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Shen Z, Zhang T, Twumasi G, Zhang J, Wang J, Xi Y, Wang R, Wang J, Zhang R, Liu H. Genetic analysis of a Kaijiang duck conservation population through genome-wide scan. Br Poult Sci 2024; 65:378-386. [PMID: 38738932 DOI: 10.1080/00071668.2024.2335937] [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: 09/02/2023] [Accepted: 03/08/2024] [Indexed: 05/14/2024]
Abstract
1. The Kaijiang duck is a native Chinese breed known for its excellent egg laying performance, killing-out percentage (88.57%), and disease resistance. The assessment of population genetic structure is the basis for understanding the genetics of indigenous breeds and for their protection and management.2. In this study, whole-genome sequencing was performed on 60 Kaijiang ducks to identify genetic variations and investigate the population structure. Homozygosity (ROH) analysis was conducted to assess inbreeding levels in the population.3. The study revealed a moderate level of inbreeding, indicated by an average inbreeding coefficient of 0.1043. This may impact the overall genetic diversity.4. Genomic Regions of Interest identified included 168 genomic regions exhibiting high levels of autozygosity. These regions were associated with processes including muscle growth, pigmentation, neuromodulation, and growth and reproduction.5. The significance of these pathways indicated their potential role in shaping the desirable traits of the Kaijiang duck. These findings provide insights into the genetic basis of the Kaijiang duck's desirable traits and can inform future breeding and conservation efforts.
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Affiliation(s)
- Z Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - T Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - G Twumasi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Y Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - R Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - J Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - R Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - H Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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2
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Llucià-Carol L, Muiño E, Cullell N, Cárcel-Márquez J, Lledós M, Gallego-Fabrega C, Martin-Campos J, Martí-Fàbregas J, Aguilera-Simón A, Planas AM, DeDiego ML, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Segura T, González-Villar E, Serrano-Heras G, Domínguez Mayoral A, Menéndez-Valladares P, Montaner J, Migeotte I, Rahmouni S, Darcis G, Bernardo D, Rojo S, Schulte EC, Protzer U, Fricke L, Winter C, Niemi MEK, Cordioli M, Delgado P, Fernández-Cadenas I. Genetic Architecture of Ischaemic Strokes after COVID-19 Shows Similarities with Large Vessel Strokes. Int J Mol Sci 2023; 24:13452. [PMID: 37686257 PMCID: PMC10487930 DOI: 10.3390/ijms241713452] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
We aimed to analyse whether patients with ischaemic stroke (IS) occurring within eight days after the onset of COVID-19 (IS-COV) are associated with a specific aetiology of IS. We used SUPERGNOVA to identify genome regions that correlate between the IS-COV cohort (73 IS-COV cases vs. 701 population controls) and different aetiological subtypes. Polygenic risk scores (PRSs) for each subtype were generated and tested in the IS-COV cohort using PRSice-2 and PLINK to find genetic associations. Both analyses used the IS-COV cohort and GWAS from MEGASTROKE (67,162 stroke patients vs. 454,450 population controls), GIGASTROKE (110,182 vs. 1,503,898), and the NINDS Stroke Genetics Network (16,851 vs. 32,473). Three genomic regions were associated (p-value < 0.05) with large artery atherosclerosis (LAA) and cardioembolic stroke (CES). We found four loci targeting the genes PITX2 (rs10033464, IS-COV beta = 0.04, p-value = 2.3 × 10-2, se = 0.02), previously associated with CES, HS6ST1 (rs4662630, IS-COV beta = -0.04, p-value = 1.3 × 10-3, se = 0.01), TMEM132E (rs12941838 IS-COV beta = 0.05, p-value = 3.6 × 10-4, se = 0.01), and RFFL (rs797989 IS-COV beta = 0.03, p-value = 1.0 × 10-2, se = 0.01). A statistically significant PRS was observed for LAA. Our results suggest that IS-COV cases are genetically similar to LAA and CES subtypes. Larger cohorts are needed to assess if the genetic factors in IS-COV cases are shared with the general population or specific to viral infection.
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Affiliation(s)
- Laia Llucià-Carol
- Stroke Pharmacogenomics and Genetics, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí 77-79, 08041 Barcelona, Spain; (L.L.-C.); (M.L.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Elena Muiño
- Stroke Pharmacogenomics and Genetics, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí 77-79, 08041 Barcelona, Spain; (L.L.-C.); (M.L.)
| | - Natalia Cullell
- Stroke Pharmacogenomics and Genetics, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí 77-79, 08041 Barcelona, Spain; (L.L.-C.); (M.L.)
- Department of Neurology, Hospital Universitari MútuaTerrassa, Fundació Docència i Recerca MútuaTerrassa, 08221 Terrassa, Spain
| | - Jara Cárcel-Márquez
- Stroke Pharmacogenomics and Genetics, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí 77-79, 08041 Barcelona, Spain; (L.L.-C.); (M.L.)
| | - Miquel Lledós
- Stroke Pharmacogenomics and Genetics, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí 77-79, 08041 Barcelona, Spain; (L.L.-C.); (M.L.)
| | - Cristina Gallego-Fabrega
- Stroke Pharmacogenomics and Genetics, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí 77-79, 08041 Barcelona, Spain; (L.L.-C.); (M.L.)
| | - Jesús Martin-Campos
- Stroke Pharmacogenomics and Genetics, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí 77-79, 08041 Barcelona, Spain; (L.L.-C.); (M.L.)
