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Wang X, Liu TX, Zhang Y, Xu LW, Yuan SL, Cui AL, Guo WW, Wang YF, Yang SM, Zhao JG. Genetically modified pigs: Emerging animal models for hereditary hearing loss. Zool Res 2024; 45:284-291. [PMID: 38485498 PMCID: PMC11017082 DOI: 10.24272/j.issn.2095-8137.2023.231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/05/2023] [Indexed: 03/19/2024] Open
Abstract
Hereditary hearing loss (HHL), a genetic disorder that impairs auditory function, significantly affects quality of life and incurs substantial economic losses for society. To investigate the underlying causes of HHL and evaluate therapeutic outcomes, appropriate animal models are necessary. Pigs have been extensively used as valuable large animal models in biomedical research. In this review, we highlight the advantages of pig models in terms of ear anatomy, inner ear morphology, and electrophysiological characteristics, as well as recent advancements in the development of distinct genetically modified porcine models of hearing loss. Additionally, we discuss the prospects, challenges, and recommendations regarding the use pig models in HHL research. Overall, this review provides insights and perspectives for future studies on HHL using porcine models.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tian-Xia Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Liang-Wei Xu
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing 100853, China
| | - Shuo-Long Yuan
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing 100853, China
| | - A-Long Cui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230022, China
| | - Wei-Wei Guo
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing 100853, China
| | - Yan-Fang Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shi-Ming Yang
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing 100853, China. E-mail:
| | - Jian-Guo Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China. E-mail:
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Punetha M, Saini S, Chaudhary S, Yadav PS, Whitworth K, Green J, Kumar D, Kues WA. Induced Pluripotent Stem Cells in the Era of Precise Genome Editing. Curr Stem Cell Res Ther 2024; 19:307-315. [PMID: 36880183 DOI: 10.2174/1574888x18666230307115326] [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: 07/14/2022] [Revised: 11/22/2022] [Accepted: 12/06/2022] [Indexed: 03/08/2023]
Abstract
Genome editing has enhanced our ability to understand the role of genetics in a number of diseases by facilitating the development of more precise cellular and animal models to study pathophysiological processes. These advances have shown extraordinary promise in a multitude of areas, from basic research to applied bioengineering and biomedical research. Induced pluripotent stem cells (iPSCs) are known for their high replicative capacity and are excellent targets for genetic manipulation as they can be clonally expanded from a single cell without compromising their pluripotency. Clustered, regularly interspaced short palindromic repeats (CRISPR) and CRISPR/Cas RNA-guided nucleases have rapidly become the method of choice for gene editing due to their high specificity, simplicity, low cost, and versatility. Coupling the cellular versatility of iPSCs differentiation with CRISPR/Cas9-mediated genome editing technology can be an effective experimental technique for providing new insights into the therapeutic use of this technology. However, before using these techniques for gene therapy, their therapeutic safety and efficacy following models need to be assessed. In this review, we cover the remarkable progress that has been made in the use of genome editing tools in iPSCs, their applications in disease research and gene therapy as well as the hurdles that remain in the actual implementation of CRISPR/Cas systems.
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Affiliation(s)
- Meeti Punetha
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Sheetal Saini
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Suman Chaudhary
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Prem Singh Yadav
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Kristin Whitworth
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jonathan Green
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Dharmendra Kumar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, 125001, Haryana, India
| | - Wilfried A Kues
- Department of Biotechnology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Höltystr 10, 31535, Neustadt, Germany
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Leng D, Ge L, Sun J. Characterization analysis of Rongchang pig population based on the Zhongxin-1 Porcine Breeding Array PLUS. Anim Biosci 2023; 36:1508-1516. [PMID: 37402459 PMCID: PMC10475371 DOI: 10.5713/ab.23.0049] [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: 02/13/2023] [Revised: 03/29/2023] [Accepted: 05/17/2023] [Indexed: 07/06/2023] Open
Abstract
OBJECTIVE To carry out a comprehensive production planning of the existing Rongchang pig population from both environmental and genetic aspects, and to establish a closed population with stable genetic diversity and strict pathogen control, it is necessary to fully understand the genetic background of the population. METHODS We genotyped 54 specific pathogen free (SPF) Rongchang pigs using the Zhongxin-1 Porcine Breeding Array PLUS, calculated their genetic diversity parameters and constructed their families. In addition, we also counted the runs of homozygosity (ROH) of each individual and calculated the value of inbreeding coefficient based on ROH for each individual. RESULTS Firstly, the results of genetic diversity analysis showed that the effective population size (Ne) of this population was 3.2, proportion of polymorphic markers (PN) was 0.515, desired heterozygosity (He) and observed heterozygosity (Ho) were 0.315 and 0.335. Ho was higher than He, indicating that the heterozygosity of all the selected loci was high. Secondly, combining the results of genomic relatedness analysis and cluster analysis, it was found that the existing Rongchang pig population could be divided into four families. Finally, we also counted the ROH of each individual and calculated the inbreeding coefficient value accordingly, whose mean value was 0.09. CONCLUSION Due to the limitation of population size and other factors, the genetic diversity of this Rongchang pig population is low. The results of this study can provide basic data to support the development of Rongchang pig breeding program, the establishment of SPF Rongchang pig closed herd and its experimental utilization.
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Affiliation(s)
- Dong Leng
- Chongqing Academy of Animal Science, Chongqing 404100,
China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130,
China
| | - Liangpeng Ge
- Chongqing Academy of Animal Science, Chongqing 404100,
China
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing 404100,
China
- National Center of Technology Innovation for Swine, Chongqing 404100,
China
| | - Jing Sun
- Chongqing Academy of Animal Science, Chongqing 404100,
China
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing 404100,
China
- National Center of Technology Innovation for Swine, Chongqing 404100,
China
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Zheng S, Xu P, Wu Z, Zhang H, Li D, Liu S, Liu B, Ren J, Chen H, Huang M. Genetic structure and domestication footprints of the tusk, coat color, and ear morphology in East Chinese pigs. J Genet Genomics 2022; 49:1053-1063. [PMID: 35413463 DOI: 10.1016/j.jgg.2022.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/29/2022]
Abstract
The domestication and artificial selection of wild boars have led to dramatic morphological and behavioral changes, especially in East Chinese (ECN) pigs. Here, we provide insights into the population structure and current genetic diversity of representative ECN pig breeds. We identify a 500-kb region containing six tooth development-relevant genes with almost completely different haplotypes between ECN pigs and Chinese wild boars or European domestic pigs. Notably, the c.195A>G missense mutation in exon 2 of AMBN may cause alterations in its protein structure associated with tusk degradation in ECN pigs. In addition, ESR1 may play an important role in the reproductive performance of ECN pigs. A major haplotype of the large lop ear-related MSRB3 gene and eight alleles in the deafness-related GRM7 gene may affect ear morphology and hearing in ECN pigs. Interestingly, we find that the two-end black (TEB) coat color in Jinhua pigs is most likely caused by EDNRB with genetic mechanisms different from other Chinese TEB pigs. This study identifies key loci that may be artificially selected in Chinese native pigs related to the tusk, coat color, and ear morphology, thus providing new insights into the genetic mechanisms of domesticated pigs.
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Affiliation(s)
- Sumei Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Pan Xu
- School of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu 225300, China
| | - Zhongping Wu
- Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong 510225, China
| | - Hui Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Desen Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Shaojuan Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Bingbing Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jun Ren
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Hao Chen
- College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, Jiangxi 330013, China.
| | - Min Huang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China.
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5
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Fontanesi L. Genetics and genomics of pigmentation variability in pigs: A review. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Sox10 Gene Is Required for the Survival of Saccular and Utricular Hair Cells in a Porcine Model. Mol Neurobiol 2022; 59:3323-3335. [DOI: 10.1007/s12035-021-02691-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/08/2021] [Indexed: 10/18/2022]
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7
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Thulasiram MR, Ogier JM, Dabdoub A. Hearing Function, Degeneration, and Disease: Spotlight on the Stria Vascularis. Front Cell Dev Biol 2022; 10:841708. [PMID: 35309932 PMCID: PMC8931286 DOI: 10.3389/fcell.2022.841708] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/20/2022] [Indexed: 11/21/2022] Open
Abstract
The stria vascularis (SV) is a highly vascularized tissue lining the lateral wall of the cochlea. The SV maintains cochlear fluid homeostasis, generating the endocochlear potential that is required for sound transduction. In addition, the SV acts as an important blood-labyrinth barrier, tightly regulating the passage of molecules from the blood into the cochlea. A healthy SV is therefore vital for hearing function. Degeneration of the SV is a leading cause of age-related hearing loss, and has been associated with several hearing disorders, including Norrie disease, Meniere's disease, Alport syndrome, Waardenburg syndrome, and Cytomegalovirus-induced hearing loss. Despite the SV's important role in hearing, there is still much that remains to be discovered, including cell-specific function within the SV, mechanisms of SV degeneration, and potential protective or regenerative therapies. In this review, we discuss recent discoveries elucidating the molecular regulatory networks of SV function, mechanisms underlying degeneration of the SV, and otoprotective strategies for preventing drug-induced SV damage. We also highlight recent clinical developments for treating SV-related hearing loss and discuss future research trajectories in the field.
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Affiliation(s)
- Matsya R Thulasiram
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jacqueline M Ogier
- Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Alain Dabdoub
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Otolaryngology–Head and Neck Surgery, University of Toronto, Toronto, ON, Canada
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Hu Q, Zang X, Ding Y, Gu T, Shi J, Li Z, Cai G, Liu D, Wu Z, Hong L. Porcine uterine luminal fluid-derived extracellular vesicles improve conceptus-endometrial interaction during implantation. Theriogenology 2022; 178:8-17. [PMID: 34735978 DOI: 10.1016/j.theriogenology.2021.10.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022]
Abstract
Successful implantation of porcine conceptus requires synergistic interaction with various signal molecules in the maternal uterus. Extracellular vesicles (EVs) in uterine luminal fluid (ULF) of mice play important roles in conceptus development. However, studies have not explored the roles of extracellular vesicles (EV) in ULF of pigs. The aim of this study was to identify characteristics, origin, and roles of ULF-derived EVs on day 9 of the estrous cycle and on day 9,12 and 15 of pregnancy in pigs. Western blot, BCA assay and HE staining analysis showed increase in EVs concentration in ULF began from day 12 of pregnancy. Immunofluorescence staining and transmission electron microscopy analysis showed that EVs were mainly derived from endometrial epithelial cells. Fluorescent labeling, CCK-8 and transwell migration assays showed that these EVs were delivered to the trophoblast or parthenogenetic activation embryos to regulate proliferation and migration of trophoblast cells. A total of 305 miRNAs were identified using small RNA sequencing analysis. Functional enrichment analysis showed that miRNAs in these EVs potentially play vital regulatory functions in EV transportation or conceptus implantation. QRT-PCR analysis was used to further verify the RNA-seq data. The findings of this study provide information on the functions of porcine ULF-derived EVs and provide a reference dataset for future translational studies on porcine ULF-derived EVs.
