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Huang Y, Zhang L, Sun Y, Liu Q, Chen J, Qian X, Gao X, Zhu GJ, Wan G. A human-specific cytotoxic neopeptide generated by the deafness gene Cingulin. J Genet Genomics 2024:S1673-8527(24)00195-4. [PMID: 39098598 DOI: 10.1016/j.jgg.2024.07.017] [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: 05/23/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 08/06/2024]
Abstract
Accumulation of mutant proteins in cells can induce proteinopathies and cause functional damage to organs. Recently, the Cingulin (CGN) protein has been shown to maintain the morphology of cuticular plates of inner ear hair cells and a frameshift mutation in CGN causes autosomal dominant non-syndromic hearing loss. Here, we find that the mutant CGN proteins form insoluble aggregates which accumulate intracellularly and lead to cell death. Expression of the mutant CGN in the inner ear results in severe hair cell death and hearing loss in mice, resembling the auditory phenotype in human patients. Interestingly, a human-specific residue (V1112) in the neopeptide generated by the frameshift mutation is critical for the aggregation and cytotoxicity of the mutant human CGN. Moreover, the expression of heat shock factor 1 (HSF1) decreases the accumulation of insoluble mutant CGN aggregates and rescues cell death. In summary, these findings identify mutant-specific toxic polypeptides as a disease-causing mechanism of the deafness mutation in CGN, which can be targeted by the expression of the cell chaperone response regulator HSF1.
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Affiliation(s)
- Yuhang Huang
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Jiangsu Key Laboratory of Molecular Medicine and National Resource Center for Mutant Mice of China, Nanjing University, Nanjing, Jiangsu 210061, China
| | - Linqing Zhang
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Jiangsu Key Laboratory of Molecular Medicine and National Resource Center for Mutant Mice of China, Nanjing University, Nanjing, Jiangsu 210061, China
| | - Yuecen Sun
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Jiangsu Key Laboratory of Molecular Medicine and National Resource Center for Mutant Mice of China, Nanjing University, Nanjing, Jiangsu 210061, China
| | - Qing Liu
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Jiangsu Key Laboratory of Molecular Medicine and National Resource Center for Mutant Mice of China, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China
| | - Jie Chen
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China
| | - Xiaoyun Qian
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China
| | - Xia Gao
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China.
| | - Guang-Jie Zhu
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China.
| | - Guoqiang Wan
- MOE Key Laboratory of Model Animal for Disease Study, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, Jiangsu 210061, China; Jiangsu Key Laboratory of Molecular Medicine and National Resource Center for Mutant Mice of China, Nanjing University, Nanjing, Jiangsu 210061, China; Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, Jiangsu 210061, China.
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Gu L, Chen J, Hu C, Wang D, Huan S, Rong G, Lv R, Xu T. Integrated transcriptomics and metabolomics study of embryonic breast muscle of Jiaji ducks. BMC Genomics 2024; 25:551. [PMID: 38824564 PMCID: PMC11144331 DOI: 10.1186/s12864-024-10452-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 05/24/2024] [Indexed: 06/03/2024] Open
Abstract
Because number of matured muscle fibers in poultry does not increase after birth, the meat yield is mainly determined during embryogenesis. We previously indicated breast muscle grew rapidly from 18th day after hatching (E18) to E27, and almost stopped from E27 to E34 of Jiaji ducks, while the mechanism is unclear. This study utilized RNA-seq to explore the related genes of muscle development and their relationship with small molecule metabolites at E18, E27 and E34 of Jiaji ducks. Several thousand differentially expressed genes (DEGs) were detected among E18, E27 and E34. DEGs expression profiles included 8 trend maps, among which trend 1 was opposite to and trend 6 was consistent with breast muscle development trend of Jiaji ducks. Through joint analysis between trend 1 of DEGs and trend 1 of differential metabolites (DEMs), protein digestion and absorption pathway stood out. The decrease of COL8A2 gene expression will lead to the decrease of arginine content, which will inhibit the development of breast muscle in embryonic Jiaji duck. Similarly, joint analysis between trend 6 of DEGs and trend 6 of DEMs indicated the increase of GAMT gene expression will cause the increase of proline content, and then promote the development of breast muscle of Jiaji duck in embryonic period. These results will be helpful for further understanding the mechanism of muscle yields of Jiaji ducks.
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Affiliation(s)
- Lihong Gu
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100, P.R. China
| | - Jile Chen
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
- School of Animal Science and Technology, School of Animal Medicine, Huazhong Agricultural University, Hubei Province, Hongshan District, Wuhan, 430072, China
| | - Chengjun Hu
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
| | - Dingfa Wang
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
| | - Shuqian Huan
- College of Animal Science, Hainan University, Haikou, 570228, P.R. China
| | - Guang Rong
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
| | - Renlong Lv
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China
| | - Tieshan Xu
- Tropical Crop Genetic Resource Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, P.R. China.
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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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Zhu G, Huang Y, Zhang L, Yan K, Qiu C, He Y, Liu Q, Zhu C, Morín M, Moreno‐Pelayo MÁ, Zhu M, Cao X, Zhou H, Qian X, Xu Z, Chen J, Gao X, Wan G. Cingulin regulates hair cell cuticular plate morphology and is required for hearing in human and mouse. EMBO Mol Med 2023; 15:e17611. [PMID: 37691516 PMCID: PMC10630877 DOI: 10.15252/emmm.202317611] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023] Open
Abstract
Cingulin (CGN) is a cytoskeleton-associated protein localized at the apical junctions of epithelial cells. CGN interacts with major cytoskeletal filaments and regulates RhoA activity. However, physiological roles of CGN in development and human diseases are currently unknown. Here, we report a multi-generation family presenting with autosomal dominant non-syndromic hearing loss (ADNSHL) that co-segregates with a CGN heterozygous truncating variant, c.3330delG (p.Leu1110Leufs*17). CGN is normally expressed at the apical cell junctions of the organ of Corti, with enriched localization at hair cell cuticular plates and circumferential belts. In mice, the putative disease-causing mutation results in reduced expression and abnormal subcellular localization of the CGN protein, abolishes its actin polymerization activity, and impairs the normal morphology of hair cell cuticular plates and hair bundles. Hair cell-specific Cgn knockout leads to high-frequency hearing loss. Importantly, Cgn mutation knockin mice display noise-sensitive, progressive hearing loss and outer hair cell degeneration. In summary, we identify CGN c.3330delG as a pathogenic variant for ADNSHL and reveal essential roles of CGN in the maintenance of cochlear hair cell structures and auditory function.
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Affiliation(s)
- Guang‐Jie Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- MOE Key Laboratory of Model Animal for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, National Resource Center for Mutant Mice of ChinaNanjing UniversityNanjingChina
- Research Institute of OtolaryngologyNanjingChina
| | - Yuhang Huang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- MOE Key Laboratory of Model Animal for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, National Resource Center for Mutant Mice of ChinaNanjing UniversityNanjingChina
| | - Linqing Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- MOE Key Laboratory of Model Animal for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, National Resource Center for Mutant Mice of ChinaNanjing UniversityNanjingChina
| | - Keji Yan
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Cui Qiu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- MOE Key Laboratory of Model Animal for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, National Resource Center for Mutant Mice of ChinaNanjing UniversityNanjingChina
| | - Yihan He
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- MOE Key Laboratory of Model Animal for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, National Resource Center for Mutant Mice of ChinaNanjing UniversityNanjingChina
| | - Qing Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- MOE Key Laboratory of Model Animal for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, National Resource Center for Mutant Mice of ChinaNanjing UniversityNanjingChina
- Research Institute of OtolaryngologyNanjingChina
| | - Chengwen Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- MOE Key Laboratory of Model Animal for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, National Resource Center for Mutant Mice of ChinaNanjing UniversityNanjingChina
- Research Institute of OtolaryngologyNanjingChina
| | - Matías Morín
- Servicio de GenéticaHospital Universitario Ramón y Cajal, IRYCISMadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades RarasInstituto de Salud Carlos III (CB06/07/0048; CIBERER‐ISCIII)MadridSpain
| | - Miguel Ángel Moreno‐Pelayo
- Servicio de GenéticaHospital Universitario Ramón y Cajal, IRYCISMadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades RarasInstituto de Salud Carlos III (CB06/07/0048; CIBERER‐ISCIII)MadridSpain
| | - Min‐Sheng Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- MOE Key Laboratory of Model Animal for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, National Resource Center for Mutant Mice of ChinaNanjing UniversityNanjingChina
- Research Institute of OtolaryngologyNanjingChina
| | - Xin Cao
- Department of Medical Genetics, School of Basic Medical ScienceNanjing Medical UniversityNanjingChina
| | - Han Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- Research Institute of OtolaryngologyNanjingChina
| | - Xiaoyun Qian
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- Research Institute of OtolaryngologyNanjingChina
| | - Zhigang Xu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life SciencesShandong UniversityQingdaoChina
| | - Jie Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- Research Institute of OtolaryngologyNanjingChina
| | - Xia Gao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- Research Institute of OtolaryngologyNanjingChina
| | - Guoqiang Wan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), The Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical SchoolNanjing UniversityNanjingChina
- MOE Key Laboratory of Model Animal for Disease Study, Jiangsu Key Laboratory of Molecular Medicine, National Resource Center for Mutant Mice of ChinaNanjing UniversityNanjingChina
- Research Institute of OtolaryngologyNanjingChina
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Lachgar-Ruiz M, Morín M, Martelletti E, Ingham NJ, Preite L, Lewis MA, Serrão de Castro LS, Steel KP, Moreno-Pelayo MÁ. Insights into the pathophysiology of DFNA44 hearing loss associated with CCDC50 frameshift variants. Dis Model Mech 2023; 16:dmm049757. [PMID: 37165931 PMCID: PMC10445743 DOI: 10.1242/dmm.049757] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 05/02/2023] [Indexed: 05/12/2023] Open
Abstract
Non-syndromic sensorineural hearing loss (SNHL) is the most common sensory disorder, and it presents a high genetic heterogeneity. As part of our clinical genetic studies, we ascertained a previously unreported mutation in CCDC50 [c.828_858del, p.(Asp276Glufs*40)] segregating with hearing impairment in a Spanish family with SNHL associated with the autosomal dominant deafness locus DFNA44, which is predicted to disrupt protein function. To gain insight into the mechanism behind DFNA44 mutations, we analysed two Ccdc50 presumed loss-of-function mouse mutants, which showed normal hearing thresholds up to 6 months of age, indicating that haploinsufficiency is unlikely to be the pathogenic mechanism. We then carried out in vitro studies on a set of artificial mutants and on the p.(Asp276Glufs*40) and p.(Phe292Hisfs*37) human mutations, and determined that only the mutants containing the six-amino-acid sequence CLENGL as part of their aberrant protein tail showed an abnormal distribution consisting of perinuclear aggregates of the CCDC50 protein (also known as Ymer). Therefore, we conclude that the CLENGL sequence is necessary to form these aggregates. Taken together, the in vivo and in vitro results obtained in this study suggest that the two identified mutations in CCDC50 exert their effect through a dominant-negative or gain-of-function mechanism rather than by haploinsufficiency.