| | - Joan Martí-Fàbregas
- Department of Neurology, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
| | - Ana Aguilera-Simón
- Department of Neurology, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain
| | - Anna M. Planas
- Institute for Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Marta L. DeDiego
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain;
| | - Alicia de Felipe Mimbrera
- Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Universitario Ramón Y Cajal, 28034 Madrid, Spain
| | - Jaime Masjuan
- Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Universitario Ramón Y Cajal, 28034 Madrid, Spain
| | - Sebastián García-Madrona
- Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Universitario Ramón Y Cajal, 28034 Madrid, Spain
| | - Tomás Segura
- Department of Neurology, University Hospital of Albacete, 02006 Albacete, Spain
| | | | - Gemma Serrano-Heras
- Department of Neurology, University Hospital of Albacete, 02006 Albacete, Spain
| | - Ana Domínguez Mayoral
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío, CSIC, Universidad de Sevilla, 410113 Seville, Spain
- Department of Neurology, Hospital Universitario Virgen Macarena, 41009 Seville, Spain
| | - Paloma Menéndez-Valladares
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío, CSIC, Universidad de Sevilla, 410113 Seville, Spain
- Department of Neurology, Hospital Universitario Virgen Macarena, 41009 Seville, Spain
| | - Joan Montaner
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío, CSIC, Universidad de Sevilla, 410113 Seville, Spain
- Department of Neurology, Hospital Universitario Virgen Macarena, 41009 Seville, Spain
| | - Isabelle Migeotte
- Fonds de la Recherche Scientifique (FNRS), 1000 Brussels, Belgium
- Centre de Génétique Humaine, Hopital Erasme, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Souad Rahmouni
- Fonds de la Recherche Scientifique (FNRS), 1000 Brussels, Belgium
- Department of Biomedical and Preclinical Sciences, Faculty of Medicine, GIGA-Insitute, University of Liege, 4000 Liège, Belgium
| | - Gilles Darcis
- Fonds de la Recherche Scientifique (FNRS), 1000 Brussels, Belgium
- CHU of Liege, 4000 Liège, Belgium
| | - David Bernardo
- Mucosal Immunology Lab, Unidad de Excelencia del Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid-CSIC, 47005 Valladolid, Spain
| | - Silvia Rojo
- Department of Microbiology, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León (SACYL), 47003 Valladolid, Spain
| | - Eva C. Schulte
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, 81377 Munich, Germany
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich University, 80336 Munich, Germany
- Department of Psychiatry, University Hospital, LMU Munich University, 80336 Munich, Germany
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, University of Bonn, 53127 Bonn, Germany
- Department of Psychiatry and Psychotherapy, University Hospital Bonn, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Ulrike Protzer
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, 81377 Munich, Germany
| | - Lisa Fricke
- Department of Internal Medicine II, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany;
| | - Christof Winter
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technische Universität München (TUM), 81675 Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Technische Universität München, 81675 Munich, Germany
| | - Mari E. K. Niemi
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland; (M.E.K.N.)
| | - Mattia Cordioli
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland; (M.E.K.N.)
| | - Pilar Delgado
- Department of Neurology, Hospital Universitari de la Vall d’Hebrón, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | - Israel Fernández-Cadenas
- Stroke Pharmacogenomics and Genetics, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí 77-79, 08041 Barcelona, Spain; (L.L.-C.); (M.L.)
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Li B, Brusman L, Dahlka J, Niswander LA. TMEM132A ensures mouse caudal neural tube closure and regulates integrin-based mesodermal migration. Development 2022; 149:dev200442. [PMID: 35950911 PMCID: PMC9482334 DOI: 10.1242/dev.200442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/25/2022] [Indexed: 09/01/2023]
Abstract
Coordinated migration of the mesoderm is essential for accurate organization of the body plan during embryogenesis. However, little is known about how mesoderm migration influences posterior neural tube closure in mammals. Here, we show that spinal neural tube closure and lateral migration of the caudal paraxial mesoderm depend on transmembrane protein 132A (TMEM132A), a single-pass type I transmembrane protein, the function of which is not fully understood. Our study in Tmem132a-null mice and cell models demonstrates that TMEM132A regulates several integrins and downstream integrin pathway activation as well as cell migration behaviors. Our data also implicates mesoderm migration in elevation of the caudal neural folds and successful closure of the caudal neural tube. These results suggest a requirement for paraxial mesodermal cell migration during spinal neural tube closure, disruption of which may lead to spina bifida.
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Affiliation(s)
| | | | | | - Lee A. Niswander
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
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4
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Imtiaz A. ARNSHL gene identification: past, present and future. Mol Genet Genomics 2022; 297:1185-1193. [DOI: 10.1007/s00438-022-01926-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 07/05/2022] [Indexed: 10/16/2022]
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5
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Wang Y, Herzig G, Molano C, Liu A. Differential expression of the Tmem132 family genes in the developing mouse nervous system. Gene Expr Patterns 2022; 45:119257. [PMID: 35690356 DOI: 10.1016/j.gep.2022.119257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/15/2022]
Abstract
The family of novel transmembrane proteins (TMEM) 132 have been associated with multiple neurological disorders and cancers in humans, but have hardly been studied in vivo. Here we report the expression patterns of the five Tmem132 genes (a, b, c, d and e) in developing mouse nervous system with RNA in situ hybridization in wholemount embryos and tissue sections. Our results reveal differential and partially overlapping expression of multiple Tmem132 family members in both the central and peripheral nervous system, suggesting potential partial redundancy among them.
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Affiliation(s)
- Yuan Wang
- Department of Occupational and Environmental Health, School of Public Health, China Medical University, Shenyang, PR China; Department of Biology, Eberly College of Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Graham Herzig
- Department of Biology, Eberly College of Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Cassandra Molano
- Department of Biology, Eberly College of Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Aimin Liu
- Department of Biology, Eberly College of Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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6
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Acharya A, Schrauwen I, Leal SM. Identification of autosomal recessive nonsyndromic hearing impairment genes through the study of consanguineous and non-consanguineous families: past, present, and future. Hum Genet 2022; 141:413-430. [PMID: 34291353 PMCID: PMC10416318 DOI: 10.1007/s00439-021-02309-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/24/2021] [Indexed: 10/20/2022]
Abstract
Hearing impairment (HI) is one of the most common sensory disabilities with exceptionally high genetic heterogeneity. Of genetic HI cases, 30% are syndromic and 70% are nonsyndromic. For nonsyndromic (NS) HI, 77% of the cases are due to autosomal recessive (AR) inheritance. ARNSHI is usually congenital/prelingual, severe-to-profound, affects all frequencies and is not progressive. Thus far, 73 ARNSHI genes have been identified. Populations with high rates of consanguinity have been crucial in the identification of ARNSHI genes, and 92% (67/73) of these genes were identified in consanguineous families. Recent changes in genomic technologies and analyses have allowed a shift towards ARNSHI gene discovery in outbred populations. The latter is crucial towards understanding the genetic architecture of ARNSHI in diverse and understudied populations. We present an overview of the 73 ARNSHI genes, the methods used to identify them, including next-generation sequencing which revolutionized the field, and new technologies that show great promise in advancing ARNSHI discoveries.
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Affiliation(s)
- Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA.
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA.