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Affiliation(s)
- Qun Hu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Xupeng Zang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Yue Ding
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Junsong Shi
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Wens Breeding Swine Technology Co. Ltd., Yunfu, China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Dewu Liu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, China.
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China.
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Huang M, Zhang H, Wu ZP, Wang XP, Li DS, Liu SJ, Zheng SM, Yang LJ, Liu BB, Li GX, Jiang YC, Chen H, Ren J. Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs. Animal 2021; 15:100354. [PMID: 34543995 DOI: 10.1016/j.animal.2021.100354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022] Open
Abstract
Pudong White (PDW) pigs, historically originating from Shanghai, are the only Chinese indigenous pigs characterised by their completely white coats, with the exception of Rongchang pigs. However, there is limited information concerning their overall genetic structure or relationship with other breeds, especially the East Chinese (ECN) and European pigs. To uncover the genetic structure, selection signatures, and potential exotic introgression in PDW pigs, we sampled 15 PDW pigs using whole-genome sequencing (~20×). We then conducted in-depth population genetic analyses in 320 pigs from 27 global pig groups, namely, European wild boars, Chinese wild boars, and outgroup. Neighbour-joining tree and principal component analysis confirmed that PDW pigs belonged to the ecotype of ECN pigs. Both f3, D-statistics, and structure analysis showed that PDW pigs shared apparent alleles with Large White (LW) pigs. Three statistics, rIBD, a haplotype heat map and copy number variation, further indicated that PDW pigs shared apparent alleles with LW pigs at the KIT Proto-Oncogene, Receptor Tyrosine Kinase (KIT) and PARG-MARCHF8 loci, suggesting that the lineage of European pigs in PDW originated from LW pigs. After further detecting the KIT mutations in different pig breeds, PDW was confirmed to have the same duplication region 1, duplication region 2, and the splicing mutation on intron 17 of KIT as LW pigs that determine the white coat colour phenotype in European white pigs. We hypothesised that LW pigs were imported to China ∼110-160 years ago according to the admixture time estimate and then crossed with ECN pigs, resulting in the introgression of the KIT alleles that produce the white coat colour phenotype in the PDW pig breed. To our knowledge, this study presents the first thorough description of the genetic structure of PDW pigs via whole-genome resequencing data; moreover, the results provide a basis for the national project for the conservation of this unique Chinese local population.
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Affiliation(s)
- M Huang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - H Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Z P Wu
- Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong Province, China
| | - X P Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - D S Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - S J Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - S M Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - L J Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - B B Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - G X Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Y C Jiang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - H Chen
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi Province, China.
| | - J Ren
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong Province, China
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10
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Analysis of Homozygous-by-Descent (HBD) Segments for Purebred and Crossbred Pigs in Russia. Life (Basel) 2021; 11:life11080861. [PMID: 34440604 PMCID: PMC8400874 DOI: 10.3390/life11080861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/30/2022] Open
Abstract
Intensive selection raises the efficiency of pig farming considerably, but it also promotes the accumulation of homozygosity, which can lead to an increase in inbreeding and the accumulation of deleterious variation. The analysis of segments homozygous-by-descent (HBD) and non-HBD segments in purebred and crossbred pigs is of great interest. Research was carried out on 657 pigs, of which there were Large White (LW, n = 280), Landrace (LR, n = 218) and F1 female (♂LR × ♀LW) (F1, n = 159). Genotyping was performed using the GeneSeek® GGP Porcine HD Genomic Profiler v1 (Illumina Inc., USA). To identify HBD segments and estimate autozygosity (inbreeding coefficient), we used the multiple HBD classes model. LW pigs exhibited 50,420 HBD segments, an average of 180 per animal; LR pigs exhibited 33,586 HBD segments, an average of 154 per animal; F1 pigs exhibited 21,068 HBD segments, an average of 132 per animal. The longest HBD segments in LW were presented in SSC1, SSC13 and SSC15; in LR, in SSC1; and in F1, in SSC15. In these segments, 3898 SNPs localized in 1252 genes were identified. These areas overlap with 441 QTLs (SSC1—238 QTLs; SSC13—101 QTLs; and SSC15—102 QTLs), including 174 QTLs for meat and carcass traits (84 QTLs—fatness), 127 QTLs for reproduction traits (100 QTLs—litter traits), 101 for production traits (69 QTLs—growth and 30 QTLs—feed intake), 21 QTLs for exterior traits (9 QTLs—conformation) and 18 QTLs for health traits (13 QTLs—blood parameters). Thirty SNPs were missense variants. Whilst estimating the potential for deleterious variation, six SNPs localized in the NEDD4, SEC11C, DCP1A, CCT8, PKP4 and TENM3 genes were identified, which may show deleterious variation. A high frequency of potential deleterious variation was noted for LR in DCP1A, and for LW in TENM3 and PKP4. In all cases, the genotype frequencies in F1 were intermediate between LR and LW. The findings presented in our work show the promise of genome scanning for HBD as a strategy for studying population history, identifying genomic regions and genes associated with important economic traits, as well as deleterious variation.
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11
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Wang L, Sun F, Wan ZY, Ye B, Wen Y, Liu H, Yang Z, Pang H, Meng Z, Fan B, Alfiko Y, Shen Y, Bai B, Lee MSQ, Piferrer F, Schartl M, Meyer A, Yue GH. Genomic Basis of Striking Fin Shapes and Colors in the Fighting Fish. Mol Biol Evol 2021; 38:3383-3396. [PMID: 33871625 PMCID: PMC8321530 DOI: 10.1093/molbev/msab110] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long-fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole-genome sequencing, quantitative trait loci mapping, genome-wide association studies, and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino, and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double-tail mutant was suggested to be caused by a deletion in a zic1/zic4 coenhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Fei Sun
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Baoqing Ye
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Yanfei Wen
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Huiming Liu
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zituo Yang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Hongyan Pang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zining Meng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Fan
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, Yangjiang, China
| | - Yuzer Alfiko
- Biotech Lab, Wilmar International, Jakarta, Indonesia
| | - Yubang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Bin Bai
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - May Shu Qing Lee
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Francesc Piferrer
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gen Hua Yue
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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12
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Wang J, Lu Y, Yan X, Shen T, Li L, Rao Y, Tan B, Xiong W, Cheng J, Zhao Y, Yuan H. Identification of novel MITF mutations in Chinese families with Waardenburg syndrome type II. Mol Genet Genomic Med 2021; 9:e1770. [PMID: 34323021 PMCID: PMC8457691 DOI: 10.1002/mgg3.1770] [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: 03/07/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Waardenburg syndrome (WS) is a rare autosomal-dominant syndrome and is characterized by sensorineural hearing loss and pigment abnormalities. It is subdivided into four types according to the clinical characteristics. MITF is one of the major pathogenic genes for type II. The aim of this study was to investigate MITF mutations and the clinical characteristics of WS type 2 (WS2) in four Chinese families. METHOD Clinical diagnoses were based on detailed clinical findings. Six WS2 patients from four unrelated Chinese families were enrolled. Massively parallel DNA sequencing was used to find pathogenic genes and Sanger sequencing was used to confirm the variants detected. RESULTS Sensorineural hearing loss was observed in four of six patients, three had heterochromia iridis, and five have freckled faces. We identified three novel MITF heterozygous mutations (c.831dupC, c.650G>A, and c.711-2A>G) and one recurrent heterozygous mutation (c.328C>T) in the four WS2 families. Intra-familial phenotypic variability and incomplete penetrance were found in WS2 patients with pathogenic variants of MITF. CONCLUSION Genetic diagnosis was performed for the involved four families based on the clinical manifestations. Four heterozygous mutations were identified in the MITF gene. Our findings expanded the phenotypic and genotypic spectrum of WS.
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Affiliation(s)
- Jing Wang
- Department of Oto-Rhino-Laryngology, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yu Lu
- Institute of Rare Disease, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaohong Yan
- Department of Oto-Rhino-Laryngology, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Tian Shen
- Department of Oto-Rhino-Laryngology, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Linke Li
- Department of Oto-Rhino-Laryngology, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yufang Rao
- Department of Oto-Rhino-Laryngology, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Bo Tan
- Institute of Rare Disease, West China Hospital of Sichuan University, Chengdu, China
| | - Wenyu Xiong
- Institute of Rare Disease, West China Hospital of Sichuan University, Chengdu, China
| | - Jing Cheng
- Institute of Rare Disease, West China Hospital of Sichuan University, Chengdu, China
| | - Yu Zhao
- Department of Oto-Rhino-Laryngology, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Huijun Yuan
- Medical Genetics Center, Southwest Hospital, Army Medical University, Chongqing, China
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13
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Seddon JM, Fortes M, Kelly-Smith M, Sommerlad SF, Hayward JJ, Burmeister L, De Risio L, Mellersh C, Freeman J, Strain GM. Deafness in Australian Cattle Dogs associated to QTL on chromosome 20 in genome-wide association study analyses. Anim Genet 2021; 52:694-702. [PMID: 34318504 DOI: 10.1111/age.13115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 11/29/2022]
Abstract
Pigment-associated deafness is a common hereditary condition in a range of dog breeds. The aim of this study was to perform a genome-wide association analysis to investigate the genetic architecture of deafness in Australian Cattle Dogs. Genotypes for 104 757 polymorphisms in 216 dogs were available for analyses after quality control. A genomic relationship matrix was used in the mixed model analyses to account for polygenic effects, as we tested each polymorphism for its association with deafness, in a case/control experimental design. Three approaches were used to code the genotypes and test for additive, recessive and dominant SNP effects. The genome-wide association study analyses identified a clear association peak on CFA20, with the most significant SNPs on this chromosome (1.29 × 10-4 ) in the vicinity of MITF. Variants in MITF have been associated with white pigmentation in dogs and with deafness in humans and other species, supporting the premise that canine deafness is associated with variants in or near this gene. A recessive inheritance for the peak in CFA20 is possible given the significant results in the recessive model; however, the estimated heritability was low (4.54 × 10-5 ). Further validation, identification of variants and testing in other dog breeds are needed.
