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Giffen KP, Liu H, Yamane KL, Li Y, Chen L, Kramer KL, Zallocchi M, He DZZ. Molecular Specializations Underlying Phenotypic Differences in Inner Ear Hair Cells of Zebrafish and Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595729. [PMID: 38826418 PMCID: PMC11142236 DOI: 10.1101/2024.05.24.595729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Hair cells (HCs) are the sensory receptors of the auditory and vestibular systems in the inner ears of vertebrates that selectively transduce mechanical stimuli into electrical activity. Although all HCs have the hallmark stereocilia bundle for mechanotransduction, HCs in non-mammals and mammals differ in their molecular specialization in the apical, basolateral and synaptic membranes. HCs of non-mammals, such as zebrafish (zHCs), are electrically tuned to specific frequencies and possess an active process in the stereocilia bundle to amplify sound signals. Mammalian cochlear HCs, in contrast, are not electrically tuned and achieve amplification by somatic motility of outer HCs (OHCs). To understand the genetic mechanisms underlying differences among adult zebrafish and mammalian cochlear HCs, we compared their RNA-seq-characterized transcriptomes, focusing on protein-coding orthologous genes related to HC specialization. There was considerable shared expression of gene orthologs among the HCs, including those genes associated with mechanotransduction, ion transport/channels, and synaptic signaling. For example, both zebrafish and mouse HCs express Tmc1, Lhfpl5, Tmie, Cib2, Cacna1d, Cacnb2, Otof, Pclo and Slc17a8 . However, there were some notable differences in expression among zHCs, OHCs, and inner HCs (IHCs), which likely underlie the distinctive physiological properties of each cell type. Tmc2 and Cib3 were not detected in adult mouse HCs but tmc2a and b and cib3 were highly expressed in zHCs. Mouse HCs express Kcna10 , Kcnj13 , Kcnj16 , and Kcnq4 , which were not detected in zHCs. Chrna9 and Chrna10 were expressed in mouse HCs. In contrast, chrna10 was not detected in zHCs. OHCs highly express Slc26a5 which encodes the motor protein prestin that contributes to OHC electromotility. However, zHCs have only weak expression of slc26a5 , and subsequently showed no voltage dependent electromotility when measured. Notably, the zHCs expressed more paralogous genes including those associated with HC-specific functions and transcriptional activity, though it is unknown whether they have functions similar to their mammalian counterparts. There was overlap in the expressed genes associated with a known hearing phenotype. Our analyses unveil substantial differences in gene expression patterns that may explain phenotypic specialization of zebrafish and mouse HCs. This dataset also includes several protein-coding genes to further the functional characterization of HCs and study of HC evolution from non-mammals to mammals.
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Manori B, Vaknin A, Vaňková P, Nitzan A, Zaidel-Bar R, Man P, Giladi M, Haitin Y. Chloride intracellular channel (CLIC) proteins function as fusogens. Nat Commun 2024; 15:2085. [PMID: 38453905 PMCID: PMC10920813 DOI: 10.1038/s41467-024-46301-z] [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: 08/27/2023] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
Chloride Intracellular Channel (CLIC) family members uniquely transition between soluble and membrane-associated conformations. Despite decades of extensive functional and structural studies, CLICs' function as ion channels remains debated, rendering our understanding of their physiological role incomplete. Here, we expose the function of CLIC5 as a fusogen. We demonstrate that purified CLIC5 directly interacts with the membrane and induces fusion, as reflected by increased liposomal diameter and lipid and content mixing between liposomes. Moreover, we show that this activity is facilitated by acidic pH, a known trigger for CLICs' transition to a membrane-associated conformation, and that increased exposure of the hydrophobic inter-domain interface is crucial for this process. Finally, mutation of a conserved hydrophobic interfacial residue diminishes the fusogenic activity of CLIC5 in vitro and impairs excretory canal extension in C. elegans in vivo. Together, our results unravel the long-sought physiological role of these enigmatic proteins.
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Grants
- 1721/16 Israel Science Foundation (ISF)
- 1653/21 Israel Science Foundation (ISF)
- 3308/20 Israel Science Foundation (ISF)
- 01214 Israel Cancer Research Fund (Israel Cancer Research Fund, Inc.)