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7
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Sandoval-Castillo J, Beheregaray LB, Wellenreuther M. Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus). G3 (BETHESDA, MD.) 2022; 12:jkac015. [PMID: 35100370 PMCID: PMC8896003 DOI: 10.1093/g3journal/jkac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Growth is one of the most important traits of an organism. For exploited species, this trait has ecological and evolutionary consequences as well as economical and conservation significance. Rapid changes in growth rate associated with anthropogenic stressors have been reported for several marine fishes, but little is known about the genetic basis of growth traits in teleosts. We used reduced genome representation data and genome-wide association approaches to identify growth-related genetic variation in the commercially, recreationally, and culturally important Australian snapper (Chrysophrys auratus, Sparidae). Based on 17,490 high-quality single-nucleotide polymorphisms and 363 individuals representing extreme growth phenotypes from 15,000 fish of the same age and reared under identical conditions in a sea pen, we identified 100 unique candidates that were annotated to 51 proteins. We documented a complex polygenic nature of growth in the species that included several loci with small effects and a few loci with larger effects. Overall heritability was high (75.7%), reflected in the high accuracy of the genomic prediction for the phenotype (small vs large). Although the single-nucleotide polymorphisms were distributed across the genome, most candidates (60%) clustered on chromosome 16, which also explains the largest proportion of heritability (16.4%). This study demonstrates that reduced genome representation single-nucleotide polymorphisms and the right bioinformatic tools provide a cost-efficient approach to identify growth-related loci and to describe genomic architectures of complex quantitative traits. Our results help to inform captive aquaculture breeding programs and are of relevance to monitor growth-related evolutionary shifts in wild populations in response to anthropogenic pressures.
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Affiliation(s)
- Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Maren Wellenreuther
- School of Biological Sciences, The New Zealand Institute for Plant and Food Research Limited, Nelson 7010, New Zealand
- Seafood Production Group, The School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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8
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Zhang X, Li T, Niu Q, Qin CJ, Zhang M, Wu GM, Li HZ, Li Y, Wang C, Du WF, Wang CY, Zhao Q, Zhao XD, Wang XL, Zhu JB. Genome-wide analysis of cell-Free DNA methylation profiling with MeDIP-seq identified potential biomarkers for colorectal cancer. World J Surg Oncol 2022; 20:21. [PMID: 35065650 PMCID: PMC8783473 DOI: 10.1186/s12957-022-02487-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 12/30/2021] [Indexed: 11/15/2022] Open
Abstract
Background Colorectal cancer is the most common malignancy and the third leading cause of cancer-related death worldwide. This study aimed to identify potential diagnostic biomarkers for colorectal cancer by genome-wide plasma cell-free DNA (cfDNA) methylation analysis. Methods Peripheral blood from colorectal cancer patients and healthy controls was collected for cfDNA extraction. Genome-wide cfDNA methylation profiling, especially differential methylation profiling between colorectal cancer patients and healthy controls, was performed by methylated DNA immunoprecipitation coupled with high-throughput sequencing (MeDIP-seq). Logistic regression models were established, and the accuracy of this diagnostic model for colorectal cancer was verified using tissue-sourced data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) due to the lack of cfDNA methylation data in public datasets. Results Compared with the control group, 939 differentially methylated regions (DMRs) located in promoter regions were found in colorectal cancer patients; 16 of these DMRs were hypermethylated, and the remaining 923 were hypomethylated. In addition, these hypermethylated genes, mainly PRDM14, RALYL, ELMOD1, and TMEM132E, were validated and confirmed in colorectal cancer by using publicly available DNA methylation data. Conclusions MeDIP-seq can be used as an optimal approach for analyzing cfDNA methylomes, and 12 probes of four differentially methylated genes identified by MeDIP-seq (PRDM14, RALYL, ELMOD1, and TMEM132E) could serve as potential biomarkers for clinical application in patients with colorectal cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12957-022-02487-4.
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Affiliation(s)
- Xin Zhang
- Department of General Surgery, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, No. 1158 Gongyuan East Road, Qingpu District, Shanghai, 201700, China
| | - Tao Li
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Qiang Niu
- Department of General Surgery, Shidong Hospital Affiliated to University of Shanghai for Science and Technology, Shanghai, 200433, China
| | - Chang-Jiang Qin
- Department of Gastrointestinal Surgery, Huaihe Hospital of Henan University, Kaifeng, 475000, Henan, China
| | - Ming Zhang
- General Surgery, The People's Hospital of Wuhai, Wuhai, 010600, Inner Mongolia, China
| | - Guang-Ming Wu
- General Surgery, The People's Hospital of Wuhai, Wuhai, 010600, Inner Mongolia, China
| | - Hua-Zhong Li
- General Surgery, The People's Hospital of Wuhai, Wuhai, 010600, Inner Mongolia, China
| | - Yan Li
- Digestive Internal, The People's Hospital of Wuhai, No. 29 Huanghe East Street, Haibowan District, Wuhai, 010600, Inner Mongolia, China
| | - Chen Wang
- Digestive Internal, The People's Hospital of Wuhai, No. 29 Huanghe East Street, Haibowan District, Wuhai, 010600, Inner Mongolia, China
| | - Wen-Fei Du
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chen-Yang Wang
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qiang Zhao
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiao-Dong Zhao
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiao-Liang Wang
- Department of General Surgery, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, No. 1158 Gongyuan East Road, Qingpu District, Shanghai, 201700, China. .,Department of General Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong, Shanghai, 201399, China.
| | - Jian-Bin Zhu
- Digestive Internal, The People's Hospital of Wuhai, No. 29 Huanghe East Street, Haibowan District, Wuhai, 010600, Inner Mongolia, China.
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9
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Azadegan-Dehkordi F, Koohiyan M, Hoseini M. An update on autosomal recessive hearing loss and loci involved in it. INDIAN JOURNAL OF OTOLOGY 2022. [DOI: 10.4103/indianjotol.indianjotol_115_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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10
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Zhu T, Qi X, Chen Y, Wang L, Lv X, Yang W, Zhang J, Li K, Ning Z, Jiang Z, Qu L. Positive selection of skeleton-related genes during duck domestication revealed by whole genome sequencing. BMC Ecol Evol 2021; 21:165. [PMID: 34488647 PMCID: PMC8419914 DOI: 10.1186/s12862-021-01894-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 08/20/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Domestication alters several phenotypic, neurological, and physiological traits in domestic animals compared to those in their wild ancestors. Domestic ducks originated from mallards, and some studies have shown that spot-billed ducks may have also made minor genetic contributions to domestication. Compared with the two ancestral species, domestic ducks generally differ in body size and bone morphology. In this study, we performed both genomic and transcriptomic analyses to identify candidate genes for elucidating the genetic mechanisms underlying phenotypic variation. METHODS In this study, the duck genome data from eight domestic breeds and two wild species were collected to study the genetic changes during domestication. And the transcriptome data of different tissues from wild ducks and seven domestic ducks were used to reveal the expression difference between wild and domestic ducks. RESULTS Using fixation index (Fst) algorithm and transcriptome data, we found that the genes related to skeletal development had high Fst values in wild and domestic breeds, and the differentially expressed genes were mainly enriched in the ossification pathway. Our data strongly suggest that the skeletal systems of domestic ducks were changed to adapt to artificial selection for larger sizes. In addition, by combining the genome and transcriptome data, we found that some Fst candidate genes exhibited different expression patterns, and these genes were found to be involved in digestive, immune, and metabolic functions. CONCLUSIONS A wide range of phenotypic differences exists between domestic and wild ducks. Through both genome and transcriptome analyses, we found that genes related to the skeletal system in domestic ducks were strongly selected. Our findings provide new insight into duck domestication and selection effects during the domestication.