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Affiliation(s)
- J M Seddon
- School of Veterinary Science, The University of Queensland, Gatton, Qld, 4343, Australia
| | - M Fortes
- School of Chemistry and Molecular Biosciences, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Qld, 4072, Australia
| | - M Kelly-Smith
- Comparative Biomedical Sciences, Louisiana State University, School of Veterinary Medicine, Baton Rouge, LA, 70803, USA
| | - S F Sommerlad
- School of Veterinary Science, The University of Queensland, Gatton, Qld, 4343, Australia
| | - J J Hayward
- Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - L Burmeister
- Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK
| | - L De Risio
- Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK
| | - C Mellersh
- Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK
| | - J Freeman
- Animal Health Trust, Newmarket, Suffolk, CB8 7UU, UK
| | - G M Strain
- Comparative Biomedical Sciences, Louisiana State University, School of Veterinary Medicine, Baton Rouge, LA, 70803, USA
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14
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Gao Z, Zhang Y, Li Z, Zeng Q, Yang F, Song Y, Song Y, He J. Genomic breed composition of Ningxiang pig via different SNP panels. J Anim Physiol Anim Nutr (Berl) 2021; 106:783-791. [PMID: 34260785 DOI: 10.1111/jpn.13603] [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: 03/07/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
The genomic breed composition (GBC) reflects the genetic relationship between individual animal and ancestor breeds in composite or hybrid breeds. Also, it can estimate the genomic contribution of each breed (ancestor) to the genome of each individual animal. Using genomic SNP information to estimate Ningxiang pig GBC is of great significance. First of all, GBC was widely used in cattle and had significant effects, but there is almost no using experience in Chinese endemic pig breeds. Importantly, High-density SNPs are expensive but can be economized by deploying a relatively small number of highly informative SNP scattered evenly across the genome. Moreover, the impact of low-density SNPs selection strategy on estimating the GBC of individual animals has not been fully explained. Using SNP data from different databases and organizations, we established reference (N = 2015) and verification (N = 302) data sets. Twelve successively smaller SNP panels (500, 1K, 5K, 10K) were built from those SNP in the reference data by three selection methods (uniform, maximized the Euclidean distance (MED) and random distribution method). For each panel, the GBC of Ningxiang pigs in the reference dataset was estimated. Then combining Shannon entropy and the GBC results, the optimal panel (the 10K SNP panel constructed by MED method) was picked out to estimate the GBC of verification Ningxiang pig, which detected that 230 individuals were purebred Ningxiang pigs and the remaining 72 impure individuals contained 6.44% blood related with Rongchang pigs and 4.09% with Bamaxiang pigs in the verification Ningxiang population. Finally, the genetic structure analysis of verification population was performed combining with the results of GBC, multi-dimensional scaling (MDS) analysis and hierarchical cluster analysis. These results showed: (a) GBC could accurately identify purebred Ningxiang pigs and, scientifically, calculate the genomic contribution of each breed of each hybrid animal. (b) GBC could carry out population genetic structure and understand the genetic background of Ningxiang pigs. Such findings highlight a variety of opportunities to better protect and identify other endangered local breeds in China facing the same situation as Ningxiang pig and provide more accurate, economical and efficient new technical support in GBC estimation breeding work.
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Affiliation(s)
- Zhendong Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Zhi Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Qinhua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Fang Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yuexiang Song
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yukun Song
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
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15
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A Missense Mutation in the KLF7 Gene Is a Potential Candidate Variant for Congenital Deafness in Australian Stumpy Tail Cattle Dogs. Genes (Basel) 2021; 12:genes12040467. [PMID: 33805165 PMCID: PMC8064056 DOI: 10.3390/genes12040467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 12/20/2022] Open
Abstract
Congenital deafness is prevalent among modern dog breeds, including Australian Stumpy Tail Cattle Dogs (ASCD). However, in ASCD, no causative gene has been identified so far. Therefore, we performed a genome-wide association study (GWAS) and whole genome sequencing (WGS) of affected and normal individuals. For GWAS, 3 bilateral deaf ASCDs, 43 herding dogs, and one unaffected ASCD were used, resulting in 13 significantly associated loci on 6 chromosomes, i.e., CFA3, 8, 17, 23, 28, and 37. CFA37 harbored a region with the most significant association (−log10(9.54 × 10−21) = 20.02) as well as 7 of the 13 associated loci. For whole genome sequencing, the same three affected ASCDs and one unaffected ASCD were used. The WGS data were compared with 722 canine controls and filtered for protein coding and non-synonymous variants, resulting in four missense variants present only in the affected dogs. Using effect prediction tools, two variants remained with predicted deleterious effects within the Heart development protein with EGF like domains 1 (HEG1) gene (NC_006615.3: g.28028412G>C; XP_022269716.1: p.His531Asp) and Kruppel-like factor 7 (KLF7) gene (NC_006619.3: g.15562684G>A; XP_022270984.1: p.Leu173Phe). Due to its function as a regulator in heart and vessel formation and cardiovascular development, HEG1 was excluded as a candidate gene. On the other hand, KLF7 plays a crucial role in the nervous system, is expressed in the otic placode, and is reported to be involved in inner ear development. 55 additional ASCD samples (28 deaf and 27 normal hearing dogs) were genotyped for the KLF7 variant, and the variant remained significantly associated with deafness in ASCD (p = 0.014). Furthermore, 24 dogs with heterozygous or homozygous mutations were detected, including 18 deaf dogs. The penetrance was calculated to be 0.75, which is in agreement with previous reports. In conclusion, KLF7 is a promising candidate gene causative for ASCD deafness.
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16
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Zu M, Guo WW, Cong T, Ji F, Zhang SL, Zhang Y, Song X, Sun W, He DZZ, Shi WG, Yang SM. SCN11A gene deletion causes sensorineural hearing loss by impairing the ribbon synapses and auditory nerves. BMC Neurosci 2021; 22:18. [PMID: 33752606 PMCID: PMC7986359 DOI: 10.1186/s12868-021-00613-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/20/2021] [Indexed: 11/10/2022] Open
Abstract
Background The SCN11A gene, encoded Nav1.9 TTX resistant sodium channels, is a main effector in peripheral inflammation related pain in nociceptive neurons. The role of SCN11A gene in the auditory system has not been well characterized. We therefore examined the expression of SCN11A in the murine cochlea, the morphological and physiological features of Nav1.9 knockout (KO) ICR mice. Results Nav1.9 expression was found in the primary afferent endings beneath the inner hair cells (IHCs). The relative quantitative expression of Nav1.9 mRNA in modiolus of wild-type (WT) mice remains unchanged from P0 to P60. The number of presynaptic CtBP2 puncta in Nav1.9 KO mice was significantly lower than WT. In addition, the number of SGNs in Nav1.9 KO mice was also less than WT in the basal turn, but not in the apical and middle turns. There was no lesion in the somas and stereocilia of hair cells in Nav1.9 KO mice. Furthermore, Nav1.9 KO mice showed higher and progressive elevated ABR threshold at 16 kHz, and a significant increase in CAP thresholds. Conclusions These data suggest a role of Nav1.9 in regulating the function of ribbon synapses and the auditory nerves. The impairment induced by Nav1.9 gene deletion mimics the characters of cochlear synaptopathy.
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Affiliation(s)
- Mian Zu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Wei-Wei Guo
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Tao Cong
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Fei Ji
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Shi-Li Zhang
- Clinical Hearing Center of Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yue Zhang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Xin Song
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Wei Sun
- Department of Communicative Disorders and Sciences, Center for Hearing and Deafness, The State University of New York at Buffalo, Buffalo, NY, USA
| | - David Z Z He
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, 68178, USA
| | - Wei-Guo Shi
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China.
| | - Shi-Ming Yang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing, China. .,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China. .,Key Lab of Hearing Science, Ministry of Education, Beijing, China. .,Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China.
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17
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Lin T, Luo L, Guo W, Ren W, Liu C, Wei H, Yang S, Wang Y. Phenotypic similarities in pigs with SOX10 c.321dupC and SOX10 c.325A>T mutations implied the correlation of SOX10 haploinsufficiency with Waardenburg syndrome. J Genet Genomics 2021; 47:770-780. [PMID: 33766494 DOI: 10.1016/j.jgg.2020.12.003] [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: 07/14/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
SOX10 is a causative gene of Waardenburg syndrome (WS) that is a rare genetic disorder characterized by hearing loss and pigment disturbance. More than 100 mutations of SOX10 have been found in patients with Type 2 WS (WS2), Type 4 WS (WS4), and more complex syndromes. However, no mutation hotspot has been detected in SOX10, and most cases are sporadic, making it difficult to establish a correlation between the high phenotypic and genetic variability. In this study, a duplication of the 321th cytosine (c.321dupC) was introduced into SOX10 in pigs, which induced premature termination of the translation of SOX10 (p.K108QfsX45). The premature stop codon in Exon 3 triggered the degradation of mutant mRNA through nonsense-mediated mRNA decay. However, SOX10c.321dupC induced a highly similar phenotype of WS2 with heterogeneous inner ear malformation compared with its adjacent missense mutation SOX10c.325A>T. In addition, a site-saturation mutation analysis of the SOX10 N-terminal nuclear localization signal (n-NLS), where these two mutations located, revealed the correlation between SOX10 haploinsufficiency and WS by an in vitro reporter assay. The analysis combining the in vitro assay with clinical cases may provide a clue to clinical diagnoses.
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Affiliation(s)
- Tingting Lin
- Department of Laboratory Animal Science, College of Basic Medical Science, Army Medical University, Chongqing 400038, China
| | - Lihua Luo
- Department of Laboratory Animal Science, College of Basic Medical Science, Army Medical University, Chongqing 400038, China
| | - Weiwei Guo
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing 100853, China
| | - Wei Ren
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing 100853, China
| | - Chuanhong Liu
- Department of Laboratory Animal Science, College of Basic Medical Science, Army Medical University, Chongqing 400038, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Science, Army Medical University, Chongqing 400038, China.
| | - Shiming Yang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing 100853, China.
| | - Yong Wang
- Department of Laboratory Animal Science, College of Basic Medical Science, Army Medical University, Chongqing 400038, China.
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18
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Zhang XB, Yang SM. Viewing the current situation of pig model application in China's medical field from the application and funding of NSFC. J Otol 2020; 16:34-39. [PMID: 33505448 PMCID: PMC7814078 DOI: 10.1016/j.joto.2020.10.004] [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: 05/08/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022] Open
Abstract
Background The National Natural Science Foundation of China (NSFC) is an important part of China’s innovation system. In the last decade, the pig has become more and more widely used in the field of medical science, especially in otology research. Objective By analyzing and summarizing the funding information over recent years, we intend to identify the characteristics and trends of funding for research using pig models and provide references for future development. Material and methods This is a comprehensive analysis of features in funding for research projects involving pig models by the NSFC in the past 10 years, with a focus on projects in the field of otolaryngology/head and neck surgery. Results Both the number and amount of funding provided by the NSFC for research involving pig models are on the rise with each passing year. Researchers at the PLA General Hospital have completed a number of studies using miniature pigs in cochlear morphology, electrophysiology, cochlear implantation, cochlear transcription analysis, gene therapy, inner ear disease modeling and Eustachian tube pathology modeling. Conclusion Pigs as an ideal large mammal model are well suited in the current national basic research strategy in China, and can help further strengthen China’s leading position in basic research in the world.