- 19202 Israel Cancer Research Fund (Israel Cancer Research Fund, Inc.)
- 20230029 Israel Cancer Association (ICA)
- CZ.1.05/1.1.00/02.0109 Ministerstvo školstva, vedy, výskumu a športu Slovenskej republiky (Ministry of Education, Science, Research and Sport of the Slovak Republic)
- 731077 EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- The Claire and Amedee Maratier Institute for the Study of Blindness and Visual Disorders, Faculty of Medicine, Tel-Aviv University.
- The Czech Infrastructure for Integrative Structural Biology (CIISB) grant (LM2023042).
- The Kahn Foundation's Orion project, Tel Aviv Sourasky Medical Center, Israel. The Claire and Amedee Maratier Institute for the Study of Blindness and Visual Disorders, Faculty of Medicine, Tel-Aviv University.
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Affiliation(s)
- Bar Manori
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | - Alisa Vaknin
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Pavla Vaňková
- Institute of Biotechnology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Anat Nitzan
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | - Ronen Zaidel-Bar
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | - Petr Man
- Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Moshe Giladi
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 6997801, Israel.
- Tel Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel.
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 6997801, Israel.
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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Loyo-Celis V, Patel D, Sanghvi S, Kaur K, Ponnalagu D, Zheng Y, Bindra S, Bhachu HR, Deschenes I, Gururaja Rao S, Singh H. Biophysical characterization of chloride intracellular channel 6 (CLIC6). J Biol Chem 2023; 299:105349. [PMID: 37838179 PMCID: PMC10641671 DOI: 10.1016/j.jbc.2023.105349] [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: 01/11/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/16/2023] Open
Abstract
Chloride intracellular channels (CLICs) are a family of proteins that exist in soluble and transmembrane forms. The newest discovered member of the family CLIC6 is implicated in breast, ovarian, lung gastric, and pancreatic cancers and is also known to interact with dopamine-(D(2)-like) receptors. The soluble structure of the channel has been resolved, but the exact physiological role of CLIC6, biophysical characterization, and the membrane structure remain unknown. Here, we aimed to characterize the biophysical properties of this channel using a patch-clamp approach. To determine the biophysical properties of CLIC6, we expressed CLIC6 in HEK-293 cells. On ectopic expression, CLIC6 localizes to the plasma membrane of HEK-293 cells. We established the biophysical properties of CLIC6 by using electrophysiological approaches. Using various anions and potassium (K+) solutions, we determined that CLIC6 is more permeable to chloride-(Cl-) as compared to bromide-(Br-), fluoride-(F-), and K+ ions. In the whole-cell configuration, the CLIC6 currents were inhibited after the addition of 10 μM of IAA-94 (CLIC-specific blocker). CLIC6 was also found to be regulated by pH and redox potential. We demonstrate that the histidine residue at 648 (H648) in the C terminus and cysteine residue in the N terminus (C487) are directly involved in the pH-induced conformational change and redox regulation of CLIC6, respectively. Using qRT-PCR, we identified that CLIC6 is most abundant in the lung and brain, and we recorded the CLIC6 current in mouse lung epithelial cells. Overall, we have determined the biophysical properties of CLIC6 and established it as a Cl- channel.
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Affiliation(s)
- Veronica Loyo-Celis
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Devendra Patel
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Shridhar Sanghvi
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio, USA; Department of Molecular Cellular and Developmental Biology, The Ohio State University, Columbus, Ohio, USA
| | - Kamalpreet Kaur
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Devasena Ponnalagu
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio, USA; Department of Pharmacology, The University of Washington, Seattle, Washington, USA
| | - Yang Zheng
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Sahej Bindra
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Harmeet Rireika Bhachu
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Isabelle Deschenes
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | | | - Harpreet Singh
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio, USA; Department of Molecular Cellular and Developmental Biology, The Ohio State University, Columbus, Ohio, USA.