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Affiliation(s)
- Tao Zhu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - Xin Qi
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - Yu Chen
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Liang Wang
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Xueze Lv
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Weifang Yang
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Jianwei Zhang
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Kaiyang Li
- Beijing General Station of Animal Husbandry, Beiyuan Road 15A#, Beijing, 100107, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China
| | - Zhihua Jiang
- Department of Animal Sciences, Center for Reproductive Biology, Veterinary and Biomedical Research Building, Washington State University, Pullman, Washington, 647010, USA
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2#, Beijing, 100193, China.
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11
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Matta JA, Gu S, Davini WB, Bredt DS. Nicotinic acetylcholine receptor redux: Discovery of accessories opens therapeutic vistas. Science 2021; 373:373/6556/eabg6539. [PMID: 34385370 DOI: 10.1126/science.abg6539] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The neurotransmitter acetylcholine (ACh) acts in part through a family of nicotinic ACh receptors (nAChRs), which mediate diverse physiological processes including muscle contraction, neurotransmission, and sensory transduction. Pharmacologically, nAChRs are responsible for tobacco addiction and are targeted by medicines for hypertension and dementia. Nicotinic AChRs were the first ion channels to be isolated. Recent studies have identified molecules that control nAChR biogenesis, trafficking, and function. These nAChR accessories include protein and chemical chaperones as well as auxiliary subunits. Whereas some factors act on many nAChRs, others are receptor specific. Discovery of these regulatory mechanisms is transforming nAChR research in cells and tissues ranging from central neurons to spinal ganglia to cochlear hair cells. Nicotinic AChR-specific accessories also enable drug discovery on high-confidence targets for psychiatric, neurological, and auditory disorders.
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Affiliation(s)
| | | | - Weston B Davini
- Neuroscience Discovery, Janssen Pharmaceutical Companies of Johnson & Johnson, San Diego, CA 92121, USA
| | - David S Bredt
- Neuroscience Discovery, Janssen Pharmaceutical Companies of Johnson & Johnson, San Diego, CA 92121, USA.
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12
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Farhadi M, Razmara E, Balali M, Hajabbas Farshchi Y, Falah M. How Transmembrane Inner Ear (TMIE) plays role in the auditory system: A mystery to us. J Cell Mol Med 2021; 25:5869-5883. [PMID: 33987950 PMCID: PMC8256367 DOI: 10.1111/jcmm.16610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/26/2021] [Indexed: 01/19/2023] Open
Abstract
Different cellular mechanisms contribute to the hearing sense, so it is obvious that any disruption in such processes leads to hearing impairment that greatly influences the global economy and quality of life of the patients and their relatives. In the past two decades, transmembrane inner ear (TMIE) protein has received a great deal of research interest because its impairments cause hereditary deafness in humans. This evolutionarily conserved membrane protein contributes to a fundamental complex that plays role in the maintenance and function of the sensory hair cells. Although the critical roles of the TMIE in mechanoelectrical transduction or hearing procedures have been discussed, there are little to no review papers summarizing the roles of the TMIE in the auditory system. In order to fill this gap, herein, we discuss the important roles of this protein in the auditory system including its role in mechanotransduction, olivocochlear synapse, morphology and different signalling pathways; we also review the genotype-phenotype correlation that can per se show the possible roles of this protein in the auditory system.
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Affiliation(s)
- Mohammad Farhadi
- ENT and Head and Neck Research Center and DepartmentThe Five Senses Health InstituteHazrat Rasoul Akram HospitalIran University of Medical SciencesTehranIran
| | - Ehsan Razmara
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVICAustralia
| | - Maryam Balali
- ENT and Head and Neck Research Center and DepartmentThe Five Senses Health InstituteHazrat Rasoul Akram HospitalIran University of Medical SciencesTehranIran
| | - Yeganeh Hajabbas Farshchi
- Department of Cellular and Molecular BiologyTehran Medical SciencesIslamic Azad UniversityTehranIran
| | - Masoumeh Falah
- ENT and Head and Neck Research Center and DepartmentThe Five Senses Health InstituteHazrat Rasoul Akram HospitalIran University of Medical SciencesTehranIran
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13
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Mahfood M, Chouchen J, Kamal Eddine Ahmad Mohamed W, Al Mutery A, Harati R, Tlili A. Whole exome sequencing, in silico and functional studies confirm the association of the GJB2 mutation p.Cys169Tyr with deafness and suggest a role for the TMEM59 gene in the hearing process. Saudi J Biol Sci 2021; 28:4421-4429. [PMID: 34354426 PMCID: PMC8324942 DOI: 10.1016/j.sjbs.2021.04.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 12/25/2022] Open
Abstract
The development of next generation sequencing techniques has facilitated the detection of mutations at an unprecedented rate. These efficient tools have been particularly beneficial for extremely heterogeneous disorders such as autosomal recessive non-syndromic hearing loss, the most common form of genetic deafness. GJB2 mutations are the most common cause of hereditary hearing loss. Amongst them the NM_004004.5: c.506G > A (p.Cys169Tyr) mutation has been associated with varying severity of hearing loss with unclear segregation patterns. In this study, we report a large consanguineous Emirati family with severe to profound hearing loss fully segregating the GJB2 missense mutation p.Cys169Tyr. Whole exome sequencing (WES), in silico, splicing and expression analyses ruled out the implication of any other variants and confirmed the implication of the p.Cys169Tyr mutation in this deafness family. We also show preliminary murine expression analysis that suggests a link between the TMEM59 gene and the hearing process. The present study improves our understanding of the molecular pathogenesis of hearing loss. It also emphasizes the significance of combining next generation sequencing approaches and segregation analyses especially in the diagnosis of disorders characterized by complex genetic heterogeneity.