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Affiliation(s)
- María Lachgar-Ruiz
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
| | - Matías Morín
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
| | - Elisa Martelletti
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Neil J. Ingham
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Lorenzo Preite
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Morag A. Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Luciana Santos Serrão de Castro
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Miguel Ángel Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Biomedical Network Research Centre on Rare Diseases (CIBERER), km 9.100, 28034 Madrid, Spain
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Erickson T, Biggers WP, Williams K, Butland SE, Venuto A. Regionalized Protein Localization Domains in the Zebrafish Hair Cell Kinocilium. J Dev Biol 2023; 11:28. [PMID: 37367482 DOI: 10.3390/jdb11020028] [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: 01/29/2023] [Revised: 05/05/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
Sensory hair cells are the receptors for auditory, vestibular, and lateral line sensory organs in vertebrates. These cells are distinguished by "hair"-like projections from their apical surface collectively known as the hair bundle. Along with the staircase arrangement of the actin-filled stereocilia, the hair bundle features a single, non-motile, true cilium called the kinocilium. The kinocilium plays an important role in bundle development and the mechanics of sensory detection. To understand more about kinocilial development and structure, we performed a transcriptomic analysis of zebrafish hair cells to identify cilia-associated genes that have yet to be characterized in hair cells. In this study, we focused on three such genes-ankef1a, odf3l2a, and saxo2-because human or mouse orthologs are either associated with sensorineural hearing loss or are located near uncharacterized deafness loci. We made transgenic fish that express fluorescently tagged versions of their proteins, demonstrating their localization to the kinocilia of zebrafish hair cells. Furthermore, we found that Ankef1a, Odf3l2a, and Saxo2 exhibit distinct localization patterns along the length of the kinocilium and within the cell body. Lastly, we have reported a novel overexpression phenotype of Saxo2. Overall, these results suggest that the hair cell kinocilium in zebrafish is regionalized along its proximal-distal axis and set the groundwork to understand more about the roles of these kinocilial proteins in hair cells.
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Affiliation(s)
- Timothy Erickson
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | | | - Kevin Williams
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Shyanne E Butland
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Alexandra Venuto
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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7
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Gan NS, Oziębło D, Skarżyński H, Ołdak M. Monogenic Causes of Low-Frequency Non-Syndromic Hearing Loss. Audiol Neurootol 2023; 28:327-337. [PMID: 37121227 DOI: 10.1159/000529464] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/23/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND Low-frequency non-syndromic hearing loss (LFNSHL) is a rare form of hearing loss (HL). It is defined as HL at low frequencies (≤2,000 Hz) resulting in a characteristic ascending audiogram. LFNSHL is usually diagnosed postlingually and is progressive, leading to HL affecting other frequencies as well. Sometimes it occurs with tinnitus. Around half of the diagnosed prelingual HL cases have a genetic cause and it is usually inherited in an autosomal recessive mode. Postlingual HL caused by genetic changes generally has an autosomal dominant pattern of inheritance and its incidence remains unknown. SUMMARY To date, only a handful of genes have been found as causing LFNSHL: well-established WFS1 and, reported in some cases, DIAPH1, MYO7A, TNC, and CCDC50 (respectively, responsible for DFNA6/14/38, DFNA1, DFNA11, DFNA56, and DFNA44). In this review, we set out audiological phenotypes, causative genetic changes, and molecular mechanisms leading to the development of LFNSHL. KEY MESSAGES LFNSHL is most commonly caused by pathogenic variants in the WFS1 gene, but it is also important to consider changes in other HL genes, which may result in similar audiological phenotype.
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Affiliation(s)
- Nina Sara Gan
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Dominika Oziębło
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Henryk Skarżyński
- Oto-Rhino-Laryngology Surgery Clinic, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Monika Ołdak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
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8
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Thorpe RK, Walls WD, Corrigan R, Schaefer A, Wang K, Huygen P, Casavant TL, Smith RJH. AudioGene: refining the natural history of KCNQ4, GSDME, WFS1, and COCH-associated hearing loss. Hum Genet 2022; 141:877-887. [PMID: 35038006 PMCID: PMC9092196 DOI: 10.1007/s00439-021-02424-7] [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: 04/12/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022]
Abstract
Autosomal dominant non-syndromic hearing loss (ADNSHL) displays gene-specific progression of hearing loss, which is amenable to sequential audioprofiling. We sought to refine the natural history of ADNSHL by examining audiometric data in 5-year increments. 2175 audiograms were included from four genetic causes of ADNSHL-KCNQ4 (DFNA2), GSDME (DFNA5), WFS1 (DFNA6/14/38), and COCH (DFNA9). Annual threshold deterioration (ATD) was calculated for each gene: for the speech-frequency pure tone average, the ATD, respectively, was 0.72 dB/year, 0.94 dB/year, 0.53 dB/year, and 1.41 dB/year, with the largest drops occurring from ages 45-50 (0.89 dB/year; KCNQ4), 5-10 (1.42 dB/year; GSDME), 40-45 (0.83 dB/year; WFS1), and 50-55 (2.09 dB/year; COCH). 5-year interval analysis of audiograms reveals the gene specific natural history of KCNQ4, GSDME, WFS1 and COCH-related progressive hearing loss. Identifying ages at which hearing loss is most rapid informs clinical care and patient expectations. Natural history data are also essential to define outcomes of clinical trials that test novel therapies designed to correct or ameliorate these genetic forms of hearing loss.
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Affiliation(s)
- Ryan K Thorpe
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - W Daniel Walls
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - Rae Corrigan
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, USA
| | - Amanda Schaefer
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA
| | - Kai Wang
- Department of Biostatistics, University of Iowa, Iowa City, Iowa, USA
| | - Patrick Huygen
- Department of Otorhinolaryngology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Thomas L Casavant
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, Iowa, USA
- Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
| | - Richard J H Smith
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, Iowa, USA.
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA.
- Department of Electrical and Computer Engineering, University of Iowa, Iowa City, Iowa, USA.
- Molecular Otolaryngology and Renal Research Laboratories and Iowa Institute of Human Genetics, Iowa City, Iowa, USA.
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9
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Warnecke A, Harre J, Shew M, Mellott AJ, Majewski I, Durisin M, Staecker H. Successful Treatment of Noise-Induced Hearing Loss by Mesenchymal Stromal Cells: An RNAseq Analysis of Protective/Repair Pathways. Front Cell Neurosci 2021; 15:656930. [PMID: 34887728 PMCID: PMC8650824 DOI: 10.3389/fncel.2021.656930] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) are an adult derived stem cell-like population that has been shown to mediate repair in a wide range of degenerative disorders. The protective effects of MSCs are mainly mediated by the release of growth factors and cytokines thereby modulating the diseased environment and the immune system. Within the inner ear, MSCs have been shown protective against tissue damage induced by sound and a variety of ototoxins. To better understand the mechanism of action of MSCs in the inner ear, mice were exposed to narrow band noise. After exposure, MSCs derived from human umbilical cord Wharton's jelly were injected into the perilymph. Controls consisted of mice exposed to sound trauma only. Forty-eight hours post-cell delivery, total RNA was extracted from the cochlea and RNAseq performed to evaluate the gene expression induced by the cell therapy. Changes in gene expression were grouped together based on gene ontology classification. A separate cohort of animals was treated in a similar fashion and allowed to survive for 2 weeks post-cell therapy and hearing outcomes determined. Treatment with MSCs after severe sound trauma induced a moderate hearing protective effect. MSC treatment resulted in an up-regulation of genes related to immune modulation, hypoxia response, mitochondrial function and regulation of apoptosis. There was a down-regulation of genes related to synaptic remodeling, calcium homeostasis and the extracellular matrix. Application of MSCs may provide a novel approach to treating sound trauma induced hearing loss and may aid in the identification of novel strategies to protect hearing.