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Ott E, Hoff S, Indorf L, Ditengou FA, Müller J, Renschler G, Lienkamp SS, Kramer-Zucker A, Bergmann C, Epting D. A novel role for the chloride intracellular channel protein Clic5 in ciliary function. Sci Rep 2023; 13:17647. [PMID: 37848494 PMCID: PMC10582032 DOI: 10.1038/s41598-023-44235-y] [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: 12/05/2022] [Accepted: 10/05/2023] [Indexed: 10/19/2023] Open
Abstract
CLIC5 belongs to a family of ion channels with six members reported so far. In vertebrates, the CLIC5 gene encodes two different isoforms, CLIC5A and CLIC5B. In addition to its ion channel activity, there is evidence for further functions of CLIC5A, such as the remodeling of the actin cytoskeleton during the formation of a functional glomerulus in the vertebrate kidney. However, its specific role is still incompletely understood and a specific functional role for CLIC5B has not been described yet. Here we report our findings on the differential expression and functions of Clic5a and Clic5b during zebrafish kidney development. Whole-mount in situ hybridization studies revealed specific expression of clic5a in the eye and pronephric glomerulus, and clic5b is expressed in the gut, liver and the pronephric tubules. Clic5 immunostainings revealed that Clic5b is localized in the cilia. Whereas knockdown of Clic5a resulted in leakiness of the glomerular filtration barrier, Clic5b deficient embryos displayed defective ciliogenesis, leading to ciliopathy-associated phenotypes such as ventral body curvature, otolith deposition defects, altered left-right asymmetry and formation of hydrocephalus and pronephric cysts. In addition, Clic5 deficiency resulted in dysregulation of cilia-dependent Wnt signalling pathway components. Mechanistically, we identified a Clic5-dependent activation of the membrane-cytoskeletal linker proteins Ezrin/Radixin/Moesin (ERM) in the pronephric tubules of zebrafish. In conclusion, our in vivo data demonstrates a novel role for Clic5 in regulating essential ciliary functions and identified Clic5 as a positive regulator of ERM phosphorylation.
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Affiliation(s)
- Elisabeth Ott
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106, Freiburg, Germany
| | - Sylvia Hoff
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106, Freiburg, Germany
| | - Lara Indorf
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106, Freiburg, Germany
| | - Franck Anicet Ditengou
- Bio Imaging Core Light Microscopy (BiMiC), Medical Faculty-Institute for Disease Modeling and Targeted Medicine (IMITATE), 79106, Freiburg, Germany
| | - Julius Müller
- Limbach Genetics, Medizinische Genetik Mainz, 55128, Mainz, Germany
| | - Gina Renschler
- Limbach Genetics, Medizinische Genetik Mainz, 55128, Mainz, Germany
| | - Soeren S Lienkamp
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106, Freiburg, Germany
- Center for Biological Signaling Studies (BIOSS), 79104, Freiburg, Germany
| | - Albrecht Kramer-Zucker
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106, Freiburg, Germany
| | - Carsten Bergmann
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106, Freiburg, Germany
- Limbach Genetics, Medizinische Genetik Mainz, 55128, Mainz, Germany
| | - Daniel Epting
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106, Freiburg, Germany.
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Alghalayini A, Hossain KR, Moghaddasi S, Turkewitz DR, D’Amario C, Wallach M, Valenzuela SM. In Vitro Enzymatic Studies Reveal pH and Temperature Sensitive Properties of the CLIC Proteins. Biomolecules 2023; 13:1394. [PMID: 37759794 PMCID: PMC10526857 DOI: 10.3390/biom13091394] [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: 08/30/2023] [Revised: 09/09/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Chloride intracellular ion channel (CLIC) proteins exist as both soluble and integral membrane proteins, with CLIC1 capable of shifting between two distinct structural conformations. New evidence has emerged indicating that members of the CLIC family act as moonlighting proteins, referring to the ability of a single protein to carry out multiple functions. In addition to their ion channel activity, CLIC family members possess oxidoreductase enzymatic activity and share significant structural and sequence homology, along with varying overlaps in their tissue distribution and cellular localization. In this study, the 2-hydroxyethyl disulfide (HEDS) assay system was used to characterize kinetic properties, as well as the temperature and pH profiles of three CLIC protein family members (CLIC1, CLIC3, CLIC4). We also assessed the effects of the drugs rapamycin and amphotericin B, on the three CLIC proteins' enzymatic activity in the HEDS assay. Our results demonstrate CLIC1 to be highly heat-sensitive, with optimal enzymatic activity observed at neutral pH7 and at a temperature of 37 °C, while CLIC3 had higher oxidoreductase activity in more acidic pH5 and was found to be relatively heat stable. CLIC4, like CLIC1, was temperature sensitive with optimal enzymatic activity observed at 37 °C; however, it showed optimal activity in more alkaline conditions of pH8. Our current study demonstrates individual differences in the enzymatic activity between the three CLIC proteins, suggesting each CLIC protein is likely regulated in discrete ways, involving changes in the subcellular milieu and microenvironment.