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Key Words
- ARNSHL, autosomal recessive non-syndromic hearing loss
- Actb, Actin beta
- BAM, Binary Alignment Map
- BWA, Burrows-Wheeler Aligner
- C1QTNF9, C1q and TNF related 9
- Cx26, Connexin 26
- ESRRAP2, Estrogen-Related Receptor Alpha Pseudogene 2
- GJB2 gene
- GJB2, Gap Junction Protein Beta 2
- HHLA1, HERV-H LTR-Associating 1
- HL, Hearing loss
- KCNQ3, Potassium Voltage-Gated Channel Subfamily Q Member 3
- Missense mutation
- NGS, next generation sequencing
- NSHL, Non-syndromic hearing loss
- Non-syndromic hearing loss
- PROVEAN, Protein Variation Effect Analyzer
- PolyPhen-2, Polymorphism Phenotyping v2
- RFLP, restriction fragment length polymorphism
- ROH, runs of homozygosity
- RT-PCR, reverse transcription PCR
- RT-qPCR, quantitative reverse transcription PCR
- SAM, Sequence Alignment/Map
- SIFT, Sorting Intolerant From Tolerant
- SJL, Swiss Jim Lambert
- SPATA13, Spermatogenesis Associated 13
- ST3GAL1, ST3 Beta-Galactoside Alpha-2,3-Sialyltransferase 1
- TMEM59, Transmembrane Protein 59
- UAE, United Arab Emirates
- VariMAT, Variation and Mutation Annotation Toolkit
- WES, Whole exome sequencing
- Whole exome sequencing
- dpSNP, Single Nucleotide Polymorphism Database
- gEAR, gene Expression Analysis Resource
- gnomAD, genome aggregation database
- qPCR, quantitative PCR
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Affiliation(s)
- Mona Mahfood
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Jihen Chouchen
- Human Genetics and Stem Cell Research Group, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Walaa Kamal Eddine Ahmad Mohamed
- Human Genetics and Stem Cell Research Group, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Abdullah Al Mutery
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates.,Human Genetics and Stem Cell Research Group, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Rania Harati
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates.,Human Genetics and Stem Cell Research Group, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
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14
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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: 12] [Impact Index Per Article: 4.0] [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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15
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Chon C, Chon G, Matsui Y, Zeng H, Lai ZC, Liu A. Efficient multiplexed genome engineering with a polycistronic tRNA and CRISPR guide-RNA reveals an important role of detonator in reproduction of Drosophila melanogaster. PLoS One 2021; 16:e0245454. [PMID: 33444382 PMCID: PMC7808601 DOI: 10.1371/journal.pone.0245454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 01/03/2021] [Indexed: 11/18/2022] Open
Abstract
Genome association studies in human and genetic studies in mouse implicated members of the transmembrane protein 132 (TMEM132) family in multiple conditions including panic disorder, hearing loss, limb and kidney malformation. However, the presence of five TMEM132 paralogs in mammalian genomes makes it extremely challenging to reveal the full requirement for these proteins in vivo. In contrast, there is only one TMEM132 homolog, detonator (dtn), in the genome of fruit fly Drosophila melanogaster, enabling straightforward research into its in vivo function. In the current study, we generate multiple loss-of-function dtn mutant fly strains through a polycistronic tRNA-gRNA approach, and show that most embryos lacking both maternal and paternal dtn fail to hatch into larvae, indicating an essential role of dtn in Drosophila reproduction.
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Affiliation(s)
- Cristin Chon
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
| | - Grace Chon
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
| | - Yurika Matsui
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
| | - Huiqing Zeng
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
| | - Zhi-Chun Lai
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
| | - Aimin Liu
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
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16
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Escalera-Balsera A, Roman-Naranjo P, Lopez-Escamez JA. Systematic Review of Sequencing Studies and Gene Expression Profiling in Familial Meniere Disease. Genes (Basel) 2020; 11:E1414. [PMID: 33260921 PMCID: PMC7761472 DOI: 10.3390/genes11121414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/21/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Familial Meniere Disease (FMD) is a rare inner ear disorder characterized by episodic vertigo associated with sensorineural hearing loss, tinnitus and/or aural fullness. We conducted a systematic review to find sequencing studies segregating rare variants in FMD to obtain evidence to support candidate genes for MD. After evaluating the quality of the retrieved records, eight studies were selected to carry out a quantitative synthesis. These articles described 20 single nucleotide variants (SNVs) in 11 genes (FAM136A, DTNA, PRKCB, COCH, DPT, SEMA3D, STRC, HMX2, TMEM55B, OTOG and LSAMP), most of them in singular families-the exception being the OTOG gene. Furthermore, we analyzed the pathogenicity of each SNV and compared its allelic frequency with reference datasets to evaluate its role in the pathogenesis of FMD. By retrieving gene expression data in these genes from different databases, we could classify them according to their gene expression in neural or inner ear tissues. Finally, we evaluated the pattern of inheritance to conclude which genes show an autosomal dominant (AD) or autosomal recessive (AR) inheritance in FMD.
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Affiliation(s)
- Alba Escalera-Balsera
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, 18016 Granada, Spain; (A.E.-B.); (P.R.-N.)
| | - Pablo Roman-Naranjo
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, 18016 Granada, Spain; (A.E.-B.); (P.R.-N.)
| | - Jose Antonio Lopez-Escamez
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, 18016 Granada, Spain; (A.E.-B.); (P.R.-N.)
- Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.GRANADA, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
- Department of Surgery, Division of Otolaryngology, Universidad de Granada, 18016 Granada, Spain
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17
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Vona B, Doll J, Hofrichter MAH, Haaf T, Varshney GK. Small fish, big prospects: using zebrafish to unravel the mechanisms of hereditary hearing loss. Hear Res 2020; 397:107906. [PMID: 32063424 PMCID: PMC7415493 DOI: 10.1016/j.heares.2020.107906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Affiliation(s)
- Barbara Vona
- Department of Otolaryngology--Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany.
| | - Julia Doll
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.
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18
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Hair cell α9α10 nicotinic acetylcholine receptor functional expression regulated by ligand binding and deafness gene products. Proc Natl Acad Sci U S A 2020; 117:24534-24544. [PMID: 32929005 DOI: 10.1073/pnas.2013762117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Auditory hair cells receive olivocochlear efferent innervation, which refines tonotopic mapping, improves sound discrimination, and mitigates acoustic trauma. The olivocochlear synapse involves α9α10 nicotinic acetylcholine receptors (nAChRs), which assemble in hair cells only coincident with cholinergic innervation and do not express in recombinant mammalian cell lines. Here, genome-wide screening determined that assembly and surface expression of α9α10 require ligand binding. Ion channel function additionally demands an auxiliary subunit, which can be transmembrane inner ear (TMIE) or TMEM132e. Both of these single-pass transmembrane proteins are enriched in hair cells and underlie nonsyndromic human deafness. Inner hair cells from TMIE mutant mice show altered postsynaptic α9α10 function and retain α9α10-mediated transmission beyond the second postnatal week associated with abnormally persistent cholinergic innervation. Collectively, this study provides a mechanism to link cholinergic input with α9α10 assembly, identifies unexpected functions for human deafness genes TMIE/TMEM132e, and enables drug discovery for this elusive nAChR implicated in prevalent auditory disorders.