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Affiliation(s)
- Xiao Bin Zhang
- Department of Health Sciences, National Natural Science Foundation of China, China
| | - Shi-Ming Yang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, No. 28 Fuxing Road, Beijing, 100853, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, 100853, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China
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19
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Yang S, Wang C, Zhou C, Kang D, Zhang X, Yuan H. A follow-up study of a Chinese family with Waardenburg syndrome type II caused by a truncating mutation of MITF gene. Mol Genet Genomic Med 2020; 8:e1520. [PMID: 33045145 PMCID: PMC7767564 DOI: 10.1002/mgg3.1520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/02/2020] [Accepted: 09/17/2020] [Indexed: 11/29/2022] Open
Abstract
Background Waardenburg syndrome (WS) is a highly clinically and genetically heterogeneous disease. The core disease phenotypes of WS are sensorineuronal hearing loss and pigmentary disturbance, which are usually caused by the absence of neural crest cell‐derived melanocytes. At present, four subtypes of WS have been defined, which are caused by seven genes. Waardenburg syndrome type 2 (WS2) is one of the most common forms. Two genes, MITF and SOX10, have been found to be responsible for majority of WS2. Methods In this study, we performed a clinical longitudinal follow‐up and mutation screening for a Chinese family with Waardenburg syndrome type II. Results A diversity of clinical manifestations was observed in this WS2 family. In addition to the congenital hearing loss of most affected family members, progressive hearing loss was also found in some WS2 patients. A nonsense mutation of c.328C>T (p.R110X) in MITF was identified in all affected family members. This mutation results in a truncated MITF protein, which is considered to be a disease‐causing mutation. Conclusion These findings offer a better understanding of the spectrum of MITF mutations and highlight the necessity of continuous hearing assessment in WS patients.
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Affiliation(s)
- Shuzhi Yang
- Department of Otolaryngology, The 4th Medical CenterChinese PLA General HospitalBeijingChina
- Department of Otorhinolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otorhinolaryngologic DiseaseChinese PLA General HospitalBeijingChina
| | - Cuicui Wang
- Center for Medical GeneticsSouthwest HospitalArmy Medical UniversityChongqingChina
| | - Chengyong Zhou
- Department of Otolaryngology, The 4th Medical CenterChinese PLA General HospitalBeijingChina
- Department of Otorhinolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otorhinolaryngologic DiseaseChinese PLA General HospitalBeijingChina
| | - DongYang Kang
- Institute Of OtolaryngologyChinese PLA General HospitalBeijingChina
| | - Xin Zhang
- Institute Of OtolaryngologyChinese PLA General HospitalBeijingChina
| | - Huijun Yuan
- Center for Medical GeneticsSouthwest HospitalArmy Medical UniversityChongqingChina
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20
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Xu C, Ren W, Zhang Y, Zheng F, Zhao H, Shang H, Guo W, Yang S. KIT gene mutation causes deafness and hypopigmentation in Bama miniature pigs. Am J Transl Res 2020; 12:5095-5107. [PMID: 33042408 PMCID: PMC7540160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
Waardenburg syndrome (WS) is a common syndromic hearing loss disease. A large group of patients affected by WS were found no mutations in the existed gene panel, indicating that there are still potential genes responsible for WS yet to be detected. In our previous study, we established an autosomal-dominant KIT (OMIM# 164920) mutation (c.2418T>A, p.Asp806Glu) pig pedigree which presented congenital bilateral severe sensorineural hearing loss and hypopigmentation, exact the same as human WS. Histological analysis showed nearly normal structures of the organ of Corti, stria vascularis (SV) and spiral neuron ganglions at E85. Scanning electron microscopy (SEM) exhibited that hair cells started to degenerate at E100, and totally gone at P1. Transmission electron microscope (TEM) showed disorganization of SV and disappearance of intermediate cells. The absence of endocochlear potentials also demonstrated the dysfunction of stria. Our study demonstrated that KIT mutation (c.2418T>A, p.Asp806Glu) interrupted the development of melanocytes in cochlea, which led to SV malformation and dysfunction, resulting in degeneration of hair cells and finally hearing loss. Therefore, KIT was highly supposed to be a newly found gene associated with WS and be added to the WS related gene screening panel clinically.
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Affiliation(s)
- Cong Xu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical SchoolNo. 28 Fuxing Road, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic DiseasesBeijing 100853, China
- State Key Lab of Hearing Science, Ministry of EducationBeijing 100853, China
- Beijing Key Lab of Hearing Impairment Prevention and TreatmentBeijing 100853, China
| | - Wei Ren
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical SchoolNo. 28 Fuxing Road, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic DiseasesBeijing 100853, China
- State Key Lab of Hearing Science, Ministry of EducationBeijing 100853, China
- Beijing Key Lab of Hearing Impairment Prevention and TreatmentBeijing 100853, China
| | - Yue Zhang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical SchoolNo. 28 Fuxing Road, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic DiseasesBeijing 100853, China
- State Key Lab of Hearing Science, Ministry of EducationBeijing 100853, China
- Beijing Key Lab of Hearing Impairment Prevention and TreatmentBeijing 100853, China
| | - Fanjun Zheng
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical SchoolNo. 28 Fuxing Road, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic DiseasesBeijing 100853, China
- State Key Lab of Hearing Science, Ministry of EducationBeijing 100853, China
- Beijing Key Lab of Hearing Impairment Prevention and TreatmentBeijing 100853, China
| | - Hui Zhao
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical SchoolNo. 28 Fuxing Road, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic DiseasesBeijing 100853, China
- State Key Lab of Hearing Science, Ministry of EducationBeijing 100853, China
- Beijing Key Lab of Hearing Impairment Prevention and TreatmentBeijing 100853, China
| | - Haitao Shang
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510080, Guangdong, China
- Department of Laboratory Animal Science, College of Basic Medical Science, Third Military Medical University (Army Medical University)Chongqing 400038, China
| | - Weiwei Guo
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical SchoolNo. 28 Fuxing Road, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic DiseasesBeijing 100853, China
- State Key Lab of Hearing Science, Ministry of EducationBeijing 100853, China
- Beijing Key Lab of Hearing Impairment Prevention and TreatmentBeijing 100853, China
| | - Shiming Yang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical SchoolNo. 28 Fuxing Road, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic DiseasesBeijing 100853, China
- State Key Lab of Hearing Science, Ministry of EducationBeijing 100853, China
- Beijing Key Lab of Hearing Impairment Prevention and TreatmentBeijing 100853, China
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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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22
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Transcript Profiles of Stria Vascularis in Models of Waardenburg Syndrome. Neural Plast 2020; 2020:2908182. [PMID: 32802035 PMCID: PMC7416267 DOI: 10.1155/2020/2908182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/18/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022] Open
Abstract
Background Waardenburg syndrome is an uncommon genetic condition characterized by at least some degree of congenital hearing loss and pigmentation deficiencies. However, the genetic pathway affecting the development of stria vascularis is not fully illustrated. Methods The transcript profile of stria vascularis of Waardenburg syndrome was studied using Mitf-M mutant pig and mice models. Therefore, GO analysis was performed to identify the differential gene expression caused by Mitf-M mutation. Results There were 113 genes in tyrosine metabolism, melanin formation, and ion transportations showed significant changes in pig models and 191 genes in mice models. In addition, there were some spice's specific gene changes in the stria vascularis in the mouse and porcine models. The expression of tight junction-associated genes, including Cadm1, Cldn11, Pcdh1, Pcdh19, and Cdh24 genes, were significantly higher in porcine models compared to mouse models. Vascular-related and ion channel-related genes in the stria vascularis were also shown significantly difference between the two species. The expression of Col2a1, Col3a1, Col11a1, and Col11a2 genes were higher, and the expression of Col8a2, Cd34, and Ncam genes were lower in the porcine models compared to mouse models. Conclusions Our data suggests that there is a significant difference on the gene expression and function between these two models.
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Sai N, Shi X, Zhang Y, Jiang QQ, Ji F, Yuan SL, Sun W, Guo WW, Yang SM, Han WJ. Involvement of Cholesterol Metabolic Pathways in Recovery from Noise-Induced Hearing Loss. Neural Plast 2020; 2020:6235948. [PMID: 32617095 PMCID: PMC7306080 DOI: 10.1155/2020/6235948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/08/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
The objective of this study was to explore the molecular mechanisms of acute noise-induced hearing loss and recovery of steady-state noise-induced hearing loss using miniature pigs. We used miniature pigs exposed to white noise at 120 dB (A) as a model. Auditory brainstem response (ABR) measurements were made before noise exposure, 1 day and 7 days after noise exposure. Proteomic Isobaric Tags for Relative and Absolute Quantification (iTRAQ) was used to observe changes in proteins of the miniature pig inner ear following noise exposure. Western blot and immunofluorescence were performed for further quantitative and qualitative analysis of proteomic changes. The average ABR-click threshold of miniature pigs before noise exposure, 1 day and 7 days after noise exposure, were 39.4 dB SPL, 67.1 dB SPL, and 50.8 dB SPL, respectively. In total, 2,158 proteins were identified using iTRAQ. Both gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analyses showed that immune and metabolic pathways were prominently involved during the impairment stage of acute hearing loss. During the recovery stage of acute hearing loss, most differentially expressed proteins were related to cholesterol metabolism. Western blot and immunofluorescence showed accumulation of reactive oxygen species and nuclear translocation of NF-κB (p65) in the hair cells of miniature pig inner ears during the acute hearing loss stage after noise exposure. Nuclear translocation of NF-κB (p65) may be associated with overexpression of downstream inflammatory factors. Apolipoprotein (Apo) A1 and Apo E were significantly upregulated during the recovery stage of hearing loss and may be related to activation of cholesterol metabolic pathways. This is the first study to use proteomics analysis to analyze the molecular mechanisms of acute noise-induced hearing loss and its recovery in a large animal model (miniature pigs). Our results showed that activation of metabolic, inflammatory, and innate immunity pathways may be involved in acute noise-induced hearing loss, while cholesterol metabolic pathways may play an important role in recovery of hearing ability following noise-induced hearing loss.
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Affiliation(s)
- Na Sai
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Science, Ministry of Education, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Xi Shi
- Clinical Hearing Center of Affiliated Hospital of Xuzhou Medical College, Xuzhou, China
| | - Yan Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Qing-qing Jiang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Science, Ministry of Education, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Fei Ji
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Science, Ministry of Education, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Shuo-long Yuan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Science, Ministry of Education, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Wei Sun
- Department of Communicative Disorders and Sciences, Center for Hearing and Deafness, The State University of New York at Buffalo, Buffalo, New York, USA
| | - Wei-Wei Guo
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Science, Ministry of Education, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Shi-Ming Yang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Science, Ministry of Education, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
| | - Wei-Ju Han
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, China
- Key Lab of Hearing Science, Ministry of Education, China
- Beijing Key Lab of Hearing Impairment for Prevention and Treatment, Beijing, China
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Hayward JJ, Kelly-Smith M, Boyko AR, Burmeister L, De Risio L, Mellersh C, Freeman J, Strain GM. A genome-wide association study of deafness in three canine breeds. PLoS One 2020; 15:e0232900. [PMID: 32413090 PMCID: PMC7228063 DOI: 10.1371/journal.pone.0232900] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/23/2020] [Indexed: 12/17/2022] Open
Abstract
Congenital deafness in the domestic dog is usually related to the presence of white pigmentation, which is controlled primarily by the piebald locus on chromosome 20 and also by merle on chromosome 10. Pigment-associated deafness is also seen in other species, including cats, mice, sheep, alpacas, horses, cows, pigs, and humans, but the genetic factors determining why some piebald or merle dogs develop deafness while others do not have yet to be determined. Here we perform a genome-wide association study (GWAS) to identify regions of the canine genome significantly associated with deafness in three dog breeds carrying piebald: Dalmatian, Australian cattle dog, and English setter. We include bilaterally deaf, unilaterally deaf, and matched control dogs from the same litter, phenotyped using the brainstem auditory evoked response (BAER) hearing test. Principal component analysis showed that we have different distributions of cases and controls in genetically distinct Dalmatian populations, therefore GWAS was performed separately for North American and UK samples. We identified one genome-wide significant association and 14 suggestive (chromosome-wide) associations using the GWAS design of bilaterally deaf vs. control Australian cattle dogs. However, these associations were not located on the same chromosome as the piebald locus, indicating the complexity of the genetics underlying this disease in the domestic dog. Because of this apparent complex genetic architecture, larger sample sizes may be needed to detect the genetic loci modulating risk in piebald dogs.