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Affiliation(s)
- Athanasia Warnecke
- Clinic for Otolaryngology–Head & Neck Surgery, Hanover Medical School, Hanover, Germany
- Cluster of Excellence “Hearing4all” of the German Research Foundation (EXC 2177/1), Oldenburg, Germany
| | - Jennifer Harre
- Clinic for Otolaryngology–Head & Neck Surgery, Hanover Medical School, Hanover, Germany
- Cluster of Excellence “Hearing4all” of the German Research Foundation (EXC 2177/1), Oldenburg, Germany
| | - Matthew Shew
- Department of Otolaryngology–Head & Neck Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | | | - Igor Majewski
- Clinic for Otolaryngology–Head & Neck Surgery, Hanover Medical School, Hanover, Germany
| | - Martin Durisin
- Clinic for Otolaryngology–Head & Neck Surgery, Hanover Medical School, Hanover, Germany
| | - Hinrich Staecker
- Department of Otolaryngology–Head & Neck Surgery, University of Kansas School of Medicine, Kansas City, KS, United States
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10
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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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11
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Wang Q, Shen Y, Pan Y, Chen K, Ding R, Zou T, Zhang A, Guo D, Ji P, Fan C, Mei L, Hu H, Ye B, Xiang M. Tlr2/4 Double Knockout Attenuates the Degeneration of Primary Auditory Neurons: Potential Mechanisms From Transcriptomic Perspectives. Front Cell Dev Biol 2021; 9:750271. [PMID: 34760891 PMCID: PMC8573328 DOI: 10.3389/fcell.2021.750271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/28/2021] [Indexed: 11/30/2022] Open
Abstract
The transcriptomic landscape of mice with primary auditory neurons degeneration (PAND) indicates key pathways in its pathogenesis, including complement cascades, immune responses, tumor necrosis factor (TNF) signaling pathway, and cytokine-cytokine receptor interaction. Toll-like receptors (TLRs) are important immune and inflammatory molecules that have been shown to disrupt the disease network of PAND. In a PAND model involving administration of kanamycin combined with furosemide to destroy cochlear hair cells, Tlr 2/4 double knockout (DKO) mice had auditory preservation advantages, which were mainly manifested at 4–16 kHz. DKO mice and wild type (WT) mice had completely damaged cochlear hair cells on the 30th day, but the density of spiral ganglion neurons (SGN) in the Rosenthal canal was significantly higher in the DKO group than in the WT group. The results of immunohistochemistry for p38 and p65 showed that the attenuation of SGN degeneration in DKO mice may not be mediated by canonical Tlr signaling pathways. The SGN transcriptome of DKO and WT mice indicated that there was an inverted gene set enrichment relationship between their different transcriptomes and the SGN degeneration transcriptome, which is consistent with the morphology results. Core module analysis suggested that DKO mice may modulate SGN degeneration by activating two clusters, and the involved molecules include EGF, STAT3, CALB2, LOX, SNAP25, CAV2, SDC4, MYL1, NCS1, PVALB, TPM4, and TMOD4.
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Affiliation(s)
- Quan Wang
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yilin Shen
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Pan
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kaili Chen
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Ding
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianyuan Zou
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Andi Zhang
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongye Guo
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peilin Ji
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cui Fan
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ling Mei
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haixia Hu
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin Ye
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingliang Xiang
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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12
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A Missense POU4F3 Variant Associated with Autosomal Dominant Midfrequency Hearing Loss Alters Subnuclear Localization and Transcriptional Capabilities. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5574136. [PMID: 34250087 PMCID: PMC8238589 DOI: 10.1155/2021/5574136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 06/09/2021] [Indexed: 11/17/2022]
Abstract
Background The pathogenic variant, POU class 4 transcription factor 3 (POU4F3), is reported to cause autosomal dominant nonsyndromic hearing loss (ADNSHL). Previously, we have examined a four-generation midfrequency sensorineural hearing loss (MFSNHL) family (no. 6126) and established POU4F3 c.602T>C (p.Leu201Pro) as a potential disease-causing variant. Objectives We explored the structural and functional alterations that the c.602T>C (p.Leu201Pro) variant enforces on the POU4F3 protein. Methods We utilized wild-type (WT) and mutant (MUT) POU4F3 c.602T>C plasmid incorporation into HeLa cells to assess functional changes, by immunofluorescence and luciferase assays. To predict protein structural alterations in the MUT versus WT POU4F3, we also generated 3D structures to compare both types of POU4F3 proteins. Results The WT POU4F3 is ubiquitously present in the nucleus, whereas the MUT form of POU4F3 exhibits a more restricted nuclear presence. This finding is different from other publications, which report a cytoplasmic localization of the MUT POU4F3. We also demonstrated that, as opposed to WT POU4F3, the MUT POU4F3 had 40% reduced luciferase activity. Conclusions The reduced nuclear presence, combined with reduced transcriptional activity, suggests that the POU4F3 c.602T>C variant alters cellular activity and may contribute to the pathogenicity of POU4F3-related hearing loss. It, also, provides more evidence of the pathophysiological characteristics of MFSNHL.
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13
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Fu X, An Y, Wang H, Li P, Lin J, Yuan J, Yue R, Jin Y, Gao J, Chai R. Deficiency of Klc2 Induces Low-Frequency Sensorineural Hearing Loss in C57BL/6 J Mice and Human. Mol Neurobiol 2021; 58:4376-4391. [PMID: 34014435 DOI: 10.1007/s12035-021-02422-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/05/2021] [Indexed: 12/19/2022]
Abstract
The transport system in cochlear hair cells (HCs) is important for their function, and the kinesin family of proteins transports numerous cellular cargos via the microtubule network in the cytoplasm. Here, we found that Klc2 (kinesin light chain 2), the light chain of kinesin-1 that mediates cargo binding and regulates kinesin-1 motility, is essential for cochlear function. We generated mice lacking Klc2, and they suffered from low-frequency hearing loss as early as 1 month of age. We demonstrated that deficiency of Klc2 resulted in abnormal transport of mitochondria and the down-regulation of the GABAA receptor family. In addition, whole-genome sequencing (WGS) of patient showed that KLC2 was related to low-frequency hearing in human. Hence, to explore therapeutic approaches, we developed adeno-associated virus containing the Klc2 wide-type cDNA sequence, and Klc2-null mice delivered virus showed apparent recovery, including decreased ABR threshold and reduced out hair cell (OHC) loss. In summary, we show that the kinesin transport system plays an indispensable and special role in cochlear HC function in mice and human and that mitochondrial localization is essential for HC survival.
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Affiliation(s)
- Xiaolong Fu
- State Key Laboratory of Bioelectronics, School of Life Sciences and Technology, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, China.,College of Laboratory Animal & Shandong Laboratory Animal Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yachun An
- School of Life Science, Shandong University, Qingdao, China
| | - Hongyang Wang
- College of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Peipei Li
- School of Life Science, Shandong University, Qingdao, China
| | - Jing Lin
- Waksman Institute, the State University of New Jersey, RutgersNew Brunswick, NJ, USA
| | - Jia Yuan
- State Key Laboratory of Bioelectronics, School of Life Sciences and Technology, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, China
| | - Rongyu Yue
- Department of Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated To Shandong University, Jinan, China
| | - Yecheng Jin
- School of Life Science, Shandong University, Qingdao, China
| | - Jiangang Gao
- College of Laboratory Animal & Shandong Laboratory Animal Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
| | - Renjie Chai
- State Key Laboratory of Bioelectronics, School of Life Sciences and Technology, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, China. .,College of Laboratory Animal & Shandong Laboratory Animal Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China. .,Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Science, Beijing, China.