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19
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Gene therapy development in hearing research in China. Gene Ther 2020; 27:349-359. [PMID: 32681137 DOI: 10.1038/s41434-020-0177-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/13/2020] [Accepted: 07/08/2020] [Indexed: 12/15/2022]
Abstract
Sensorineural hearing loss, the most common form of hearing impairment, is mainly attributable to genetic mutations or acquired factors, such as aging, noise exposure, and ototoxic drugs. In the field of gene therapy, advances in genetic and physiological studies and profound increases in knowledge regarding the underlying mechanisms have yielded great progress in terms of restoring the auditory function in animal models of deafness. Nonetheless, many challenges associated with the translation from basic research to clinical therapies remain to be overcome before a total restoration of auditory function can be expected. In recent years, Chinese research teams have promoted various developmental efforts in this field, including gene sequencing to identify additional potential loci that cause deafness, studies to elucidate the underlying molecular mechanisms, and research to optimize vectors and delivery routes. In this review, we summarize the state of the field and focus mainly on the progress of gene therapy in animal model studies and the optimization of therapeutic strategies in China.
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20
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Lee S, Dondzillo A, Gubbels SP, Raphael Y. Practical aspects of inner ear gene delivery for research and clinical applications. Hear Res 2020; 394:107934. [PMID: 32204962 DOI: 10.1016/j.heares.2020.107934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/24/2022]
Abstract
The application of gene therapy is widely expanding in research and continuously improving in preparation for clinical applications. The inner ear is an attractive target for gene therapy for treating environmental and genetic diseases in both the auditory and vestibular systems. With the lack of spontaneous cochlear hair cell replacement, hair cell regeneration in adult mammals is among the most important goals of gene therapy. In addition, correcting gene defects can open up a new era for treating inner ear diseases. The relative isolation and small size of the inner ear dictate local administration routes and carefully calculated small volumes of reagents. In the current review, we will cover effective timing, injection routes and types of vectors for successful gene delivery to specific target cells within the inner ear. Differences between research purposes and clinical applications are also discussed.
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Affiliation(s)
- Sungsu Lee
- Kresge Hearing Research Institute, Department of Otolaryngology, Head and Neck Surgery, Michigan Medicine, Ann Arbor, MI, USA
| | - Anna Dondzillo
- Department of Otolaryngology, Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Samuel P Gubbels
- Department of Otolaryngology, Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Yehoash Raphael
- Kresge Hearing Research Institute, Department of Otolaryngology, Head and Neck Surgery, Michigan Medicine, Ann Arbor, MI, USA.
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21
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Liaqat K, Hussain S, Bilal M, Nasir A, Acharya A, Ali RH, Nawaz S, Umair M, Schrauwen I, Ahmad W, Leal SM. Further evidence of involvement of TMEM132E in autosomal recessive nonsyndromic hearing impairment. J Hum Genet 2019; 65:187-192. [PMID: 31656313 PMCID: PMC8216908 DOI: 10.1038/s10038-019-0691-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/01/2019] [Accepted: 10/09/2019] [Indexed: 12/25/2022]
Abstract
Autosomal-recessive (AR) nonsyndromic hearing impairment (NSHI) displays a high degree of genetic heterogeneity with >100 genes identified. Recently, TMEM132E, which is highly expressed in inner hair cells, was suggested as a novel ARNSHI gene for DFNB99. A missense variant c.1259G>A: p.(Arg420Gln) in TMEM132E was identified that segregated with ARNSHI in a single Chinese family with two affected members. In the present study, a family of Pakistani origin with prelingual profound sensorineural hearing impairment displaying AR mode of inheritance was investigated via exome and Sanger sequencing. Compound heterozygous variants c.382G>T: p.(Ala128Ser) and c.2204C>T: p.(Pro735Leu) in TMEM132E were observed in affected but not in unaffected family members. TMEM132E variants identified in this and the previously reported ARNSHI family are located in the extracellular domain. In conclusion, we present a second ARNSHI family with TMEM132E variants which strengthens the evidence of the involvement of this gene in the etiology of ARNSHI.
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Affiliation(s)
- Khurram Liaqat
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Center of Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shabir Hussain
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Center of Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, Suwon, 443-749, South Korea
| | - Anushree Acharya
- Center of Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Center for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Raja Hussain Ali
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Shoaib Nawaz
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Science, Ministry of National Guard-Health Affairs (MNGHA), P.O. Box 3660, Riyadh, 11481, Saudi Arabia
| | - Isabelle Schrauwen
- Center of Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Center for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Suzanne M Leal
- Center of Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Center for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA.
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22
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Megdiche S, Mastrangelo S, Ben Hamouda M, Lenstra JA, Ciani E. A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds. Front Genet 2019; 10:1025. [PMID: 31708969 PMCID: PMC6824410 DOI: 10.3389/fgene.2019.01025] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/24/2019] [Indexed: 12/24/2022] Open
Abstract
Merino sheep represents a valuable genetic resource worldwide. In this study, we investigated selection signatures in Merino (and Merino-derived) sheep breeds using genome-wide SNP data and two different approaches: a classical FST-outlier method and an approach based on the analysis of local ancestry in admixed populations. In order to capture the most reliable signals, we adopted a combined, multi-cohort approach. In particular, scenarios involving four Merino breeds (Spanish Merino, Australian Merino, Chinese Merino, and Sopravissana) were tested via the local ancestry approach, while nine pair-wise breed comparisons contrasting the above breeds, as well as the Gentile di Puglia breed, with non-Merino breeds from the same geographic area were tested via the FST-outlier method. Signals observed using both methods were compared with genome-wide patterns of distribution of runs of homozygosity (ROH) islands. Novel and known selection signatures were detected. The most reliable signals were observed on OAR 3 (MSRB3 and LEMD3), OAR10 (FRY and RXFP2), OAR 13 (RALY), OAR17 (FAM101A), and OAR18 (NFKBIA, SEC23A, and PAX9). All the above overlapped with known QTLs for wool traits, and evidences from the literature of their involvement in skin/hair/wool biology, as well as gene network analysis, further corroborated these results. The signal on OAR10 also contains well known evidence for association with horn morphology and polledness. More elusive biological evidences of association with the Merino phenotype were observed for a number of other genes, notably LOC101120019 and TMEM132B (OAR17), LOC105609948 (OAR3), LOC101110773 (OAR10), and EIF2S2 (OAR17). Taken together, the above results further contribute to decipher the genetic basis underlying the Merino phenotype.