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Affiliation(s)
- Amani Alghalayini
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia; (A.A.); (K.R.H.); (S.M.); (D.R.T.); (C.D.); (M.W.)
- ARC Research Hub for Integrated Device for End-User Analysis at Low-Levels (IDEAL), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Khondker Rufaka Hossain
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia; (A.A.); (K.R.H.); (S.M.); (D.R.T.); (C.D.); (M.W.)
- ARC Research Hub for Integrated Device for End-User Analysis at Low-Levels (IDEAL), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Saba Moghaddasi
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia; (A.A.); (K.R.H.); (S.M.); (D.R.T.); (C.D.); (M.W.)
| | - Daniel R. Turkewitz
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia; (A.A.); (K.R.H.); (S.M.); (D.R.T.); (C.D.); (M.W.)
| | - Claudia D’Amario
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia; (A.A.); (K.R.H.); (S.M.); (D.R.T.); (C.D.); (M.W.)
| | - Michael Wallach
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia; (A.A.); (K.R.H.); (S.M.); (D.R.T.); (C.D.); (M.W.)
| | - Stella M. Valenzuela
- School of Life Sciences, University of Technology Sydney, Sydney, NSW 2007, Australia; (A.A.); (K.R.H.); (S.M.); (D.R.T.); (C.D.); (M.W.)
- ARC Research Hub for Integrated Device for End-User Analysis at Low-Levels (IDEAL), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
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6
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Huang Q, Lv Q, Tang W, Pan Y, Xing Y, He M, Wu H, Huang J, Huang C, Lan H, Chen J, Xiao G. A comprehensively prognostic and immunological analysis of chloride intracellular channel protein 5 (CLIC5) in pan-cancer and identification in ovarian cancer. J Cancer Res Clin Oncol 2023; 149:10561-10583. [PMID: 37286734 DOI: 10.1007/s00432-023-04927-4] [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: 03/21/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023]
Abstract
CLIC5 encoded protein associates with actin-based cytoskeletal and is increasingly thought to play significant roles in human cancers. We use TCGA and GEO to explore CLIC5 expression differences, mutation and DNA methylation, TMB, MSI, and immune cell infiltration. We verified the mRNA expression of CLIC5 in human ovarian cancer cells by real-time PCR and detected the expression of CLIC5 as well as immune marker genes in ovarian cancer by immunohistochemistry. The pan-cancer analysis showed that CLIC5 is highly expressed in several malignant tumors. In some cancers, CLIC5 expression in tumor samples is associated with poorer overall survival. For example, patients with ovarian cancer with high expression of CLIC5 have a poor prognosis. CLIC5 mutation frequency increased in all tumor types. The CLIC5 promoter is hypomethylated in most tumors. CLIC5 was associated with tumor immunity and different immune cells of different tumor types, such as CD8 + T cells, tumor-associated fibroblasts, macrophages, etc. CLIC5 was positively correlated with various immune checkpoints, and TMB and MSI were correlated with dysregulation of CLIC5 in tumors. The expression of CLIC5 in ovarian cancer was detected by qPCR and IHC, and the results were consistent with the bioinformatics results. There were a strong positive correlation between CLIC5 expression and M2 macrophage (CD163) infiltration and a negative correlation with CD8 + T-cell infiltration. In conclusions, our first pan-cancer analysis offered a detailed grasp of the cancerogenic functions of CLIC5 in a variety of malignancies. CLIC5 participated in immunomodulation and performed a crucial function in the tumor microenvironment.