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14
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Tumane RG, Thakkar L, Pingle SK, Jain RK, Jawade AA, Raje DV. Expression of serum proteins in noise induced hearing loss workers of mining based industry. J Proteomics 2021; 240:104185. [PMID: 33737237 DOI: 10.1016/j.jprot.2021.104185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/28/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022]
Abstract
Noise Induced Hearing Loss (NIHL) is caused by excessive noise exposure due to occupational activities thus affects communication and quality of life. Prolonged occupational and environmental exposure to loud noise damages key molecules present in the micro-machinery of the ear which are required for the mechano-electrical transduction of sound waves in cochlea. Specific proteins are known to be associated with hearing loss and related structural and functional disabilities in the human inner, outer hair cells and cochlea. Rationale of this study was to identify the cochlear proteins associated with the pathophysiology of NIHL using proteomic approaches in mining based industrial workers. Total (n = 210) samples were collected from mining based industrial workers of central India. Subjects were categorized based on audiometric analysis. Proteome changes of the host serum were investigated using one and two-dimensional electrophoresis in combination with LC-MS/MS and MALDI-TOF-MS. Up-regulated 46 cochlear proteins among confirmed NIHL cases were identified by MASCOT. Shrinkage discriminant analysis provided top 25 discriminating feature proteins namely myosin, transthyretin, SERPIN, CCDC50, enkurin, transferin etc. The identified potential proteins may be used as biomarkers for early detection and to understand the pathogenic mechanism of NIHL. Evaluation of these biomarkers in follow-up cases may further aid in improving NIHL diagnosis. SIGNIFICANCE: Human proteome study in Noise Induced Hearing Loss (NIHL) cases has not been published till date. This study represents most comprehensive proteomic analysis in NIHL cases taken from Indian mine workers. The identified key twenty-five discriminating feature proteins which are upregulated when an individual develops (or is in stage of development of) NIHL, provides insights into the potential roles of these varied proteins in disease progression. The proteins thus identified by proteomic approach may be used as early diagnostic biomarker to predict the occurrence of disease at very early stage.
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Affiliation(s)
- Rajani G Tumane
- Department of Biochemistry, National Institute of Miners' Health, JNARDDC Campus, Wadi, Nagpur 440023, Maharashtra, India
| | - Lucky Thakkar
- Department of Biochemistry, National Institute of Miners' Health, JNARDDC Campus, Wadi, Nagpur 440023, Maharashtra, India
| | - Shubhangi K Pingle
- Department of Biochemistry, National Institute of Miners' Health, JNARDDC Campus, Wadi, Nagpur 440023, Maharashtra, India.
| | - Ruchika K Jain
- Department of Biochemistry, National Institute of Miners' Health, JNARDDC Campus, Wadi, Nagpur 440023, Maharashtra, India
| | - Aruna A Jawade
- Department of Biochemistry, National Institute of Miners' Health, JNARDDC Campus, Wadi, Nagpur 440023, Maharashtra, India
| | - Dhananjay V Raje
- MDS Analytics, First Floor Sakar Enclave, Plot No. 127, Shankar Nagar, Nagpur, Maharashtra, India
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15
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Lee JH, Hwang YJ, Li H, Kim H, Suh MW, Han D, Oh SH. In-depth proteome of perilymph in guinea pig model. Proteomics 2021; 21:e2000138. [PMID: 33459488 DOI: 10.1002/pmic.202000138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
The vast majority of sensorineural hearing loss is caused by impairment of the inner ear cells. Proteomic analysis of perilymph may therefore improve our understanding of inner ear diseases and hearing loss. However, the investigation of the human perilymph proteome was limited due to technical difficulties in perilymph sampling. The guinea pig (Cavia porcellus) is frequently used as an experimental model in preclinical hearing research. In this study, we analyzed samples of perilymph collected from 12 guinea pigs to overcome limited experimental information regarding its proteome. We identified a total of 1413 proteins, establishing a greatly expanded proteome of the previously inferred guinea pig perilymph. This provides a comprehensive proteomic resource for the research community, which will facilitate future molecular-phenotypic studies using the guinea pig as an experimental model of relevance to human inner ear biology.
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Affiliation(s)
- Jung Hun Lee
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Yu-Jung Hwang
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Hui Li
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Hyeyoon Kim
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Myung-Whan Suh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Seung-Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea
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16
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Coiled-coil domain containing 50-V2 protein positively regulates neurite outgrowth. Sci Rep 2020; 10:21295. [PMID: 33277610 PMCID: PMC7718278 DOI: 10.1038/s41598-020-78304-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 11/23/2020] [Indexed: 11/10/2022] Open
Abstract
The coiled-coil domain containing 50 (CCDC50) protein is a phosphotyrosine-dependent signalling protein stimulated by epidermal growth factor. It is highly expressed in neuronal cells in the central nervous system; however, the roles of CCDC50 in neuronal development are largely unknown. In this study, we showed that the depletion of CCDC50-V2 impeded the neuronal development process, including arbor formation, spine density development, and axonal outgrowth, in primary neurons. Mechanistic studies revealed that CCDC50-V2 positively regulated the nerve growth factor receptor, while it downregulated the epidermal growth factor receptor pathway. Importantly, JNK/c-Jun activation was found to be induced by the CCDC50-V2 overexpression, in which the interaction between CCDC50-V2 and JNK2 was also observed. Overall, the present study demonstrates a novel mechanism of CCDC50 function in neuronal development and provides new insight into the link between CCDC50 function and the aetiology of neurological disorders.
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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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Zhang L, Wu X, Lin X. Gene therapy for genetic mutations affecting non-sensory cells in the cochlea. Hear Res 2020; 394:107858. [PMID: 31791650 DOI: 10.1016/j.heares.2019.107858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/13/2019] [Accepted: 11/22/2019] [Indexed: 01/15/2023]
Abstract
Congenital hearing loss (HL) affects about 1 in every 500 infants. Among those affected more than half are caused by genetic mutations. According to the cellular sites affected by mutations in the cochlea, deafness genes could be classified into three major groups: those affecting the function of hair cells and synapses, cochlear supporting cells, and cells in the stria vascularis (SV) as well as in the lateral wall. The second and third groups account for more than half of all sensorineural hearing loss (SNHL) cases caused by genetic mutations. Current major treatment options for SNHL patients are hearing aids and cochlear implants (CIs). Hearing aids can only help patients with moderate to severe HL. Resolution of CIs is still improving and these devices are quite expensive especially when lifetime rehabilitation and maintenance costs are included. Tremendous efforts have been made to find novel treatments that are expected to restore hearing with higher-resolution and more natural quality, and to have a significantly lower cost over the lifetime of uses. Gene therapy studies have made impressive progresses in preclinical trials. This review focuses on deafness genes that affect supporting cells and cells in the SV of the cochlea. We will discuss recent progresses and remaining challenges for gene therapies targeting mutations in deafness genes belonging to this category.
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Affiliation(s)
- Li Zhang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China; Department of Otolaryngology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322-3030, USA
| | - Xuewen Wu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital of Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China; Department of Otolaryngology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322-3030, USA
| | - Xi Lin
- Department of Otolaryngology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322-3030, USA.
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19
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Sun G, Zhou H, Chen K, Zeng J, Zhang Y, Yan L, Yao W, Hu J, Wang T, Xing J, Xiao K, Wu L, Ye Z, Xu H. HnRNP A1 - mediated alternative splicing of CCDC50 contributes to cancer progression of clear cell renal cell carcinoma via ZNF395. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:116. [PMID: 32560659 PMCID: PMC7304168 DOI: 10.1186/s13046-020-01606-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/28/2020] [Indexed: 01/26/2023]
Abstract
BACKGROUND Aberrant alternative splicing events play critical roles in carcinogenesis and progression of many cancers, while sparse studies regarding to alternative splicing are available for clear cell renal cell carcinoma (ccRCC). We identified that alternative splicing of coiled-coil domain containing 50 (CCDC50) was dysregulated in ccRCC, whereas the clinical significance of this splicing event and its splicing regulation mechanisms were still elusive. METHODS Bioinformatic algorithm was utilized to identify significant exon skipping events in ccRCC via exon sequencing data from The Cancer Genome Atlas. Semi-quantitative real-time polymerase chain reaction and western blot were used to validate the aberrant expression of different transcripts in renal cancer tissues, cell lines and corresponding noncancerous controls. Short hairpin RNA targeting CCDC50 and overexpressing plasmids for each transcript were introduced into ccRCC cell lines, followed by a series of in vitro and in vivo functional experiments. Moreover, a panel of splicing factors were identified and their roles on splicing regulation of CCDC50 precursor mRNA (pre-mRNA) were studied. Furthermore, RNAseq data were analyzed to elucidate downstream molecules of CCDC50. Two-way analysis of variance and unpaired Student t test were used in statistical analysis. RESULTS Pre-mRNA of CCDC50 generated two transcripts, full-length transcript (CCDC50-FL) and truncated transcript (CCDC50-S) with exon 6 skipped. CCDC50-S was overexpressed in ccRCC tissues and cell lines compared to noncancerous counterparts, but CCDC50-FL was only detected in noncancerous tissues and normal renal epithelial cells. Higher percent spliced-in index was associated with better survival in ccRCC patients. In vitro and in vivo functional experiments indicated that CCDC50-S transcript promoted the proliferation, migration, invasion and tumorigenesis of ccRCC, while CCDC50-FL exerted opposite tumor suppressive functions. Besides, we identified that heterogeneous nuclear ribonucleoprotein A1 (HnRNP A1) could promote the skipping of exon 6, which resulted in higher portion of CCDC50-S and oncogenic transformation. Moreover, zinc finger protein 395 (ZNF395) was identified as a downstream protein of CCDC50-S, and the interaction initiated oncogenic pathways which were involved in ccRCC progression. CONCLUSIONS Aberrant alternative splicing of CCDC50 is regulated by HnRNP A1 in ccRCC. This splicing event contributes to cancer progression through the downstream pathway involving ZNF395.