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Affiliation(s)
- Jessica J. Hayward
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Maria Kelly-Smith
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Adam R. Boyko
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | | | - Luisa De Risio
- Animal Health Trust, Newmarket, Suffolk, England, United Kingdom
| | - Cathryn Mellersh
- Animal Health Trust, Newmarket, Suffolk, England, United Kingdom
| | - Julia Freeman
- Animal Health Trust, Newmarket, Suffolk, England, United Kingdom
| | - George M. Strain
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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Kelly-Smith M, Strain GM. STRING data mining of GWAS data in canine hereditary pigment-associated deafness. Vet Anim Sci 2020; 9:100118. [PMID: 32734119 PMCID: PMC7386748 DOI: 10.1016/j.vas.2020.100118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies may fail to identify significant associations between a disorder and causative genes in complex hereditary disorders. STRING software is a bioinformatics data mining tool that identifies known and predicted physical and functional relationship networks among the proteins of candidate genes. STRING analysis provides a mechanism to identify gene-gene interactions that might not otherwise have been recognized. Relationships identified from STRING analysis can uncover function-based gene-gene relationships that may not be easily extracted from literature, thereby providing genes for pursuit as a cause of a complex hereditary disorder. In this study STRING analysis was applied to identification of candidate genes to pursue as the cause of pigment-associated hereditary deafness in dogs.
Most canine deafness is linked to white pigmentation caused by the piebald locus, shown to be the gene MITF (melanocyte inducing transcription factor), but studies have failed to identify a deafness cause. The coding regions of MITF have not been shown to be mutated in deaf dogs, leading us to pursue genes acting on or controlled by MITF. We have genotyped DNA from 502 deaf and hearing Australian cattle dogs, Dalmatians, and English setters, breeds with a high deafness prevalence. Genome-wide significance was not attained in any of our analyses, but we did identify several suggestive associations. Genome-wide association studies (GWAS) in complex hereditary disorders frequently fail to identify causative gene variants, so advanced bioinformatics data mining techniques are needed to extract information to guide future studies. STRING diagrams are graphical representations of known and predicted networks of protein-protein interactions, identifying documented relationships between gene proteins based on the scientific literature, to identify functional gene groupings to pursue for further scrutiny. The STRING program predicts associations at a preset confidence level and suggests biological functions based on the identified genes. Starting with (1) genes within 500 kb of GWAS-suggested SNPs, (2) known pigmentation genes, (3) known human deafness genes, and (4) genes identified from proteomic analysis of the cochlea, we generated STRING diagrams that included these genes. We then reduced the number of genes by excluding genes with no relationship to auditory function, pigmentation, or relevant structures, and identified clusters of genes that warrant further investigation.
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Affiliation(s)
- Maria Kelly-Smith
- Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803 USA
| | - George M Strain
- Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803 USA
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Wang Y, Jiang T, Tang P, Wu Y, Jiang Z, Dai J, Gu Y, Xu J, Da M, Ma H, Jin G, Mo X, Li Q, Wang X, Hu Z. Family-based whole-genome sequencing identifies compound heterozygous protein-coding and noncoding mutations in tetralogy of Fallot. Gene 2020; 741:144555. [PMID: 32165302 DOI: 10.1016/j.gene.2020.144555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/08/2020] [Indexed: 12/28/2022]
Abstract
Tetralogy of Fallot (TOF) is one of most serious cyanotic congenital heart disease (CHD) and the prevalence is estimated to be 1 in 3000 live births worldwide. Though multiple studies have found genetic variants as risk factors for TOF, they could only explain a small fraction of the pathogenesis. Here, we performed whole genome sequencing (WGS) for 6 individuals derived from 2 families to evaluate pathogenic mutations located in both coding and noncoding regions. We characterized the annotated deleterious coding mutations and impaired noncoding mutations in regulatory elements by various data analysis. Additionally, functional assays were conducted to validate function regulatory elements and noncoding mutations. Interestingly, a compound heterozygous pattern with pathogenic coding and noncoding mutations was identified in probands. In proband 1, biallelic mutations (g.139409115A > T, encoding p.Asn685Ile; g.139444949C > A) in NOTCH1 exon and its regulatory element were detected. In vitro experiments revealed that the regulatory element acted as a silencer and the noncoding mutation decreased the expression of NOTCH1. In proband 2, we also found compound heterozygous mutations (g. 216235029C > T, encoding p.Val2281Met; g. 216525154A > C) which potentially regulated the function of FN1 gene. In summary, our study firstly reported an instance of newly identified noncoding mutation in regulatory element within the compound heterozygous pattern in TOF. The results provided a deeper understanding of TOF genetic architectures.
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Affiliation(s)
- Yifeng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Tao Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Pushi Tang
- Department of Cardiovascular Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, China
| | - Yifei Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhu Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Yayun Gu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Jing Xu
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Min Da
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Xuming Mo
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Qingguo Li
- Department of Cardiovascular Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, China.
| | - Xiaowei Wang
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China; Department of Epidemiology and Biostatistics, Center for Global Health, Nanjing Medical University, Nanjing 211166, China.
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Khalil A, Karroum SB, Barake R, Dunya G, Abou-Rizk S, Kamar A, Nemer G, Bassim M. Post-lingual non-syndromic hearing loss phenotype: a polygenic case with 2 biallelic mutations in MYO15A and MITF. BMC MEDICAL GENETICS 2020; 21:1. [PMID: 31898538 PMCID: PMC6941291 DOI: 10.1186/s12881-019-0942-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 12/24/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND Hearing loss (HL) represents the most common congenital sensory impairment with an incidence of 1-5 per 1000 live births. Non-syndromic hearing loss (NSHL) is an isolated finding that is not part of any other disorder accounting for 70% of all genetic hearing loss cases. METHODS In the current study, we reported a polygenic mode of inheritance in an NSHL consanguineous family using exome sequencing technology and we evaluated the possible effect of the detected single nucleotide variants (SNVs) using in silico methods. RESULTS Two bi-allelic SNVs were detected in the affected patients; a MYO15A (. p.V485A) variant, and a novel MITF (p.P338L) variant. Along with these homozygous mutations, we detected two heterozygous variants in well described hearing loss genes (MYO7A and MYH14). The novel MITF p. Pro338Leu missense mutation was predicted to change the protein structure and function. CONCLUSION A novel MITF mutation along with a previously described MYO15A mutation segregate with an autosomal recessive non-syndromic HL case with a post-lingual onset. The findings highlight the importance of carrying whole exome sequencing for a comprehensive assessment of HL genetic heterogeneity.
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Affiliation(s)
- Athar Khalil
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Samer Bou Karroum
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Rana Barake
- Otolaryngology - Head and Neck Surgery, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Gabriel Dunya
- Otolaryngology - Head and Neck Surgery, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Samer Abou-Rizk
- Otolaryngology - Head and Neck Surgery, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Amina Kamar
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Georges Nemer
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon. .,Genomics and Precision Medicine Program, College of Health and Life Siences, Hamad Bin Khalifa University, Doha, Qatar.
| | - Marc Bassim
- Otolaryngology - Head and Neck Surgery, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
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OSBPL2-disrupted pigs recapitulate dual features of human hearing loss and hypercholesterolaemia. J Genet Genomics 2019; 46:379-387. [PMID: 31451425 DOI: 10.1016/j.jgg.2019.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 02/06/2023]
Abstract
Oxysterol binding protein like 2 (OSBPL2), an important regulator in cellular lipid metabolism and transport, was identified as a novel deafness-causal gene in our previous work. To resemble the phenotypic features of OSBPL2 mutation in animal models and elucidate the potential genotype-phenotype associations, the OSBPL2-disrupted Bama miniature (BM) pig model was constructed using CRISPR/Cas9-mediated gene editing, somatic cell nuclear transfer (SCNT) and embryo transplantation approaches, and then subjected to phenotypic characterization of auditory function and serum lipid profiles. The OSBPL2-disrupted pigs displayed progressive hearing loss (HL) with degeneration/apoptosis of cochlea hair cells (HCs) and morphological abnormalities in HC stereocilia, as well as hypercholesterolaemia. High-fat diet (HFD) feeding aggravated the development of HL and led to more severe hypercholesterolaemia. The dual phenotypes of progressive HL and hypercholesterolaemia resembled in OSBPL2-disrupted pigs confirmed the implication of OSBPL2 mutation in nonsydromic hearing loss (NSHL) and contributed to the potential linkage between auditory dysfunction and dyslipidaemia/hypercholesterolaemia.
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Wu Z, Deng Z, Huang M, Hou Y, Zhang H, Chen H, Ren J. Whole-Genome Resequencing Identifies KIT New Alleles That Affect Coat Color Phenotypes in Pigs. Front Genet 2019; 10:218. [PMID: 30949195 PMCID: PMC6436083 DOI: 10.3389/fgene.2019.00218] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/27/2019] [Indexed: 12/13/2022] Open
Abstract
The Duroc × (Landrace × Large White) hybrid pig (DLY) is the most popular commercial pig used in the Chinese pig industry. DLY pigs are usually white but sometimes show colored phenotypes. Colored DLY pigs are not favored by slaughterhouses and retailers, thus causing certain economic losses to farmers in China. In this study, we first conducted a genome-wide association study and RNA sequencing to demonstrate that KIT variants are responsible for diversifying coat color phenotypes segregating in a DLY population. We then defined the precise sizes and locations of four duplications (DUP1-4), four candidate causative mutations at the KIT locus, in the pig reference genome using the whole-genome sequence data of representative colored individuals. The sequence data also enabled us to identify a list of new KIT alleles. By investigating the association between these new alleles and coat color phenotypes, we provide further evidence that DUP2 is another causative mutation for the solid white coat color in pigs. DUP1 (the KIT gene duplication), DUP2 and the splice mutation are all required for the manifestation of a solid white coat color. DUP4 had a more significant effect on the formation of the belt phenotype compared with DUP3. Given the necessity of DUP2 for the solid white coat color, we detected IN/IN homozygotes lacking DUP2 in Large White and Landrace pigs and found that French Landrace pigs had the highest frequency (8.98%) of IN/IN individuals. This study not only advances our understanding of the molecular mechanism of the color phenotype in pigs, but also establishes a simple and accurate method for the screening of KIT IN/IN homozygotes in Large White and Landrace that would cause colored DLY pigs.