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Affiliation(s)
- Qiaoling Huang
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
- Central Laboratory, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Quankun Lv
- Emergency Department, the Sixth Affiliated Hospital, South China University of Technology, Foshan, 528000, Guangdong, People's Republic of China
| | - Waner Tang
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
- Central Laboratory, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Yuhua Pan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Yue Xing
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, 510120, Guangdong, People's Republic of China
| | - Min He
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Huiyi Wu
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Jiamin Huang
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Che Huang
- Hubei University of Medicine, Shiyan, 442000, China
| | - Haifeng Lan
- Department of Orthopaedic Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, People's Republic of China
| | - Jingqi Chen
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China.
- Oncology Department, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China.
| | - Guohong Xiao
- Translational Medicine Center, Guangzhou Key Laboratory for Research and Development of Nano-Biomedical Technology for Diagnosis and Therapy and Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, Department of Gynecology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, Guangdong, People's Republic of China.
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Zhang L, Chen X, Yao S, Zheng L, Yang X, Wang Y, Li X, Wu E, Tuo B. Intracellular chloride channel 1 and tumor. Am J Cancer Res 2023; 13:3300-3314. [PMID: 37693147 PMCID: PMC10492100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/08/2023] [Indexed: 09/12/2023] Open
Abstract
As the major intracellular anion, chloride plays an important role in maintaining intracellular and extracellular ion homeostasis, osmotic pressure, and cell volume. Intracellular chloride channel 1, which has the physiological role of forming membrane proteins in the lipid bilayer and playing ion channels, is a hot research topic in recent years. It has been found that CLIC1 does not only act as an ion channel but also participates in cell cycle regulation, apoptosis, and intracellular oxidation; thus, it participates in the proliferation, invasion, and migration of various tumor cells in various systems throughout the body. At the same time, CLIC1 is highly expressed in tumor cells and is associated with malignancy and a poor prognosis. This paper reviews the pathological mechanisms of CLIC1 in systemic diseases, which is important for the early diagnosis, treatment, and prognosis of systemic diseases associated with CLIC1 expression.
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Affiliation(s)
- Li Zhang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical UniversityZunyi, Guizhou, China
| | - Xingyue Chen
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical UniversityZunyi, Guizhou, China
| | - Shun Yao
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical UniversityZunyi, Guizhou, China
| | - Liming Zheng
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical UniversityZunyi, Guizhou, China
| | - Xingyue Yang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical UniversityZunyi, Guizhou, China
| | - Yongfeng Wang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical UniversityZunyi, Guizhou, China
| | - Xin Li
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical UniversityZunyi, Guizhou, China
| | - Enqin Wu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical UniversityZunyi, Guizhou, China
| | - Biguang Tuo
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical UniversityZunyi, Guizhou, China
- The Collaborative Innovation Center of Tissue Damage Repair and Regenerative Medicine of Zunyi Medical UniversityZunyi, Guizhou, China
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8
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Li J, Liu C, Müller U, Zhao B. RIPOR2-mediated autophagy dysfunction is critical for aminoglycoside-induced hearing loss. Dev Cell 2022; 57:2204-2220.e6. [PMID: 36113482 PMCID: PMC9529990 DOI: 10.1016/j.devcel.2022.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/25/2022] [Accepted: 08/23/2022] [Indexed: 01/18/2023]
Abstract
Aminoglycosides (AGs) are potent antibiotics that are capable of treating a wide variety of life-threatening infections; however, they are ototoxic and cause irreversible damage to cochlear hair cells. Despite substantial progress, little is known about the molecular pathways critical for hair cell function and survival that are affected by AG exposure. We demonstrate here that gentamicin, a representative AG antibiotic, binds to and within minutes triggers translocation of RIPOR2 in murine hair cells from stereocilia to the pericuticular area. Then, by interacting with a central autophagy component, GABARAP, RIPOR2 affects autophagy activation. Reducing the expression of RIPOR2 or GABARAP completely prevents AG-induced hair cell death and subsequent hearing loss in mice. Additionally, abolishing the expression of PINK1 or Parkin, two key mitochondrial autophagy proteins, prevents hair cell death and subsequent hearing loss caused by AG. In summary, our study demonstrates that RIPOR2-mediated autophagic dysfunction is essential for AG-induced hearing loss.