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Affiliation(s)
- Guoliang Sun
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Hui Zhou
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Ke Chen
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Jin Zeng
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Yangjun Zhang
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Libin Yan
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Weimin Yao
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Junhui Hu
- Hubei Institute of Urology, Wuhan, 430030 P.R. China ,grid.19006.3e0000 0000 9632 6718Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095 USA
| | - Tao Wang
- grid.412625.6Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen, 361000 P.R. China
| | - Jinchun Xing
- grid.412625.6Department of Urology, The First Affiliated Hospital of Xiamen University, Xiamen, 361000 P.R. China
| | - Kefeng Xiao
- Department of Urology, The People’s Hospital of Shenzhen City, Shenzhen, 518000 P.R. China
| | - Lily Wu
- grid.19006.3e0000 0000 9632 6718Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095 USA
| | - Zhangqun Ye
- grid.33199.310000 0004 0368 7223Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 P.R. China ,Hubei Institute of Urology, Wuhan, 430030 P.R. China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P.R. China. .,Hubei Institute of Urology, Wuhan, 430030, P.R. China.
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20
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Lee J, Ha S, Lee ST, Park SG, Shin S, Choi JR, Cheon KA. Next-Generation Sequencing in Korean Children With Autism Spectrum Disorder and Comorbid Epilepsy. Front Pharmacol 2020; 11:585. [PMID: 32477112 PMCID: PMC7240034 DOI: 10.3389/fphar.2020.00585] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/16/2020] [Indexed: 12/23/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social communication and restricted and repetitive behaviors and interests. Identifying the genetic background may be one of the key features for the future diagnosis and treatment of ASD. With the tremendous development in genetic diagnosis techniques, next-generation sequencing (NGS) can be used to analyze multiple genes simultaneously with a single test in laboratory and clinical settings and is well suited for investigating autism genetics. According to previous studies, there are two types of genetic variants in ASD, rare variants and common variants, and both are important in explaining pathogenesis. In this study, NGS data from 137 participants with ASD were reviewed retrospectively with consideration for comorbid epilepsy. Diagnostic yield was 17.51% (24/137), and pathogenic/likely pathogenic variants were seen more frequently in female participants. Fourteen participants were diagnosed with comorbid epilepsy, six of them had pathogenic/likely pathogenic variants (43%). Genes with variants of unknown significance (VOUS) which have one or more evidence of pathogenicity following the American College of Medical Genetics (ACMG) criteria were also reviewed in both ASD and ASD with comorbid epilepsy groups. We found that most frequently found VOUS genes have previously been reported as genes related to ASD or other developmental disorders. These results suggest that when interpreting the NGS results in the clinical setting, careful observation of VOUS with some pathological evidence might contribute to the discovery of genetic pathogenesis of neurodevelopmental disorders such as ASD and epilepsy.
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Affiliation(s)
- Junghan Lee
- Division of Child and Adolescent Psychiatry, Department of Psychiatry, Severance Hospital, Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Sungji Ha
- Department of Psychiatry, Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung-Gyun Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Keun-Ah Cheon
- Division of Child and Adolescent Psychiatry, Department of Psychiatry, Severance Hospital, Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, South Korea
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21
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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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22
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Lin HC, Ren Y, Lysaght AC, Kao SY, Stankovic KM. Proteome of normal human perilymph and perilymph from people with disabling vertigo. PLoS One 2019; 14:e0218292. [PMID: 31185063 PMCID: PMC6559673 DOI: 10.1371/journal.pone.0218292] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022] Open
Abstract
The vast majority of hearing loss, the most common sensory impairment, and vertigo, which commonly causes falls, both reflect underlying dysfunction of inner ear cells. Perilymph sampling can thus provide molecular cues to hearing and balance disorders. While such "liquid biopsy" of the inner ear is not yet in routine clinical practice, previous studies have uncovered alterations in perilymph in patients with certain types of hearing loss. However, the proteome of perilymph from patients with intact hearing has been unknown. Furthermore, no complete characterization of perilymph from patients with vestibular dysfunction has been reported. Here, using liquid-chromatography with tandem mass spectrometry, we analyzed samples of normal perilymph collected from three patients with skull base meningiomas and intact hearing. We identified 228 proteins that were common across the samples, establishing a greatly expanded proteome of the previously inferred normal human perilymph. Further comparison to perilymph obtained from three patients with vestibular dysfunction with drop attacks due to Meniere's disease showed 38 proteins with significantly differential abundance. The abundance of four protein candidates with previously unknown roles in inner ear biology was validated in murine cochleae by immunohistochemistry and in situ hybridization: AACT, HGFAC, EFEMP1, and TGFBI. Together, these results motivate future work in characterizing the normal human perilymph and identifying biomarkers of inner ear disease.
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Affiliation(s)
- Hsiao-Chun Lin
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, United States of America
- Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, Massachusetts, United States of America
| | - Yin Ren
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, United States of America
- Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, Massachusetts, United States of America
| | - Andrew C. Lysaght
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, United States of America
- Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, Massachusetts, United States of America
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, United States of America
| | - Shyan-Yuan Kao
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, United States of America
- Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, Massachusetts, United States of America
| | - Konstantina M. Stankovic
- Department of Otolaryngology, Harvard Medical School, Boston, Massachusetts, United States of America
- Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, Massachusetts, United States of America
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, United States of America
- Harvard Program in Therapeutic Science, Harvard University, Boston, United States of America
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23
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Wang H, Zhang CZ, Lu SX, Zhang MF, Liu LL, Luo RZ, Yang X, Wang CH, Chen SL, He YF, Xie D, Xu RH, Yun JP. A Coiled-Coil Domain Containing 50 Splice Variant Is Modulated by Serine/Arginine-Rich Splicing Factor 3 and Promotes Hepatocellular Carcinoma in Mice by the Ras Signaling Pathway. Hepatology 2019; 69:179-195. [PMID: 30028541 DOI: 10.1002/hep.30147] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 06/14/2018] [Indexed: 12/22/2022]
Abstract
Deregulation of alternative splicing contributes to the malignant progression of cancer. Little is known about the significant alternative splicing events in hepatocellular carcinoma (HCC). High-throughput sequencing revealed that coiled-coil domain containing 50 (CCDC50) pre-mRNA is aberrantly spliced in 50% of our HCC cases. A BaseScope assay was performed to examine the expression of CCDC50S (a truncated oncogenic splice variant) in HCC tissues. Compared with benign liver tumors and several other types of solid tumors, CCDC50S mRNA was up-regulated in HCC, with a diagnostic potential (sensitivity, 0.711; specificity, 0.793). High expression of CCDC50S mRNA in HCC was significantly correlated with poor tumor differentiation, advanced tumor node metastasis (TNM) stage, and unfavorable prognosis. Overexpression of CCDC50S exerted tumorigenic activities that promoted HCC growth and metastasis by activation of Ras/forkhead box protein O4 (Foxo4) signaling. Either suppression of mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) phosphorylation or overexpression of Foxo4 markedly attenuated CCDC50S-mediated phenotypes. Furthermore, serine- and arginine-rich splicing factor 3 (SRSF3) directly bound to CCDC50S mRNA to maintain its stability in the cytoplasm. The cytosolic retention of SRSF3 was mediated by the interaction of hepatitis B virus-encoded X protein (HBx) and 14-3-3β. Ectopic HBx expression induced expression of cytosolic SRSF3 and CCDC50S. Conclusion: Our study provided compelling evidence that up-regulation of CCDC50S was modulated by HBx/SRSF3/14-3-3β complex and enhanced oncogenic progression of HCC through the Ras/Foxo4 signaling pathway. These data suggest that CCDC50S may serve as a diagnostic and prognostic biomarker and probably a promising therapeutic target in HCC.
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Affiliation(s)
- Hong Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chris Zhiyi Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shi-Xun Lu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Mei-Fang Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Li-Li Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rong-Zhen Luo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xia Yang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chun-Hua Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shi-Lu Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yang-Fan He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Rui-Hua Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jing-Ping Yun
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
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24
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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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25
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DiStefano MT, Hemphill SE, Cushman BJ, Bowser MJ, Hynes E, Grant AR, Siegert RK, Oza AM, Gonzalez MA, Amr SS, Rehm HL, Abou Tayoun AN. Curating Clinically Relevant Transcripts for the Interpretation of Sequence Variants. J Mol Diagn 2018; 20:789-801. [PMID: 30096381 PMCID: PMC6204605 DOI: 10.1016/j.jmoldx.2018.06.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/20/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022] Open
Abstract
Variant interpretation depends on accurate annotations using biologically relevant transcripts. We have developed a systematic strategy for designating primary transcripts and have applied it to 109 hearing loss-associated genes that were divided into three categories. Category 1 genes (n = 38) had a single transcript; category 2 genes (n = 33) had multiple transcripts, but a single transcript was sufficient to represent all exons; and category 3 genes (n = 38) had multiple transcripts with unique exons. Transcripts were curated with respect to gene expression reported in the literature and the Genotype-Tissue Expression Project. In addition, high-frequency loss-of-function variants in the Genome Aggregation Database and disease-causing variants in ClinVar and the Human Gene Mutation Database across the 109 genes were queried. These data were used to classify exons as clinically significant, insignificant, or of uncertain significance. Interestingly, 6% of all exons, containing 124 reportedly disease-causing variants, were of uncertain significance. Finally, we used exon-level next-generation sequencing quality metrics generated at two clinical laboratories and identified a total of 43 technically challenging exons in 20 different genes that had inadequate coverage and/or homology issues that might lead to false-variant calls. We have demonstrated that transcript analysis plays a critical role in accurate clinical variant interpretation.