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Affiliation(s)
- Zhongping Wu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zheng Deng
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Min Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yong Hou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Hui Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Hao Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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An FW, Yuan H, Guo W, Hou ZH, Cai JM, Luo CC, Yu N, Jiang QQ, Cheng W, Liu W, Yang SM. Establishment of a Large Animal Model for Eustachian Tube Functional Study in Miniature Pigs. Anat Rec (Hoboken) 2019; 302:1024-1038. [PMID: 30779320 DOI: 10.1002/ar.24098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 10/14/2018] [Accepted: 11/10/2018] [Indexed: 12/21/2022]
Abstract
This study was performed to investigate whether miniature pigs are a suitable animal model for studies of the Eustachian tube (ET). Sixteen Chinese experimental miniature pigs were used in this investigation. Ten animals were used for anatomical and morphometric analyses to obtain qualitative and quantitative information regarding the ET. Three animals were used for histological analysis to determine the fine structure of ET cross-sections. Three animals were used to investigate the feasibility of balloon dilation of the Eustachian tube (BDET). The anatomical study indicated that the pharyngeal orifice and tympanic orifice of the miniature pig ET are located at the posterior end of the nasal lateral wall and anterior wall of the middle ear cavity, respectively. The cartilaginous tube was seen to pass through the whole length of the ET, the length of the cartilaginous part of the ET and the diameter of the isthmus were similar between humans and miniature pigs. The inclination of the ET in miniature pigs was larger than that in humans. The gross histology seemed to be slightly different between miniature pig and human, but the fine structures were essentially the same in both species. BDET experiments verified that the miniature pig model is suitable as a model for clinical operations. The miniature pig ET corresponds very well to that of humans. In addition, the miniature pig ET is suitable as a model for clinical operations. Therefore, the miniature pig is a valid animal model for ET study. Anat Rec, 302:1024-1038, 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Feng-Wei An
- Department of Otolaryngology and Head Neck Surgery, Chinese PLA General Hospital, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing City, Chinese PLA Medical School, Beijing, China
| | - Hu Yuan
- Department of Otolaryngology and Head Neck Surgery, Chinese PLA General Hospital, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing City, Chinese PLA Medical School, Beijing, China
| | - Weiwei Guo
- Department of Otolaryngology and Head Neck Surgery, Chinese PLA General Hospital, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing City, Chinese PLA Medical School, Beijing, China
| | - Zhao-Hui Hou
- Department of Otolaryngology and Head Neck Surgery, Chinese PLA General Hospital, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing City, Chinese PLA Medical School, Beijing, China
| | - Jian-Ming Cai
- Department of Radiology, Chinese PLA General Hospital, Beijing, China
| | - Chun-Cai Luo
- Department of Radiology, Chinese PLA General Hospital, Beijing, China
| | - Ning Yu
- Department of Otolaryngology and Head Neck Surgery, Chinese PLA General Hospital, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing City, Chinese PLA Medical School, Beijing, China
| | - Qing-Qing Jiang
- Department of Otolaryngology and Head Neck Surgery, Chinese PLA General Hospital, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing City, Chinese PLA Medical School, Beijing, China
| | - Wei Cheng
- Department of Otolaryngology and Head Neck Surgery, Chinese PLA General Hospital, Beijing, China.,Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing City, Chinese PLA Medical School, Beijing, China
| | - Wei Liu
- Department of Surgical Sciences, Section of Otolaryngology Head and Neck Surgery, Uppsala University Hospital, Uppsala, Sweden.,Department of Otolaryngology, Uppsala University Hospital, Uppsala, Sweden
| | - Shi-Ming Yang
- Key Lab of Hearing Impairment Science of Ministry of Education, Key Lab of Hearing Impairment Prevention and Treatment of Beijing City, Chinese PLA Medical School, Beijing, China
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Du Y, Ren LL, Jiang QQ, Liu XJ, Ji F, Zhang Y, Yuan SL, Wu ZM, Guo WW, Yang SM. Degeneration of saccular hair cells caused by MITF gene mutation. Neural Dev 2019; 14:1. [PMID: 30635004 PMCID: PMC6330439 DOI: 10.1186/s13064-019-0126-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/03/2019] [Indexed: 02/01/2023] Open
Abstract
Background Waardenburg syndrome (WS) is the consequence of an inherited autosomal dominant mutation which causes the early degeneration of intermediate cells of cochlear stria vascularis (SV) and profound hearing loss. Patients with WS may also experience primary vestibular symptoms. Most of the current WS studies did not discuss the relationship between WS and abnormal vestibular function. Our study found that a spontaneous mutant pig showed profound hearing loss and depigmentation. MITF-M, a common gene mutation causes type WS which affect the development of the intermediate cell of SV, was then identified for animal modeling. Results In this study, the degeneration of vestibular hair cells was found in pigs with MITF-M. The morphology of hair cells in vestibular organs of pigs was examined using electron microscopy from embryonic day E70 to postnatal two weeks. Significant hair cell loss in the mutant saccule was found in this study through E95 to P14. Conversely, there was no hair cell loss in either utricle or semi-circular canals. Conclusions Our study suggested that MITF-M gene mutation only affects hair cells of the saccule, but has no effect on other vestibular organs. The study also indicated that the survival of cochlear and saccular hair cells was dependent on the potassium release from the cochlear SV, but hair cells of the utricle and semi-circular canals were independent on SV.
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Affiliation(s)
- Yi Du
- Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School, Beijng, China
| | - Li-Li Ren
- Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School, Beijng, China
| | - Qing-Qing Jiang
- Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School, Beijng, China
| | - Xing-Jian Liu
- Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School, Beijng, China
| | - Fei Ji
- Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School, Beijng, China
| | - Yue Zhang
- Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School, Beijng, China
| | - Shuo-Long Yuan
- Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School, Beijng, China
| | - Zi-Ming Wu
- Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School, Beijng, China.
| | - Wei-Wei Guo
- Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School, Beijng, China.
| | - Shi-Ming Yang
- Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School, Beijng, China.
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32
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Pan Z, Li S, Liu Q, Wang Z, Zhou Z, Di R, Miao B, Hu W, Wang X, Hu X, Xu Z, Wei D, He X, Yuan L, Guo X, Liang B, Wang R, Li X, Cao X, Dong X, Xia Q, Shi H, Hao G, Yang J, Luosang C, Zhao Y, Jin M, Zhang Y, Lv S, Li F, Ding G, Chu M, Li Y. Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization. Gigascience 2018; 7:4924504. [PMID: 29668959 PMCID: PMC5905515 DOI: 10.1093/gigascience/giy019] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 02/22/2018] [Indexed: 12/30/2022] Open
Abstract
Background Animal domestication has been extensively studied, but the process of feralization remains poorly understood. Results Here, we performed whole-genome sequencing of 99 sheep and identified a primary genetic divergence between 2 heterogeneous populations in the Tibetan Plateau, including 1 semi-feral lineage. Selective sweep and candidate gene analysis revealed local adaptations of these sheep associated with sensory perception, muscle strength, eating habit, mating process, and aggressive behavior. In particular, a horn-related gene, RXFP2, showed signs of rapid evolution specifically in the semi-feral breeds. A unique haplotype and repressed horn-related tissue expression of RXFP2 were correlated with higher horn length, as well as spiral and horizontally extended horn shape. Conclusions Semi-feralization has an extensive impact on diverse phenotypic traits of sheep. By acquiring features like those of their wild ancestors, semi-feral sheep were able to regain fitness while in frequent contact with wild surroundings and rare human interventions. This study provides a new insight into the evolution of domestic animals when human interventions are no longer dominant.
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Affiliation(s)
- Zhangyuan Pan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Shengdi Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiuyue Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhengkui Zhou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Benpeng Miao
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenping Hu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangyu Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoxiang Hu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Ze Xu
- BasePair BioTechonology Co., Ltd., Suzhou, China
| | - Dongkai Wei
- BasePair BioTechonology Co., Ltd., Suzhou, China
| | - Xiaoyun He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liyun Yuan
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaofei Guo
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Benmeng Liang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruichao Wang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoyu Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohan Cao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinlong Dong
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qing Xia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongcai Shi
- Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, China
| | - Geng Hao
- Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, China
| | - Jean Yang
- Research Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Cuicheng Luosang
- Research Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yiqiang Zhao
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Mei Jin
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Yingjie Zhang
- College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China
| | - Shenjin Lv
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Fukuan Li
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Guohui Ding
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China
| | - Mingxing Chu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China
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33
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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 DOI: 10.1016/j.jmoldx.2018.06.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [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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34
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Li WX, Peng H, Yang L, Hao QQ, Sun W, Ji F, Guo WW, Yang SM. Familial nonsyndromic hearing loss with incomplete partition type II caused by novel DSPP gene mutations. Acta Otolaryngol 2018; 138:685-690. [PMID: 29741433 DOI: 10.1080/00016489.2018.1459832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
BACKGROUND Familial nonsyndromic hearing loss (NSHL) with incomplete partition type II (IP-II) is a very rare condition. AIMS/OBJECTIVES To determine the audiological feature, inheritance patterns and genetic etiology of familial NSHL with IP-II in a Chinese family with eight family members. MATERIAL AND METHODS Clinical data were collected from all eight family members, selected deafness genes were sequenced in proband and whole genome sequencing of seven family members was performed. RESULTS The proband were a pair of male nonidentical twins (III:1, III:2). Three patients in this family, including the twins and their father (II:1), were diagnosed with bilateral NSHL with IP-II, and no mutation was found in the genes of SLC26A4, GJB2, GJB3, mitochondrial 12S rRNA, and MITF. Whole genome sequencing data indicated de novo mutations of the gene DSPP, c.3085A > G and c.3087C > T, which resulted in p.N1029D and co-segregated with deafness phenotype, were the underlying genetic etiology. CONCLUSION AND SIGNIFICANCE Familial NSHL with IP-II is extremely rare. In this family, de novo DSPP gene mutations, were considered to be the most probable genetic etiology. And this is the first report to reveal DSPP gene mutations leading to familial NSHL with IP-II.