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Affiliation(s)
- Jinan Li
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Chang Liu
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ulrich Müller
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bo Zhao
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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Adadey SM, Wonkam-Tingang E, Alves de Souza Rios L, Aboagye ET, Esoh K, Manyisa N, De Kock C, Awandare GA, Mowla S, Wonkam A. Cell-based analysis of CLIC5A and SLC12A2 variants associated with hearing impairment in two African families. Front Genet 2022; 13:924904. [PMID: 36035115 PMCID: PMC9403182 DOI: 10.3389/fgene.2022.924904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/18/2022] [Indexed: 01/18/2023] Open
Abstract
We have previously reported CLIC5A and SLC12A2 variants in two families from Cameroon and Ghana, segregating non-syndromic hearing impairment (NSHI). In this study, biological assays were performed to further functionally investigate the pathogenicity of CLIC5 [c.224T>C; p.(L75P)] and SCL12A2 [c.2935G>A: p.(E979K)] variants. Ectopic expression of the proteins in a cell model shows that compared to wild-type, both the CLIC5A and SLC12A2 variants were overexpressed. The mutant CLIC5A protein appears as aggregated perinuclear bodies while the wild-type protein was evenly distributed in the cytoplasm. Furthermore, cells transfected with the wild-type CLIC5A formed thin membrane filopodia-like protrusions which were absent in the CLIC5A mutant expressing and control cells. On the other hand, the wild-type SLC12A2 expressing cells had an axon-like morphology which was not observed in the mutant expressing and control cells. A network analysis revealed that CLIC5A can interact with at least eight proteins at the base of the stereocilia. This study has generated novel biological data associated with the pathogenicity of targeted variants in CLIC5A and SLC12A2, found in two African families, and therefore expands our understanding of their pathobiology in hearing impairment.
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Affiliation(s)
- Samuel Mawuli Adadey
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Edmond Wonkam-Tingang
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Leonardo Alves de Souza Rios
- Department of Pathology, Division of Haematology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Elvis Twumasi Aboagye
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Kevin Esoh
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Noluthando Manyisa
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Carmen De Kock
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gordon A. Awandare
- Department of Biochemistry, Cell, and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Shaheen Mowla
- Department of Pathology, Division of Haematology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Ambroise Wonkam
- Department of Pathology, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- McKusick-Nathans Institute and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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10
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Miller KK, Atkinson P, Mendoza KR, Ó Maoiléidigh D, Grillet N. Dimensions of a Living Cochlear Hair Bundle. Front Cell Dev Biol 2021; 9:742529. [PMID: 34900993 PMCID: PMC8657763 DOI: 10.3389/fcell.2021.742529] [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: 07/16/2021] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
The hair bundle is the mechanosensory organelle of hair cells that detects mechanical stimuli caused by sounds, head motions, and fluid flows. Each hair bundle is an assembly of cellular-protrusions called stereocilia, which differ in height to form a staircase. Stereocilia have different heights, widths, and separations in different species, sensory organs, positions within an organ, hair-cell types, and even within a single hair bundle. The dimensions of the stereociliary assembly dictate how the hair bundle responds to stimuli. These hair-bundle properties have been measured previously only to a limited degree. In particular, mammalian data are either incomplete, lack control for age or position within an organ, or have artifacts owing to fixation or dehydration. Here, we provide a complete set of measurements for postnatal day (P) 11 C57BL/6J mouse apical inner hair cells (IHCs) obtained from living tissue, tissue mildly-fixed for fluorescent imaging, or tissue strongly fixed and dehydrated for scanning electronic microscopy (SEM). We found that hair bundles mildly-fixed for fluorescence had the same dimensions as living hair bundles, whereas SEM-prepared hair bundles shrank uniformly in stereociliary heights, widths, and separations. By determining the shrinkage factors, we imputed live dimensions from SEM that were too small to observe optically. Accordingly, we created the first complete blueprint of a living IHC hair bundle. We show that SEM-prepared measurements strongly affect calculations of a bundle’s mechanical properties – overestimating stereociliary deflection stiffness and underestimating the fluid coupling between stereocilia. The methods of measurement, the data, and the consequences we describe illustrate the high levels of accuracy and precision required to understand hair-bundle mechanotransduction.