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Affiliation(s)
- Sami Megdiche
- Départment des Ressources Animales, Agroalimentaire et Développement Rural, Institut Supérieur Agronomique de Chott-Mariem, Université de Sousse, Sousse, Tunisia
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | | | | | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro,”Bari, Italy
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23
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Skarp S, Kanervo L, Kotimäki J, Sorri M, Männikkö M, Hietikko E. Whole-exome sequencing suggests multiallelic inheritance for childhood-onset Ménière's disease. Ann Hum Genet 2019; 83:389-396. [PMID: 31106404 DOI: 10.1111/ahg.12327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 03/18/2019] [Accepted: 04/29/2019] [Indexed: 01/22/2023]
Abstract
The genetic background of Ménière's disease (MD) was studied in one patient with childhood-onset MD and his grandfather affected with middle age-onset MD. Whole-exome sequencing was performed and the data were compared to 76 exomes from unrelated subjects without MD. Thirteen rare inner ear expressed variants with pathogenic estimations were observed in the case of childhood-onset MD. These variants were in genes involved in the formation of cell membranes or the cytoskeleton and in genes participating in cell death or gene-regulation pathways. His grandfather shared two of the variants: p.Y273N in HMX2 and p.L229F in TMEM55B. HMX2 p.Y273N was considered the more likely candidate for MD, as the gene is known to affect both hearing and vestibular function. The variant in the HMX2 gene may affect inner ear development and structural integrity and thus might predispose to the onset of MD. As there was a significant difference in onset between the patients, an accumulation of defects in several pathways is probably responsible for the exceptionally early onset of the disease, and the genetic etiology of childhood-onset MD is most likely multifactorial. This is the first molecular genetic study of childhood-onset MD.
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Affiliation(s)
- Sini Skarp
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Laura Kanervo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Jouko Kotimäki
- Department of Otorhinolaryngology, Kainuu Central Hospital, Kajaani, Finland
| | - Martti Sorri
- Department of Otorhinolaryngology and Head and Neck Surgery, Oulu University Hospital, Finland & PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Minna Männikkö
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elina Hietikko
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
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24
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Pickett SB, Raible DW. Water Waves to Sound Waves: Using Zebrafish to Explore Hair Cell Biology. J Assoc Res Otolaryngol 2019; 20:1-19. [PMID: 30635804 DOI: 10.1007/s10162-018-00711-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023] Open
Abstract
Although perhaps best known for their use in developmental studies, over the last couple of decades, zebrafish have become increasingly popular model organisms for investigating auditory system function and disease. Like mammals, zebrafish possess inner ear mechanosensory hair cells required for hearing, as well as superficial hair cells of the lateral line sensory system, which mediate detection of directional water flow. Complementing mammalian studies, zebrafish have been used to gain significant insights into many facets of hair cell biology, including mechanotransduction and synaptic physiology as well as mechanisms of both hereditary and acquired hair cell dysfunction. Here, we provide an overview of this literature, highlighting some of the particular advantages of using zebrafish to investigate hearing and hearing loss.
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Affiliation(s)
- Sarah B Pickett
- Department of Biological Structure, University of Washington, Health Sciences Building H-501, 1959 NE Pacific Street, Box 357420, Seattle, WA, 98195-7420, USA
- Graduate Program in Neuroscience, University of Washington, 1959 NE Pacific Street, Box 357270, Seattle, WA, 98195-7270, USA
| | - David W Raible
- Department of Biological Structure, University of Washington, Health Sciences Building H-501, 1959 NE Pacific Street, Box 357420, Seattle, WA, 98195-7420, USA.
- Graduate Program in Neuroscience, University of Washington, 1959 NE Pacific Street, Box 357270, Seattle, WA, 98195-7270, USA.
- Virginia Merrill Bloedel Hearing Research Center, University of Washington, 1701 NE Columbia Rd, Box 357923, Seattle, WA, 98195-7923, USA.
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25
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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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26
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Sanchez-Pulido L, Ponting CP. TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules. Bioinformatics 2018; 34:721-724. [PMID: 29088312 PMCID: PMC6030884 DOI: 10.1093/bioinformatics/btx689] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 09/29/2017] [Accepted: 10/26/2017] [Indexed: 11/26/2022] Open
Abstract
Summary The molecular functions of TMEM132 genes remain poorly understood and under-investigated despite their mutations associated with non-syndromic hearing loss, panic disorder and cancer. Here we show the full domain architecture of human TMEM132 family proteins solved using in-depth sequence and structural analysis. We reveal them to be five previously unappreciated cell adhesion molecules whose domain architecture has an early holozoan origin prior to the emergence of choanoflagellates and metazoa. The extra-cellular portions of TMEM132 proteins contain five conserved domains including three tandem immunoglobulin domains, and a cohesin domain homologue, the first such domain found in animals. These findings strongly predict a cellular adhesion function for TMEM132 family, connecting the extracellular medium with the intracellular actin cytoskeleton. Contact luis.sanchez-pulido@igmm.ed.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Luis Sanchez-Pulido
- Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Chris P Ponting
- Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
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27
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Abstract
PURPOSE OF REVIEW In the age of targeted genomic enrichment and massively parallel sequencing, there is no more efficient genetic testing method for the diagnosis of hereditary hearing loss. More clinical tests are on the market, which can make choosing good tests difficult. RECENT FINDINGS More and larger comprehensive genetic studies in patients with hearing loss have been published recently. They remind us of the importance of looking for both single nucleotide variation and copy number variation in all genes implicated in nonsyndromic hearing loss. They also inform us of how a patient's history and phenotype provide essential information in the interpretation of genetic data. SUMMARY Choosing the most comprehensive genetic test improves the chances of a genetic diagnosis and thereby impacts clinical care.
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28
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Blanco-Sánchez B, Clément A, Phillips JB, Westerfield M. Zebrafish models of human eye and inner ear diseases. Methods Cell Biol 2016; 138:415-467. [PMID: 28129854 DOI: 10.1016/bs.mcb.2016.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Eye and inner ear diseases are the most common sensory impairments that greatly impact quality of life. Zebrafish have been intensively employed to understand the fundamental mechanisms underlying eye and inner ear development. The zebrafish visual and vestibulo-acoustic systems are very similar to these in humans, and although not yet mature, they are functional by 5days post-fertilization (dpf). In this chapter, we show how the zebrafish has significantly contributed to the field of biomedical research and how researchers, by establishing disease models and meticulously characterizing their phenotypes, have taken the first steps toward therapies. We review here models for (1) eye diseases, (2) ear diseases, and (3) syndromes affecting eye and/or ear. The use of new genome editing technologies and high-throughput screening systems should increase considerably the speed at which knowledge from zebrafish disease models is acquired, opening avenues for better diagnostics, treatments, and therapies.