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Affiliation(s)
- Wan-Xin Li
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Peng
- Department of Otolaryngology-Head and Neck Surgery, Guangdong No. 2 Provincial People’s Hospital affiliated Southern Medical University, Guangzhou, China
| | - Le Yang
- Department of Otolaryngology-Head and Neck Surgery, Guangdong No. 2 Provincial People’s Hospital affiliated Southern Medical University, Guangzhou, China
| | - Qing-Qing Hao
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Wei Sun
- Department of Communicative Disorders and Sciences, Center for Hearing and Deafness, the State University of New York at Buffalo, Buffalo, NY, USA
| | - Fei Ji
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Wei-Wei Guo
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Shi-Ming Yang
- Department of Otolaryngology, Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
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35
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An intercross population study reveals genes associated with body size and plumage color in ducks. Nat Commun 2018; 9:2648. [PMID: 30018292 PMCID: PMC6050300 DOI: 10.1038/s41467-018-04868-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 05/31/2018] [Indexed: 12/15/2022] Open
Abstract
Comparative population genomics offers an opportunity to discover the signatures of artificial selection during animal domestication, however, their function cannot be directly revealed. We discover the selection signatures using genome-wide comparisons among 40 mallards, 36 indigenous-breed ducks, and 30 Pekin ducks. Then, the phenotypes are fine-mapped based on resequencing of 1026 ducks from an F2 segregating population generated by wild × domestic crosses. Interestingly, the two key economic traits of Pekin duck are associated with two selective sweeps with fixed mutations. A novel intronic insertion most possibly leads to a splicing change in MITF accounted for white duck down feathers. And a putative long-distance regulatory mutation causes continuous expression of the IGF2BP1 gene after birth which increases body size by 15% and feed efficiency by 6%. This study provides new insights into genotype-phenotype associations in animal research and constitutes a promising resource on economically important genes in fowl.
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36
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Chen W, Hao QQ, Ren LL, Ren W, Lin HS, Guo WW, Yang SM. Cochlear morphology in the developing inner ear of the porcine model of spontaneous deafness. BMC Neurosci 2018; 19:28. [PMID: 29716524 PMCID: PMC5930852 DOI: 10.1186/s12868-018-0426-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/18/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Auditory function and cochlear morphology have previously been described in a porcine model with spontaneous WS2-like phenotype. In the present study, cochlear histopathology was further investigated in the inner ear of the developing spontaneous deafness pig. RESULTS We found that the stria vascularis transformed into a complex tri-laminar tissue at embryonic 85 days (E85) in normal pigs, but not in the MITF-/- pigs. As the neural crest (NC) of cochlea was derived by melanocytes. MITF mutation caused failure of development of melanocytes which caused a subsequent collapse of cochlear duct and deficits of the epithelium after E100. Furthermore, the spiral ganglion neurons of cochlea in the MITF-/- pigs began to degenerate at postnatal 30 days (P30). Thus, our histopathological results indicated that the malformation of the stria vascularis was a primary defect in MITF-/- induced WT pigs which was resulted from the loss of NC-derived melanocytes. Subsequently, the cochleae underwent secondary degeneration of the vestibular organs. As the degeneration of spiral ganglion neurons happened after P30, it suggests that WS patients should be considered as candidates for cochlear implant. CONCLUSIONS Our porcine model of MITF-M mutation may provide a crucial animal model for cochlear implant, cell therapy in patients with congenital hereditary hearing loss.
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Affiliation(s)
- Wei Chen
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School,Ministry of Education, Beijng, China
| | - Qing-Qing Hao
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School,Ministry of Education, Beijng, China
| | - Li-Li Ren
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School,Ministry of Education, Beijng, China
| | - Wei Ren
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School,Ministry of Education, Beijng, China
| | - Hui-Sang Lin
- Department of Biotechnology, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Wei-Wei Guo
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School,Ministry of Education, Beijng, China.
| | - Shi-Ming Yang
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Key Laboratory of Hearing Impairment Science, Chinese PLA Medical School,Ministry of Education, Beijng, China.
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37
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Wang C, Wang X, Tang J, Chen H, Zhang J, Li Y, Lei S, Ji H, Yang B, Ren J, Ding N. Genome-wide association studies for two exterior traits in Chinese Dongxiang spotted pigs. Anim Sci J 2018; 89:868-875. [DOI: 10.1111/asj.13003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/11/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Chengbin Wang
- State Key Laboratory of Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; Nanchang China
| | - Xiaopeng Wang
- State Key Laboratory of Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; Nanchang China
| | - Jianhong Tang
- State Key Laboratory of Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; Nanchang China
| | - Hao Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; Nanchang China
| | - Junjie Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; Nanchang China
| | - Yiping Li
- State Key Laboratory of Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; Nanchang China
| | - Shengrong Lei
- National Conservation Farm of Dongxiang Spotted Pigs; Dongxiang China
| | - Huayuan Ji
- Institute of Animal Husbandry and Veterinary; Jiangxi Academy of Agricultural Science; Nanchang China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; Nanchang China
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; Nanchang China
| | - Nengshui Ding
- State Key Laboratory of Pig Genetic Improvement and Production Technology; Jiangxi Agricultural University; Nanchang China
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38
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A novel variant in MITF in a child from Yunnan-Guizhou Plateau with autosomal dominant inheritance of nonsyndromic hearing loss: A case report. Mol Med Rep 2018; 17:6054-6058. [PMID: 29484430 DOI: 10.3892/mmr.2018.8627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/02/2018] [Indexed: 11/05/2022] Open
Abstract
Deafness and hearing loss may have functional, economic, social and emotional impacts on humans, including the ability of an individual to communicate with others, feelings of isolation and frustration, and health sector costs. The World Health Organization reported that there are 32 million children worldwide with hearing loss. In order to investigate genetic mutations in children of 26 nationalities with hearing loss in Yunnan, Sanger sequencing was employed to screen for mutations in four of the most common pathological genes, including gap junction protein β2 and 3, solute carrier family 26 member 4 and mitochondrial DNA. Whole exome sequencing was used to detect the mutation in the proband of a family in which these four genes were normal. Subsequently, the mutation was identified by Sanger sequencing. The present study reports a novel mutation, c.718C>G; p. (Arg240Gly) in the melanogenesis associated transcription factor gene, in Han people with hearing loss. The results of the present study may provide parents and children an accurate diagnosis, which may allow physicians to how to rehabilitate children's hearing.
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39
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Hai T, Guo W, Yao J, Cao C, Luo A, Qi M, Wang X, Wang X, Huang J, Zhang Y, Zhang H, Wang D, Shang H, Hong Q, Zhang R, Jia Q, Zheng Q, Qin G, Li Y, Zhang T, Jin W, Chen ZY, Wang H, Zhou Q, Meng A, Wei H, Yang S, Zhao J. Creation of miniature pig model of human Waardenburg syndrome type 2A by ENU mutagenesis. Hum Genet 2017; 136:1463-1475. [PMID: 29094203 DOI: 10.1007/s00439-017-1851-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/22/2017] [Indexed: 02/08/2023]
Abstract
Human Waardenburg syndrome 2A (WS2A) is a dominant hearing loss (HL) syndrome caused by mutations in the microphthalmia-associated transcription factor (MITF) gene. In mouse models with MITF mutations, WS2A is transmitted in a recessive pattern, which limits the study of hearing loss (HL) pathology. In the current study, we performed ENU (ethylnitrosourea) mutagenesis that resulted in substituting a conserved lysine with a serine (p. L247S) in the DNA-binding domain of the MITF gene to generate a novel miniature pig model of WS2A. The heterozygous mutant pig (MITF +/L247S) exhibits a dominant form of profound HL and hypopigmentation in skin, hair, and iris, accompanied by degeneration of stria vascularis (SV), fused hair cells, and the absence of endocochlear potential, which indicate the pathology of human WS2A. Besides hypopigmentation and bilateral HL, the homozygous mutant pig (MITF L247S/L247S) and CRISPR/Cas9-mediated MITF bi-allelic knockout pigs both exhibited anophthalmia. Three WS2 patients carrying MITF mutations adjacent to the corresponding region were also identified. The pig models resemble the clinical symptom and molecular pathology of human WS2A patients perfectly, which will provide new clues for better understanding the etiology and development of novel treatment strategies for human HL.
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Affiliation(s)
- Tang Hai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Weiwei Guo
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jing Yao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Chunwei Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Ailing Luo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Meng Qi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xianlong Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Jiaojiao Huang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Hongyong Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Dayu Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Haitao Shang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, 400038, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qianlong Hong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Rui Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qitao Jia
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qiantao Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Guosong Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Yongshun Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Tao Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Weiwu Jin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Zheng-Yi Chen
- Department of Otolaryngology, Harvard Medical School and Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA, 02114, USA
| | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Chinese Swine Mutagenesis Consortium, Beijing, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Anming Meng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, 400038, China. .,Chinese Swine Mutagenesis Consortium, Beijing, China.
| | - Shiming Yang
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Jianguo Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,Chinese Swine Mutagenesis Consortium, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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40
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Hai T, Cao C, Shang H, Guo W, Mu Y, Yang S, Zhang Y, Zheng Q, Zhang T, Wang X, Liu Y, Kong Q, Li K, Wang D, Qi M, Hong Q, Zhang R, Wang X, Jia Q, Wang X, Qin G, Li Y, Luo A, Jin W, Yao J, Huang J, Zhang H, Li M, Xie X, Zheng X, Guo K, Wang Q, Zhang S, Li L, Xie F, Zhang Y, Weng X, Yin Z, Hu K, Cong Y, Zheng P, Zou H, Xin L, Xia J, Ruan J, Li H, Zhao W, Yuan J, Liu Z, Gu W, Li M, Wang Y, Wang H, Yang S, Liu Z, Wei H, Zhao J, Zhou Q, Meng A. Pilot study of large-scale production of mutant pigs by ENU mutagenesis. eLife 2017. [PMID: 28639938 PMCID: PMC5505698 DOI: 10.7554/elife.26248] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
N-ethyl-N-nitrosourea (ENU) mutagenesis is a powerful tool to generate mutants on a large scale efficiently, and to discover genes with novel functions at the whole-genome level in Caenorhabditis elegans, flies, zebrafish and mice, but it has never been tried in large model animals. We describe a successful systematic three-generation ENU mutagenesis screening in pigs with the establishment of the Chinese Swine Mutagenesis Consortium. A total of 6,770 G1 and 6,800 G3 pigs were screened, 36 dominant and 91 recessive novel pig families with various phenotypes were established. The causative mutations in 10 mutant families were further mapped. As examples, the mutation of SOX10 (R109W) in pig causes inner ear malfunctions and mimics human Mondini dysplasia, and upregulated expression of FBXO32 is associated with congenital splay legs. This study demonstrates the feasibility of artificial random mutagenesis in pigs and opens an avenue for generating a reservoir of mutants for agricultural production and biomedical research. DOI:http://dx.doi.org/10.7554/eLife.26248.001
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Affiliation(s)
- Tang Hai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Chunwei Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Haitao Shang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Weiwei Guo
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Yanshuang Mu
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Shulin Yang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qiantao Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Tao Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xianlong Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Yu Liu
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Qingran Kong
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Kui Li
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dayu Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Meng Qi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qianlong Hong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Rui Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xiupeng Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qitao Jia
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Guosong Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Yongshun Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Ailing Luo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Weiwu Jin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Jing Yao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Jiaojiao Huang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Hongyong Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Menghua Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xiangmo Xie
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Xuejuan Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Kenan Guo
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Qinghua Wang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Shibin Zhang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Liang Li
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Fei Xie
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Yu Zhang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Xiaogang Weng
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Zhi Yin
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Kui Hu
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Yimei Cong
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Peng Zheng
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Hailong Zou
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,College of Life Science, Northeast Agricultural University of China, Harbin, China
| | - Leilei Xin
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jihan Xia
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinxue Ruan
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hegang Li
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiming Zhao
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Yuan
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zizhan Liu
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiwang Gu
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Pearl Laboratory Animal Sci. & Tech. Co. Ltd, Guangzhou, China
| | - Ming Li
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Pearl Laboratory Animal Sci. & Tech. Co. Ltd, Guangzhou, China
| | - Yong Wang
- Chinese Swine Mutagenesis Consortium Working Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Shiming Yang
- Department of Otolaryngology-Head and Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University of China, Harbin, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medicine, Third Military Medical University, Chongqing, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Jianguo Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China
| | - Anming Meng
- Chinese Swine Mutagenesis Consortium Guide Group, Chinese Swine Mutagenesis Consortium, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
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41
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Chen W, Yi H, Zhang L, Ji F, Yuan S, Zhang Y, Ren L, Li J, Chen L, Guo W, Yang S. Establishing the standard method of cochlear implant in Rongchang pig. Acta Otolaryngol 2017; 137:503-510. [PMID: 28079462 DOI: 10.1080/00016489.2016.1267406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
CONCLUSIONS In this investigation, a large mammal, Rongchang pigs were used to successfully establish a research platform for cochlear implant study on the routine use of it in clinic. OBJECTIVE The aim of this study was to establish a standard method of cochlear implant in a large mammal-pig. METHODS Rongchang pigs were selected, then divided into two groups: normal-hearing group (Mitf +/+) and mutation group with hearing loss (Mitf -/-). Cochlear implants were used and ABR and EABR were recorded. The implanted electrodes were observed by X-ray and HE stains. RESULTS The success with cochlear implant and the best electrode position could be defined in all animals, the coiling of the cochlea reached 1.5-1.75 turns. Immediately after the operation of cochlear implants, the ABR threshold of the operated ear (right) could not be derived for each frequency at 120 dB SPL. Moreover, 7 days after surgery, the low-frequency ABR threshold of the operated ear (right) could be derived partly at 100 dB SPL, but the high-frequency ABR threshold could not be derived at 120 dB SPL. Immediately or 1 week after cochlear implants, the EABR threshold was 90 CL in the Mitf +/+ group. This was obviously lower than the 190 CL in the Mitf -/- group.