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Affiliation(s)
- Katharine K Miller
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Stanford University, Stanford, CA, United States
| | - Patrick Atkinson
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Stanford University, Stanford, CA, United States
| | - Kyssia Ruth Mendoza
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Stanford University, Stanford, CA, United States
| | - Dáibhid Ó Maoiléidigh
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Stanford University, Stanford, CA, United States
| | - Nicolas Grillet
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Stanford University, Stanford, CA, United States
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11
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Mackowetzky K, Yoon KH, Mackowetzky EJ, Waskiewicz AJ. Development and evolution of the vestibular apparatuses of the inner ear. J Anat 2021; 239:801-828. [PMID: 34047378 PMCID: PMC8450482 DOI: 10.1111/joa.13459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/07/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
The vertebrate inner ear is a labyrinthine sensory organ responsible for perceiving sound and body motion. While a great deal of research has been invested in understanding the auditory system, a growing body of work has begun to delineate the complex developmental program behind the apparatuses of the inner ear involved with vestibular function. These animal studies have helped identify genes involved in inner ear development and model syndromes known to include vestibular dysfunction, paving the way for generating treatments for people suffering from these disorders. This review will provide an overview of known inner ear anatomy and function and summarize the exciting discoveries behind inner ear development and the evolution of its vestibular apparatuses.
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Affiliation(s)
- Kacey Mackowetzky
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Kevin H. Yoon
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Andrew J. Waskiewicz
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Women & Children’s Health Research InstituteUniversity of AlbertaEdmontonAlbertaCanada
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12
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Mao QY, Xie S, Wu LL, Xiang RL, Cai ZG. MicroRNA-mRNA expression profiles and functional network after injection of botulinum toxin type A into submandibular glands. Toxicon 2021; 199:31-40. [PMID: 34052235 DOI: 10.1016/j.toxicon.2021.05.011] [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: 02/16/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 11/28/2022]
Abstract
Botulinum toxin type A (BTXA) is effective for the treatment of sialorrhea. MicroRNAs (miRNAs) have significant functions in salivary diseases, but the role of miRNAs during BTXA-inhibited salivary secretion is not yet clear. A total of 19 differentially expressed (DE) miRNAs and 1072 DE mRNAs were identified following BTXA injected into submandibular glands of rats (n = 4) through miRNA sequencing and microarray analysis. Bioinformatic analysis identified that several pathways may be associated with the inhibition of salivary secretion, such as the MAPK signalling pathway, tight junctions, and cytokine-cytokine receptor interaction. We predicted the target genes of DE miRNAs and established the miRNA-mRNA interaction network. The intersection of DE mRNAs and target genes of DE miRNAs was performed and seven mRNAs were obtained: Egr2, Paqr9, Zkscan1, Usp6n, Cyb561a3, Zfhx4, and Clic5. These findings explore the mechanism of BTXA in inhibiting salivary secretion and probably will provide new ideas for clinical application.
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Affiliation(s)
- Qian-Ying Mao
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Shang Xie
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Li-Ling Wu
- Department of Physiology and Pathophysiology, Peking University School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing, 100191, China
| | - Ruo-Lan Xiang
- Department of Physiology and Pathophysiology, Peking University School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing, 100191, China.
| | - Zhi-Gang Cai
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, China.
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13
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Li J, Liu C, Zhao B. N-Terminus of GRXCR2 Interacts With CLIC5 and Is Essential for Auditory Perception. Front Cell Dev Biol 2021; 9:671364. [PMID: 34026762 PMCID: PMC8131845 DOI: 10.3389/fcell.2021.671364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/13/2021] [Indexed: 11/17/2022] Open
Abstract
Stereocilia of cochlear hair cells are specialized mechanosensing organelles that convert sound-induced vibration to electrical signals. Glutaredoxin domain-containing cysteine-rich protein 2 (GRXCR2) is localized at the base of stereocilia and is necessary for stereocilia morphogenesis and auditory perception. However, the detailed functions of GRXCR2 in hair cells are still largely unknown. Here, we report that GRXCR2 interacts with chloride intracellular channel protein 5 (CLIC5) which is also localized at the base of stereocilia and required for normal hearing in human and mouse. Immunolocalization analyses suggest that GRXCR2 is not required for the localization of CLIC5 to the stereociliary base during development, or vice versa. Using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, we deleted 60 amino acids near the N-terminus of GRXCR2 essential for its interaction with CLIC5. Interestingly, mice harboring this in-frame deletion in Grxcr2 exhibit moderate hearing loss at lower frequencies and severe hearing loss at higher frequencies although the morphogenesis of stereocilia is minimally affected. Thus, our findings reveal that the interaction between GRXCR2 and CLIC5 is crucial for normal hearing.