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Affiliation(s)
- Marina T DiStefano
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Sarah E Hemphill
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Brandon J Cushman
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Mark J Bowser
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Elizabeth Hynes
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Andrew R Grant
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Rebecca K Siegert
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Andrea M Oza
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Michael A Gonzalez
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts; Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Medical and Population Genetics, The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Ahmad N Abou Tayoun
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Genetics Department, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates.
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Guillen‐Ahlers H, Erbe CB, Chevalier FD, Montoya MJ, Zimmerman KD, Langefeld CD, Olivier M, Runge CL. TMTC2 variant associated with sensorineural hearing loss and auditory neuropathy spectrum disorder in a family dyad. Mol Genet Genomic Med 2018; 6:653-659. [PMID: 29671961 PMCID: PMC6081214 DOI: 10.1002/mgg3.397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 02/02/2018] [Accepted: 03/09/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Sensorineural hearing loss (SNHL) is a common form of hearing loss that can be inherited or triggered by environmental insults; auditory neuropathy spectrum disorder (ANSD) is a SNHL subtype with unique diagnostic criteria. The genetic factors associated with these impairments are vast and diverse, but causal genetic factors are rarely characterized. METHODS A family dyad, both cochlear implant recipients, presented with a hearing history of bilateral, progressive SNHL, and ANSD. Whole-exome sequencing was performed to identify coding sequence variants shared by both family members, and screened against genes relevant to hearing loss and variants known to be associated with SNHL and ANSD. RESULTS Both family members are successful cochlear implant users, demonstrating effective auditory nerve stimulation with their devices. Genetic analyses revealed a mutation (rs35725509) in the TMTC2 gene, which has been reported previously as a likely genetic cause of SNHL in another family of Northern European descent. CONCLUSION This study represents the first confirmation of the rs35725509 variant in an independent family as a likely cause for the complex hearing loss phenotype (SNHL and ANSD) observed in this family dyad.
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Affiliation(s)
- Hector Guillen‐Ahlers
- Department of GeneticsTexas Biomedical Research InstituteSan AntonioTXUSA
- Present address:
Department of Internal MedicineSection of Molecular MedicineWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Christy B. Erbe
- Department of Otolaryngology and Communication SciencesMedical College of WisconsinMilwaukeeWIUSA
| | | | - Maria J. Montoya
- Department of GeneticsTexas Biomedical Research InstituteSan AntonioTXUSA
| | - Kip D. Zimmerman
- Department of Biostatistical SciencesWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Carl D. Langefeld
- Department of Biostatistical SciencesWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Michael Olivier
- Department of GeneticsTexas Biomedical Research InstituteSan AntonioTXUSA
- Present address:
Department of Internal MedicineSection of Molecular MedicineWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Christina L. Runge
- Department of Otolaryngology and Communication SciencesMedical College of WisconsinMilwaukeeWIUSA
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A Missense Mutation in POU4F3 Causes Midfrequency Hearing Loss in a Chinese ADNSHL Family. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5370802. [PMID: 29850532 PMCID: PMC5904794 DOI: 10.1155/2018/5370802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 03/05/2018] [Indexed: 11/18/2022]
Abstract
Hereditary nonsyndromic hearing loss is extremely heterogeneous. Mutations in the POU class 4 transcription factor 3 (POU4F3) are known to cause autosomal dominant nonsyndromic hearing loss linked to the loci of DFNA15. In this study, we describe a pathogenic missense mutation in POU4F3 in a four-generation Chinese family (6126) with midfrequency, progressive, and postlingual autosomal dominant nonsyndromic hearing loss (ADNSHL). By combining targeted capture of 129 known deafness genes, next-generation sequencing, and bioinformatic analysis, we identified POU4F3 c.602T>C (p.Leu201Pro) as the disease-causing variant. This variant cosegregated with hearing loss in other family members but was not detected in 580 normal controls or the ExAC database and could be classified as a “pathogenic variant” according to the American College of Medical Genetics and Genomics guidelines. We conclude that POU4F3 c.602T>C (p.Leu201Pro) is related to midfrequency hearing loss in this family. Routine examination of POU4F3 is necessary for the genetic diagnosis of midfrequency hearing loss.
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Yamamoto N, Mutai H, Namba K, Morita N, Masuda S, Nishi Y, Nakano A, Masuda S, Fujioka M, Kaga K, Ogawa K, Matsunaga T. Prevalence of TECTA mutation in patients with mid-frequency sensorineural hearing loss. Orphanet J Rare Dis 2017; 12:157. [PMID: 28946916 PMCID: PMC5613382 DOI: 10.1186/s13023-017-0708-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/07/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND To date, 102 genes have been reported as responsible for non-syndromic hearing loss, some of which are associated with specific audiogram features. Four genes have been reported as causative for mid-frequency sensorineural hearing loss (MFSNHL), among which TECTA is the most frequently reported; however, the prevalence of TECTA mutations is unknown. To elucidate the prevalence of TECTA mutation in MFSNHL and clarify genotype-phenotype correlations, we analyzed the genetic and clinical features of patients with MFSNHL. METHODS Subjects with bilateral non-syndromic hearing loss were prescreened for GJB2 and m.1555A > G and m.3243A > G mitochondrial DNA mutations, and patients with inner ear malformations were excluded. We selected MFSNHL patients whose audiograms met the U-shaped criterion proposed by the GENDEAF study group, along with those with shallow U-shaped audiograms, for TECTA analysis. All TECTA exons were analyzed by Sanger sequencing. Novel missense variants were classified as possibly pathogenic, non-pathogenic, and variants of uncertain significance, based on genetic data. To evaluate novel possibly pathogenic variants, we predicted changes in protein structure by molecular modeling. RESULTS Pathogenic and possibly pathogenic variants of TECTA were found in 4 (6.0%) of 67 patients with MFSNHL. In patients with U-shaped audiograms, none (0%) of 21 had pathogenic or possibly pathogenic variants. In patients with shallow U-shaped audiograms, four (8.7%) of 46 had pathogenic or possibly pathogenic variants. Two novel possibly pathogenic variants were identified and two previously reported mutations were considered as variant of unknown significance. The clinical features of patients with pathogenic and possibly pathogenic variants were consistent with those in previous studies. Pathogenic or possibly pathogenic variants were identified in 3 of 23 families (13.0%) which have the family histories compatible with autosomal dominant and 1 of 44 families (2.3%) which have the family histories compatible with sporadic or autosomal recessive. CONCLUSIONS TECTA mutations were identified in 6.0% of MFSNHL. These mutations were more frequent in patients with shallow U-shaped audiograms than those with U-shaped audiograms, and in families which have the family histories compatible with autosomal dominant than those with the family histories compatible with sporadic or autosomal recessive.
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Affiliation(s)
- Nobuko Yamamoto
- Department of Otolaryngology, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo, 152-8902, Japan.,Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo, 152-8902, Japan.,Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Hideki Mutai
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo, 152-8902, Japan
| | - Kazunori Namba
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo, 152-8902, Japan
| | - Noriko Morita
- Department of Otolaryngology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo, 173-8606, Japan
| | - Shin Masuda
- Department of Pediatric Rehabilitation, Hiroshima Prefectural Hospital, 1-5-54 Ujina-Kanda, Minami, Hiroshima, 734-8530, Japan
| | - Yasuyuki Nishi
- Department of Otolaryngology, National Hospital Organization Kure Medical Center, 3-1 Aoyama, Kure, Hiroshima, 737-0023, Japan
| | - Atsuko Nakano
- Division of Otorhinolaryngology, Chiba Children's Hospital, 579-1 Heta, Midori, Chiba, 266-0007, Japan
| | - Sawako Masuda
- Department of Otorhinolaryngology, National Mie Hospital, 357 Osato-Kubota, Tsu, Mie, 514-0125, Japan
| | - Masato Fujioka
- Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Kimitaka Kaga
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo, 152-8902, Japan
| | - Kaoru Ogawa
- Department of Otolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Tatsuo Matsunaga
- Department of Otolaryngology, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo, 152-8902, Japan. .,Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo, 152-8902, Japan.