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Affiliation(s)
- Wei Chen
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, PR China
- Department of Otolaryngology, Chinese PLA General Hospital of Air Force, Beijing, PR China
| | - Haijin Yi
- Department of Otolaryngology, Head & Neck Surgery, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing, PR China
| | - Liang Zhang
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, PR China
| | - Fei Ji
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, PR China
| | - Shuolong Yuan
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, PR China
| | - Yue Zhang
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, PR China
| | - Lili Ren
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, PR China
| | - Jianan Li
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, PR China
| | - Lei Chen
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, PR China
| | - Weiwei Guo
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, PR China
| | - Shiming Yang
- Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, PR China
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42
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Sun J, Hao Z, Luo H, He C, Mei L, Liu Y, Wang X, Niu Z, Chen H, Li JD, Feng Y. Functional analysis of a nonstop mutation in MITF gene identified in a patient with Waardenburg syndrome type 2. J Hum Genet 2017; 62:703-709. [PMID: 28356565 PMCID: PMC5489919 DOI: 10.1038/jhg.2017.30] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/30/2017] [Accepted: 02/07/2017] [Indexed: 11/09/2022]
Abstract
Waardenburg syndrome (WS) is an autosomal dominant inherited neurogenic disorder with the combination of various degrees of sensorineural deafness and pigmentary abnormalities affecting the skin, hair and eye. The four subtypes of WS were defined on the basis of the presence or absence of additional symptoms. Mutation of human microphthalmia-associated transcription factor (MITF) gene gives rise to WS2. Here, we identified a novel WS-associated mutation at the stop codon of MITF (p.X420Y) in a Chinese WS2 patient. This mutation resulted in an extension of extra 33 amino-acid residues in MITF. The mutant MITF appeared in both the nucleus and the cytoplasm, whereas the wild-type MITF was localized in the nucleus exclusively. The mutation led to a reduction in the transcriptional activities, whereas the DNA-binding activity was not altered. We show that the foremost mechanism was haploinsufficiency for the mild phenotypes of WS2 induced in X420Y MITF.
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Affiliation(s)
- Jie Sun
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,Department of Otolaryngology, First Affiliated Hospital, Xinjiang Medical University, Xinjiang, People's Republic of China.,Province Key Laboratory of Otolaryngology Critical Disease, Xiangya Hospital, Central south University, Hunan, People's Republic of China
| | - Ziqi Hao
- Department of Center Laboratory, Taiyuan Central Hospital, Shanxi, People's Republic of China
| | - Hunjin Luo
- State Key Laboratory of Medical Genetics, Central South University, Hunan, People's Republic of China
| | - Chufeng He
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,Province Key Laboratory of Otolaryngology Critical Disease, Xiangya Hospital, Central south University, Hunan, People's Republic of China
| | - Lingyun Mei
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,Province Key Laboratory of Otolaryngology Critical Disease, Xiangya Hospital, Central south University, Hunan, People's Republic of China
| | - Yalan Liu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,Province Key Laboratory of Otolaryngology Critical Disease, Xiangya Hospital, Central south University, Hunan, People's Republic of China
| | - Xueping Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Zhijie Niu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China
| | - Hongsheng Chen
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China
| | - Jia-Da Li
- State Key Laboratory of Medical Genetics, Central South University, Hunan, People's Republic of China
| | - Yong Feng
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Hunan, People's Republic of China.,Province Key Laboratory of Otolaryngology Critical Disease, Xiangya Hospital, Central south University, Hunan, People's Republic of China.,Department of Center Laboratory, Taiyuan Central Hospital, Shanxi, People's Republic of China.,State Key Laboratory of Medical Genetics, Central South University, Hunan, People's Republic of China
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43
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Liu H, Li Y, Chen L, Zhang Q, Pan N, Nichols DH, Zhang WJ, Fritzsch B, He DZZ. Organ of Corti and Stria Vascularis: Is there an Interdependence for Survival? PLoS One 2016; 11:e0168953. [PMID: 28030585 PMCID: PMC5193441 DOI: 10.1371/journal.pone.0168953] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/08/2016] [Indexed: 01/08/2023] Open
Abstract
Cochlear hair cells and the stria vascularis are critical for normal hearing. Hair cells transduce mechanical stimuli into electrical signals, whereas the stria is responsible for generating the endocochlear potential (EP), which is the driving force for hair cell mechanotransduction. We questioned whether hair cells and the stria interdepend for survival by using two mouse models. Atoh1 conditional knockout mice, which lose all hair cells within four weeks after birth, were used to determine whether the absence of hair cells would affect function and survival of stria. We showed that stria morphology and EP remained normal for long time despite a complete loss of all hair cells. We then used a mouse model that has an abnormal stria morphology and function due to mutation of the Mitf gene to determine whether hair cells are able to survive and transduce sound signals without a normal electrochemical environment in the endolymph. A strial defect, reflected by missing intermediate cells in the stria and by reduction of EP, led to systematic outer hair cell death from the base to the apex after postnatal day 18. However, an 18-mV EP was sufficient for outer hair cell survival. Surprisingly, inner hair cell survival was less vulnerable to reduction of the EP. Our studies show that normal function of the stria is essential for adult outer hair cell survival, while the survival and normal function of the stria vascularis do not depend on functional hair cells.
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Affiliation(s)
- Huizhan Liu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Yi Li
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska, United States of America
- Department of Otorhinolaryngology, Beijing Tongren Hospital, Beijing Capital Medical University, Beijing, China
| | - Lei Chen
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska, United States of America
- Chongqing Academy of Animal Science, Chongqing, China
| | - Qian Zhang
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Ning Pan
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - David H. Nichols
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Weiping J. Zhang
- Department of Pathophysiology, Second Military Medical University, Shanghai, China
| | - Bernd Fritzsch
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - David Z. Z. He
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska, United States of America
- * E-mail:
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44
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Ma Y, Guo W, Yi H, Ren L, Zhao L, Zhang Y, Yuan S, Liu R, Xu L, Cong T, EK O, Zhai S, Yang S. Transplantation of human umbilical cord mesenchymal stem cells in cochlea to repair sensorineural hearing. Am J Transl Res 2016; 8:5235-5245. [PMID: 28077998 PMCID: PMC5209478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/25/2016] [Indexed: 06/06/2023]
Abstract
To examine if transplantation of human umbilical cord mesenchymal stem cells (UMSC) into cochlea can be used to repair sensorineural hearing. Here we transplanted the fifth and sixth generations of UMSCs through the subarachnoid cavity of congenital deaf albino pigs. Auditory brainstem responses (ABR) were measured before and after UMSC transplantation. Cochlear samples were collected at 2 hrs, 3 days, 1, 2, 3, 4 and 8 weeks after transplantation. Immunohistochemistry was used to detect the proliferated cell nuclear antigen (PCNA). The UMSCs were found in different regions of the cochlea, including the stria vascularis, the basal membrane and the spiral ganglions, 3 days to 4 weeks after the transplantation. UMSCs and their DNA were found also in the areas of the brain, the heart, the liver, the kidney and the lung. ABR tests displayed a new waveform in the congenital deaf albino pigs after the UMSCs transplantation. We conclude that human UMSCs injected into the subarachnoid space can migrate into the inner ear, the central nervous system and the periphery organs. The presence of UMSCs in the cochlea maybe associated with changes of ABR waveforms in the congenital deaf albino pigs.
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Affiliation(s)
- Yueying Ma
- Department of Otolaryngology, Head and Neck Surgery, Beijing Friendship Hospital, Capital Medical UniversityBeijing, China
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General HospitalBeijing, China
| | - Weiwei Guo
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General HospitalBeijing, China
| | - Haijin Yi
- Department of Otolaryngology, Head & Neck Surgery, Beijing Tsinghua Changgung Hospital, Medical center, Tsinghua University168# Litang Street, Changping District, Beijing, China
| | - Lili Ren
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General HospitalBeijing, China
| | - Lidong Zhao
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General HospitalBeijing, China
| | - Yue Zhang
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General HospitalBeijing, China
| | - Shuolong Yuan
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General HospitalBeijing, China
| | - Riyuan Liu
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General HospitalBeijing, China
| | - Liangwei Xu
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General HospitalBeijing, China
| | - Tao Cong
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General HospitalBeijing, China
| | - Oghagbon EK
- Department of Chemical Pathology, Faculty of Basic & Allied Medical Sciences, College of Heath Sciences, Benue State UniversityMakurdi, Nigeria
| | - Suoqiang Zhai
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General HospitalBeijing, China
| | - Shiming Yang
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General HospitalBeijing, China
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