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Affiliation(s)
| | - A Clément
- University of Oregon, Eugene, OR, United States
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29
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Pediatric otolaryngology, molecular diagnosis of hereditary hearing loss: next-generation sequencing approach. Curr Opin Otolaryngol Head Neck Surg 2016; 23:480-4. [PMID: 26488533 DOI: 10.1097/moo.0000000000000208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Sensorineural hearing loss (SNHL) is the most common sensory birth defect. The purpose of this article is to review the advances in next-generation sequencing (NGS) and molecular diagnosis of hereditary hearing loss. RECENT FINDINGS Early diagnosis and detection of SNHL is critical for the development of appropriate speech and language, as neuroplasticity peaks in the first few years of life. There has been increased accuracy of NGS genetic testing, which has helped created a paradigm shift in the diagnosis of hearing loss. The diagnostic yield of genetic testing now approaches that of radiographic imaging; however, there remains a difference in cost and time delay. With the introduction of comprehensive genetic panels, 23-129 genes can be sequenced from the same blood sample. SUMMARY Diagnostic genetic testing of SNHL in the past has been confined to a few genes through Sanger sequencing. The advent of NGS allows for development of comprehensive genetic panels, which test for up to 129 genes while improving the accuracy and efficiency of testing. This type of testing may become more common as the costs decrease and more genes are discovered.
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30
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Hosoya M, Fujioka M, Ogawa K, Okano H. Distinct Expression Patterns Of Causative Genes Responsible For Hereditary Progressive Hearing Loss In Non-Human Primate Cochlea. Sci Rep 2016; 6:22250. [PMID: 26915689 PMCID: PMC4768099 DOI: 10.1038/srep22250] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/10/2016] [Indexed: 12/18/2022] Open
Abstract
Hearing impairment is the most frequent sensory deficit in humans. Deafness genes, which harbor pathogenic mutations that have been identified in families with hereditary hearing loss, are commonly expressed in the auditory end organ or the cochlea and may contribute to normal hearing function, yet some of the mouse models carrying these mutations fail to recapitulate the hearing loss phenotype. In this study, we find that distinct expression patterns of those deafness genes in the cochlea of a non-human primate, the common marmoset (Callithrix jacchus). We examined 20 genes whose expression in the cochlea has already been reported. The deafness genes GJB3, CRYM, GRHL2, DFNA5, and ATP6B1 were expressed in marmoset cochleae in patterns different from those in mouse cochleae. Of note, all those genes are causative for progressive hearing loss in humans, but not in mice. The other tested genes, including the deafness gene COCH, in which mutation recapitulates deafness in mice, were expressed in a similar manner in both species. The result suggests that the discrepancy in the expression between rodents and primates may account for the phenotypic difference. This limitation of the rodent models can be bypassed by using non-human primate models such as the marmoset.
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Affiliation(s)
- Makoto Hosoya
- Keio University School of Medicine, Department of Otorhinolaryngology, Head and Neck Surgery, 35 Shinanomachi Shinjyuku-ku Tokyo, 160-8582, Japan
| | - Masato Fujioka
- Keio University School of Medicine, Department of Otorhinolaryngology, Head and Neck Surgery, 35 Shinanomachi Shinjyuku-ku Tokyo, 160-8582, Japan
| | - Kaoru Ogawa
- Keio University School of Medicine, Department of Otorhinolaryngology, Head and Neck Surgery, 35 Shinanomachi Shinjyuku-ku Tokyo, 160-8582, Japan
| | - Hideyuki Okano
- Keio University School of Medicine, Department of Physiology, 35 Shinanomachi Shinjyuku-ku Tokyo, 160-8582, Japan
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31
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Egilmez OK, Kalcioglu MT. Genetics of Nonsyndromic Congenital Hearing Loss. SCIENTIFICA 2016; 2016:7576064. [PMID: 26989561 PMCID: PMC4775805 DOI: 10.1155/2016/7576064] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/19/2016] [Indexed: 06/05/2023]
Abstract
Congenital hearing impairment affects nearly 1 in every 1000 live births and is the most frequent birth defect in developed societies. Hereditary types of hearing loss account for more than 50% of all congenital sensorineural hearing loss cases and are caused by genetic mutations. HL can be either nonsyndromic, which is restricted to the inner ear, or syndromic, a part of multiple anomalies affecting the body. Nonsyndromic HL can be categorised by mode of inheritance, such as autosomal dominant (called DFNA), autosomal recessive (DFNB), mitochondrial, and X-linked (DFN). To date, 125 deafness loci have been reported in the literature: 58 DFNA loci, 63 DFNB loci, and 4 X-linked loci. Mutations in genes that control the adhesion of hair cells, intracellular transport, neurotransmitter release, ionic hemeostasis, and cytoskeleton of hair cells can lead to malfunctions of the cochlea and inner ear. In recent years, with the increase in studies about genes involved in congenital hearing loss, genetic counselling and treatment options have emerged and increased in availability. This paper presents an overview of the currently known genes associated with nonsyndromic congenital hearing loss and mutations in the inner ear.
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Affiliation(s)
- Oguz Kadir Egilmez
- Department of Otorhinolaryngology, Faculty of Medicine, Istanbul Medeniyet University, 34722 Istanbul, Turkey
| | - M. Tayyar Kalcioglu
- Department of Otorhinolaryngology, Faculty of Medicine, Istanbul Medeniyet University, 34722 Istanbul, Turkey
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32
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Vona B, Nanda I, Hofrichter MAH, Shehata-Dieler W, Haaf T. Non-syndromic hearing loss gene identification: A brief history and glimpse into the future. Mol Cell Probes 2015; 29:260-70. [PMID: 25845345 DOI: 10.1016/j.mcp.2015.03.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 11/27/2022]
Abstract
From the first identified non-syndromic hearing loss gene in 1995, to those discovered in present day, the field of human genetics has witnessed an unparalleled revolution that includes the completion of the Human Genome Project in 2003 to the $1000 genome in 2014. This review highlights the classical and cutting-edge strategies for non-syndromic hearing loss gene identification that have been used throughout the twenty year history with a special emphasis on how the innovative breakthroughs in next generation sequencing technology have forever changed candidate gene approaches. The simplified approach afforded by next generation sequencing technology provides a second chance for the many linked loci in large and well characterized families that have been identified by linkage analysis but have presently failed to identify a causative gene. It also discusses some complexities that may restrict eventual candidate gene discovery and calls for novel approaches to answer some of the questions that make this simple Mendelian disorder so intriguing.
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Affiliation(s)
- Barbara Vona
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany.
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | - Wafaa Shehata-Dieler
- Comprehensive Hearing Center, Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Surgery, University Hospital, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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33
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Abstract
Next-generation sequencing (NGS) technologies have played a central role in the genetic revolution. These technologies, especially whole-exome sequencing, have become the primary tool of geneticists to identify the causative DNA variants in Mendelian disorders, including hereditary deafness. Current research estimates that 1% of all human genes have a function in hearing. To date, mutations in over 80 genes have been reported to cause nonsyndromic hearing loss (NSHL). Strikingly, more than a quarter of all known genes related to NSHL were discovered in the past 5 years via NGS technologies. In this article, we review recent developments in the usage of NGS for hereditary deafness, with an emphasis on whole-exome sequencing.
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