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Ma Z, Xia W, Liu F, Ma J, Sun S, Zhang J, Jiang N, Wang X, Hu J, Ma D. SLC44A4 mutation causes autosomal dominant hereditary postlingual non-syndromic mid-frequency hearing loss. Hum Mol Genet 2017; 26:383-394. [PMID: 28013291 DOI: 10.1093/hmg/ddw394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/11/2016] [Indexed: 01/28/2023] Open
Abstract
Clinical, genetic, and functional investigations were performed to identify the causative mutation in a distinctive Chinese family with postlingual non-syndromic mid-frequency sensorineural hearing loss. Whole-exome sequencing revealed SLC44A4, which encodes the choline transport protein, as the pathogenic gene in this family. In the zebrafish model, downregulation of slc44a4 using morpholinos led to significant abnormalities in the zebrafish inner ear and lateral line neuromasts and contributed, to some extent, to disabilities in hearing and balance. SH-SY5Y cells transfected with SLC44A4 showed higher choline uptake and acetylcholine release than that of cells transfected with mutant SLC44A4. We concluded that mutation of SLC44A4 may cause defects in the Choline- acetylcholine system, which is crucial to the efferent innervation of hair cells in the olivocochlear bundle for the maintenance of physiological function of outer hair cells and the protection of hair cells from acoustic injury, leading to hearing loss.
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Affiliation(s)
- Zhaoxin Ma
- Department of Otorhinolaryngology, Shanghai East Hospital, Tongji University, Shanghai, 200120, People's Republic of China
| | - Wenjun Xia
- Institute of Biomedical Science, Fudan University, Shanghai, 200032, People's Republic of China
| | - Fei Liu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Jing Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Shaoyang Sun
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Nan Jiang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Xu Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Jiongjiong Hu
- Department of Otorhinolaryngology, Shanghai East Hospital, Tongji University, Shanghai, 200120, People's Republic of China
| | - Duan Ma
- Institute of Biomedical Science, Fudan University, Shanghai, 200032, People's Republic of China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and.,Children's Hospital, Fudan University, 200032, People's Republic of China
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Iwasa YI, Nishio SY, Usami SI. Comprehensive Genetic Analysis of Japanese Autosomal Dominant Sensorineural Hearing Loss Patients. PLoS One 2016; 11:e0166781. [PMID: 27911912 PMCID: PMC5135052 DOI: 10.1371/journal.pone.0166781] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 11/03/2016] [Indexed: 11/18/2022] Open
Abstract
Background In general, autosomal dominant inherited hearing loss does not have a founder mutation, with the causative mutation different in each family. For this reason, there has been a strong need for efficient diagnosis methods for autosomal dominant sensorineural hearing loss (ADSNHL) patients. This study sought to verify the effectiveness of our analysis algorithm for the screening of ADSNHL patients as well as the usefulness of the massively parallel DNA sequencing (MPS). Subjects and Methods Seventy-five Japanese ADSNHL patients from 53 ENT departments nationwide participated in this study. We conducted genetic analysis of 75 ADSNHL patients using the Invader assay, TaqMan genotyping assay and MPS-based genetic screening. Results A total of 46 (61.3%) ADSNHL patients were found to have at least one candidate gene variant. Conclusion We were able to achieve a high mutation detection rate through the combination of the Invader assay, TaqMan genotyping assay and MPS. MPS could be used to successfully identify mutations in rare deafness genes.
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Affiliation(s)
- Yoh-ichiro Iwasa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390–8621, Japan
| | - Shin-ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390–8621, Japan
| | - Shin-ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390–8621, Japan
- * E-mail:
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Research progress in pathogenic genes of hereditary non-syndromic mid-frequency deafness. Front Med 2016; 10:137-42. [DOI: 10.1007/s11684-016-0449-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/07/2016] [Indexed: 10/21/2022]
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Targeted Exome Sequencing of Deafness Genes After Failure of Auditory Phenotype-Driven Candidate Gene Screening. Otol Neurotol 2016; 36:1096-102. [PMID: 25830873 DOI: 10.1097/mao.0000000000000747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To demonstrate the efficacy and advantages of targeted exome sequencing (TES) of known deafness genes in cases with failed or misleading auditory phenotype-driven candidate gene screening. STUDY DESIGN Prospective cohort survey. SETTING Otolaryngology department of a tertiary referral hospital. PATIENTS Six hearing-impaired probands with seemingly non-syndromic features from six deaf families were enrolled in this study after failure of genetic diagnosis using auditory phenotype-driven candidate gene screening. INTERVENTION TES of known deafness genes was performed in the six probands, and a final causative variant was pursued using subsequent filtering steps. MAIN OUTCOME MEASURE Potential causative variants determined using TES were confirmed by previously introduced filtering steps. RESULTS We detected causative variants in three (50%) of six families, and these variants were in the COCH, PAX3, and GJB2 genes. Additionally, we also recapitulated the recent finding from other report arguing for the non-pathogenic potential of MYO1A variant. CONCLUSIONS TES of a deafness panel provides a comprehensive genetic screening tool that can be implemented without being misled by the audiogram configuration information and can complement incomplete clinical physical examinations. In addition, the secondary incidental finding obtained by TES contributes useful information regarding the deafness field.
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Conserved proline-directed phosphorylation regulates SR protein conformation and splicing function. Biochem J 2015; 466:311-22. [PMID: 25529026 DOI: 10.1042/bj20141373] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The alternative splicing of human genes is dependent on SR proteins, a family of essential splicing factors whose name derives from a signature C-terminal domain rich in arginine-serine dipeptide repeats (RS domains). Although the SRPKs (SR-specific protein kinases) phosphorylate these repeats, RS domains also contain prolines with flanking serines that are phosphorylated by a second family of protein kinases known as the CLKs (Cdc2-like kinases). The role of specific serine-proline phosphorylation within the RS domain has been difficult to assign since CLKs also phosphorylate arginine-serine dipeptides and, thus, display overlapping residue specificities with the SRPKs. In the present study, we address the effects of discrete serine-proline phosphorylation on the conformation and cellular function of the SR protein SRSF1 (SR protein splicing factor 1). Using chemical tagging and dephosphorylation experiments, we show that modification of serine-proline dipeptides broadly amplifies the conformational ensemble of SRSF1. The induction of these new structural forms triggers SRSF1 mobilization in the nucleus and alters its binding mechanism to an exonic splicing enhancer in precursor mRNA. These physical events correlate with changes in the alternative splicing of over 100 human genes based on a global splicing assay. Overall, these studies draw a direct causal relationship between a specific type of chemical modification in an SR protein and the regulation of alternative gene splicing programmes.
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Nishio SY, Hattori M, Moteki H, Tsukada K, Miyagawa M, Naito T, Yoshimura H, Iwasa YI, Mori K, Shima Y, Sakuma N, Usami SI. Gene expression profiles of the cochlea and vestibular endorgans: localization and function of genes causing deafness. Ann Otol Rhinol Laryngol 2015; 124 Suppl 1:6S-48S. [PMID: 25814645 DOI: 10.1177/0003489415575549] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OBJECTIVES We sought to elucidate the gene expression profiles of the causative genes as well as the localization of the encoded proteins involved in hereditary hearing loss. METHODS Relevant articles (as of September 2014) were searched in PubMed databases, and the gene symbols of the genes reported to be associated with deafness were located on the Hereditary Hearing Loss Homepage using localization, expression, and distribution as keywords. RESULTS Our review of the literature allowed us to systematize the gene expression profiles for genetic deafness in the inner ear, clarifying the unique functions and specific expression patterns of these genes in the cochlea and vestibular endorgans. CONCLUSIONS The coordinated actions of various encoded molecules are essential for the normal development and maintenance of auditory and vestibular function.
