absence of human OSBPL2 orthologues by RNA-seq analysis. In total, 2112 differentially expressed genes (DEGs) were identified between wild-type (WT) and Osbpl2-/- OC-1 cells, and 877 DEGs were identified between WT and osbpl2b-/- zebrafish inner ear tissues. Functional annotation implicated Osbpl2/osbpl2b in lipid metabolism, cell adhesion and the extracellular matrix in both OC-1 cells and zebrafish inner ear tissues. Protein-protein interaction (PPI) analysis indicated that Osbpl2/osbpl2b were also involved in ubiquitination. Further experiments showed that Osbpl2-/- OC-1 cells exhibited an abnormal focal adhesion morphology characterized by inhibited FAK activity and impaired cell adhesion. In conclusion, we identified novel pathways modulated by OSBPL2 orthologues, providing new insight into the mechanism of hearing loss induced by OSBPL2 deficiency.
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Affiliation(s)
- Hairong Shi
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, China
| | - Hongshun Wang
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, China
| | - Jun Yao
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, China; Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, China
| | - Changsong Lin
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, China
| | - Qinjun Wei
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, China; Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, China
| | - Yajie Lu
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, China; Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, China
| | - Xin Cao
- Department of Medical Genetics, School of Basic Medical Science, Nanjing Medical University, Nanjing, China; Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, China.
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Carpena NT, Lee MY. Genetic Hearing Loss and Gene Therapy. Genomics Inform 2018; 16:e20. [PMID: 30602081 PMCID: PMC6440668 DOI: 10.5808/gi.2018.16.4.e20] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022] Open
Abstract
Genetic hearing loss crosses almost all the categories of hearing loss which includes the following: conductive, sensory, and neural; syndromic and nonsyndromic; congenital, progressive, and adult onset; high-frequency, low-frequency, or mixed frequency; mild or profound; and recessive, dominant, or sex-linked. Genes play a role in almost half of all cases of hearing loss but effective treatment options are very limited. Genetic hearing loss is considered to be extremely genetically heterogeneous. The advancements in genomics have been instrumental to the identification of more than 6,000 causative variants in more than 150 genes causing hearing loss. Identification of genes for hearing impairment provides an increased insight into the normal development and function of cells in the auditory system. These defective genes will ultimately be important therapeutic targets. However, the auditory system is extremely complex which requires tremendous advances in gene therapy including gene vectors, routes of administration, and therapeutic approaches. This review summarizes and discusses recent advances in elucidating the genomics of genetic hearing loss and technologies aimed at developing a gene therapy that may become a treatment option for in the near future.
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Affiliation(s)
- Nathanial T Carpena
- Department of Otolaryngology-Head and Neck Surgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Min Young Lee
- Department of Otolaryngology-Head and Neck Surgery, Dankook University College of Medicine, Cheonan 31116, Korea.,Beckman Laser Institute Korea, Dankook University, Cheonan 31116, Korea
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Lessons learned from the DFNA37 gene discovery odyssey. Genet Med 2018; 21:1481-1482. [DOI: 10.1038/s41436-018-0395-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/20/2018] [Indexed: 01/23/2023] Open
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