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Affiliation(s)
- Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Mitsuru Hattori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hideaki Moteki
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Keita Tsukada
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Maiko Miyagawa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Takehiko Naito
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hidekane Yoshimura
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yoh-Ichiro Iwasa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kentaro Mori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yutaka Shima
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Naoko Sakuma
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Otorhinolaryngology and Head and Neck Surgery, Yokohama City University School of Medicine, Yokohama, Japan
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
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Schmutz SM. An analysis of the inheritance pattern of an adult-onset hearing loss in Border Collie dogs. Canine Genet Epidemiol 2014; 1:6. [PMID: 26401323 PMCID: PMC4574391 DOI: 10.1186/2052-6687-1-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 04/22/2014] [Indexed: 11/10/2022] Open
Abstract
Background During routine diagnostic BAER testing of dogs of various breeds for private owners at the Western College of Veterinary Medicine in Saskatoon, it became evident that some individual dogs developed hearing loss as adults. Although inherited congenital deafness has been widely reported in dogs, this type of deafness had not. Findings Special clinics were set up to screen working Border Collies at herding competitions. To determine the typical age that geriatric deafness might be expected, retired dogs were also recruited. Five of the 10 Border Collies 12 years of age or older had hearing loss (1 bilaterally deaf and 4 had reduced hearing). The adult onset deafness which exhibited in three families, did not usually occur until 5 years of age, too young to be geriatric deafness. This adult onset deafness fits an autosomal dominant pattern of inheritance. Several of these dogs had been BAER tested at younger ages with no sign of deafness. The deaf dogs were not associated with either gender. A survey was developed which was completed by the dog owners, that indicated that the hearing loss was gradual, not sudden. In addition, some family studies were conducted. Conclusions Dogs at 5 years of age were often in the prime of their herding careers and then did not respond appropriately to distant commands. This type of deafness is important to dog owners but is also a potential medical model for some forms of hearing loss in humans. This report also suggests that geriatric hearing loss is common in dogs older than 12 years. Electronic supplementary material The online version of this article (doi:10.1186/2052-6687-1-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sheila M Schmutz
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
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Liao M, Shi D, Wang Y, Zhang K, Chen X, Gao Y, Tan A, Xuan Q, Yang X, Hu Y, Qin X, Zhang H, Mo Z. Genome-wide scan on total serum IgE levels identifies no common variants in a healthy Chinese male population. Immunogenetics 2013; 65:561-8. [PMID: 23661040 DOI: 10.1007/s00251-013-0706-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 04/18/2013] [Indexed: 12/30/2022]
Abstract
Immunoglobulin E (IgE) provides important information on the humoral immune status, and the IgE level is routinely detected in clinical practice. There are many diseases associated with IgE, such as atopic disease, autoimmune diseases, and so on. IgE is a genetically complex trait, but comprehensive genetic assessment of the variability in serum IgE levels is lacking. Previous genome-wide association studies (GWAS) on total serum IgE levels have identified FCER1A as the susceptibility locus; however, the candidate gene association study in southern Chinese patients reported no association. Given the genetic difference in different populations, we firstly conducted this two-stage GWAS in a Chinese population of 3,495 men, including 1,999 unrelated subjects in the first stage and 1,496 independent individuals replicated in the second stage. In the first stage, we totally identified three single nucleotide polymorphisms (SNPs) which reached a P value of 1.0 × 10⁻⁵. Rs17090302 on chromosome 3 and Rs28708846 on chromosome 13 are intergenic. Rs432085 from chromosome 3p28 is located in the gene CCDC50. When the two-stage data was combined, none of the SNPs reached the genome-wide significant level. Collectively, we did not identify novel loci associated with the serum IgE level in Chinese males, but we hypothesized that CCDC50 was a candidate gene in regulation on IgE level.
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Affiliation(s)
- Ming Liao
- Institute of Urology and Nephrology, First Affiliated Hospital of Guangxi Medical University, No. 22 Shuangyong Road, 530021, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
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Park SJ, Jang HR, Kim M, Kim JH, Kwon OH, Park JL, Noh SM, Song KS, Kim SY, Kim YH, Kim YS. Epigenetic alteration of CCDC67 and its tumor suppressor function in gastric cancer. Carcinogenesis 2012; 33:1494-501. [PMID: 22610074 DOI: 10.1093/carcin/bgs178] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this study, the promoter of the gene coiled-coil domain-containing 67 (CCDC67) was found to be frequently methylated in gastric cancer cell lines and in primary gastric tumors, as examined by restriction landmark genomic scanning. In addition, CCDC67 expression was down-regulated in 72.7% of gastric cancer cell lines tested. In most cases, gene down-regulation was associated with CpG hypermethylation in the CCDC67 promoter. Treatment with 5-aza-2'-deoxycytidine and/or trichostatin A restored CCDC67 expression in down-regulated cell lines. Pyrosequencing analysis of 150 paired primary gastric cancer samples revealed that promoter CpG methylation was increased in 74% of tested tumors compared with paired adjacent normal tissues, and this hypermethylation correlated significantly with down-regulation of CCDC67. CCDC67 protein was localized to the cell membrane by immunocytochemistry. Stable transfection of a CCDC67 gene in one gastric cancer cell line inhibited adhesion-dependent and -independent colony formation, and CCDC67 expression suppressed tumorigenesis in nude mice. We suggest that CCDC67 is a putative tumor suppressor gene that is silenced in gastric cancers by promoter CpG methylation and that it may play an important role in cell signaling and migration related to tumorigenesis.
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Affiliation(s)
- Sung-Joon Park
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
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Finding new genes for non-syndromic hearing loss through an in silico prioritization study. PLoS One 2010; 5. [PMID: 20927407 PMCID: PMC2946934 DOI: 10.1371/journal.pone.0012742] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 08/17/2010] [Indexed: 11/19/2022] Open
Abstract
At present, 51 genes are already known to be responsible for Non-Syndromic hereditary Hearing Loss (NSHL), but the knowledge of 121 NSHL-linked chromosomal regions brings to the hypothesis that a number of disease genes have still to be uncovered. To help scientists to find new NSHL genes, we built a gene-scoring system, integrating Gene Ontology, NCBI Gene and Map Viewer databases, which prioritizes the candidate genes according to their probability to cause NSHL. We defined a set of candidates and measured their functional similarity with respect to the disease gene set, computing a score () that relies on the assumption that functionally related genes might contribute to the same (disease) phenotype. A Kolmogorov-Smirnov test, comparing the pair-wise distribution on the disease gene set with the distribution on the remaining human genes, provided a statistical assessment of this assumption. We found at a p-value that the former pair-wise is greater than the latter, justifying a prioritization strategy based on the functional similarity of candidate genes respect to the disease gene set. A cross-validation test measured to what extent the ranking for NSHL is different from a random ordering: adding 15% of the disease genes to the candidate gene set, the ranking of the disease genes in the first eight positions resulted statistically different from a hypergeometric distribution with a p-value and a power. The twenty top-scored genes were finally examined to evaluate their possible involvement in NSHL. We found that half of them are known to be expressed in human inner ear or cochlea and are mainly involved in remodeling and organization of actin formation and maintenance of the cilia and the endocochlear potential. These findings strongly indicate that our metric was able to suggest excellent NSHL candidates to be screened in patients and controls for causative mutations.
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Abstract
Hearing loss (HL), or deafness in its most severe form, affects an estimated 28 and 22.5 million Americans and Europeans, respectively. The numbers are higher in regions such as India and the Middle East, where consanguinity contributes to larger numbers of recessively inherited hearing impairment (HI). As a result of work-related difficulties, educational and developmental delays, and social stigmas and exclusion, the economic impact of HL is very high. At the other end of the spectrum, a rich deaf culture, particularly for individuals whose parents and even grandparents were deaf, is a social movement that believes that deafness is a difference in human experience rather than a disability. This review attempts to cover the remarkable progress made in the field of the genetics of HL over the past 20 years. Mutations in a significant number of genes have been discovered over the years that contribute to clinically heterogeneous forms of HL, enabling genetic counseling and prediction of progression of HL. Cell biological assays, protein localization in the inner ear, and detailed analysis of spontaneous and transgenic mouse models have provided an incredibly rich resource for elucidating mechanisms of hereditary hearing loss (HHL). This knowledge is providing answers for the families with HL, who contribute a great deal to the research being performed worldwide.
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Affiliation(s)
- Amiel A Dror
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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Pollazzon M, Grosso S, Papa F, Katzaki E, Marozza A, Mencarelli M, Uliana V, Balestri P, Mari F, Renieri A. A 9.3Mb microdeletion of 3q27.3q29 associated with psychomotor and growth delay, tricuspid valve dysplasia and bifid thumb. Eur J Med Genet 2009; 52:131-3. [DOI: 10.1016/j.ejmg.2009.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 03/13/2009] [Indexed: 11/27/2022]
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Current World Literature. Curr Opin Otolaryngol Head Neck Surg 2008; 16:490-5. [DOI: 10.1097/moo.0b013e3283130f63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Mid-frequency DFNA8/12 hearing loss caused by a synonymous TECTA mutation that affects an exonic splice enhancer. Eur J Hum Genet 2008; 16:1430-6. [PMID: 18575463 DOI: 10.1038/ejhg.2008.110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Autosomal dominant hearing loss is highly heterogeneous. Hearing impairment mainly involves the mid-frequencies (500-2000 Hz) in only a low percentage of the cases. In a Dutch family with autosomal dominant mid-frequency/flat hearing loss, genome-wide SNP analysis combined with fine mapping using microsatellite markers mapped the defect to the DFNA8/12 locus, with a maximum two-point LOD score of 3.52. All exons and intron-exon boundaries of the TECTA gene, of which mutations are causative for DFNA8/12, were sequenced. Only one heterozygous synonymous change in exon 16 (c.5331G>A; p.L1777L) was found to segregate with the hearing loss. This change was predicted to cause the loss of an exonic splice enhancer (ESE). RT-PCR using primers flanking exon 16 revealed, besides the expected PCR product from the wild-type allele, a smaller fragment only in the affected individual, representing part of an aberrant TECTA transcript lacking exon 16. The aberrant splicing is predicted to result in a deletion of 37 amino acids (p.S1758Y/G1759_N1795del) in alpha-tectorin. Subsequently, the same mutation was detected in two out of 36 individuals with a comparable phenotype. Owing to the position of the protein deletion just N-terminal of the zona pellucida (ZP) domain of alpha-tectorin, it is likely that the deletion of 37 amino acids may affect the proteolytic processing, structure and/or function of this domain, which results in a clinical phenotype comparable to that of missense mutations in the ZP domain. In addition, this is the first report of a synonymous mutation that affects an ESE and causes hereditary hearing loss.
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