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Affiliation(s)
- Jinan Li
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Chang Liu
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Bo Zhao
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
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14
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Radixin modulates the function of outer hair cell stereocilia. Commun Biol 2020; 3:792. [PMID: 33361775 PMCID: PMC7758333 DOI: 10.1038/s42003-020-01506-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 11/18/2020] [Indexed: 01/07/2023] Open
Abstract
The stereocilia of the inner ear sensory cells contain the actin-binding protein radixin, encoded by RDX. Radixin is important for hearing but remains functionally obscure. To determine how radixin influences hearing sensitivity, we used a custom rapid imaging technique to visualize stereocilia motion while measuring electrical potential amplitudes during acoustic stimulation. Radixin inhibition decreased sound-evoked electrical potentials. Other functional measures, including electrically induced sensory cell motility and sound-evoked stereocilia deflections, showed a minor amplitude increase. These unique functional alterations demonstrate radixin as necessary for conversion of sound into electrical signals at acoustic rates. We identified patients with RDX variants with normal hearing at birth who showed rapidly deteriorating hearing during the first months of life. This may be overlooked by newborn hearing screening and explained by multiple disturbances in postnatal sensory cells. We conclude radixin is necessary for ensuring normal conversion of sound to electrical signals in the inner ear. Sonal Prasad et al. identify several mutations in the radixin (RDX) gene that are associated with early-life hearing loss. Using a guinea pig model, they propose that radixin helps convert sound into electrical signals in the mature inner ear.
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15
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Abstract
The delivery of therapies to the cochlea is notoriously challenging. It is an organ protected by a number of barriers that need to be overcome in the drug delivery process. Additionally, there are multiple sites of possible damage within the cochlea. Despite the many potential sites of damage, acquired otologic insults preferentially damage a single location. While progress has been made in techniques for inner ear drug delivery, the current techniques remain non-specific and our ability to deliver therapies in a cell-specific manner are limited. Fortunately, there are proteins specific to various cell-types within the cochlea (e.g., hair cells, spiral ganglion cells, stria vascularis) that function as biomarkers of site-specific damage. These protein biomarkers have potential to serve as targets for cell-specific inner ear drug delivery. In this manuscript, we review the concept of biomarkers and targeted- inner ear drug delivery and the well-characterized protein biomarkers within each of the locations of interest within the cochlea. Our review will focus on targeted drug delivery in the setting of acquired otologic insults (e.g., ototoxicity, noise-induce hearing loss). The goal is not to discuss therapies to treat acquired otologic insults, rather, to establish potential concepts of how to deliver therapies in a targeted, cell-specific manner. Based on our review, it is clear that future of inner ear drug delivery is a discipline filled with potential that will require collaborative efforts among clinicians and scientists to optimize treatment of otologic insults. Graphical Abstract ![]()
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16
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Wonkam-Tingang E, Schrauwen I, Esoh KK, Bharadwaj T, Nouel-Saied LM, Acharya A, Nasir A, Adadey SM, Mowla S, Leal SM, Wonkam A. Bi-Allelic Novel Variants in CLIC5 Identified in a Cameroonian Multiplex Family with Non-Syndromic Hearing Impairment. Genes (Basel) 2020; 11:genes11111249. [PMID: 33114113 PMCID: PMC7690789 DOI: 10.3390/genes11111249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
DNA samples from five members of a multiplex non-consanguineous Cameroonian family, segregating prelingual and progressive autosomal recessive non-syndromic sensorineural hearing impairment, underwent whole exome sequencing. We identified novel bi-allelic compound heterozygous pathogenic variants in CLIC5. The variants identified, i.e., the missense [NM_016929.5:c.224T>C; p.(L75P)] and the splicing (NM_016929.5:c.63+1G>A), were validated using Sanger sequencing in all seven available family members and co-segregated with hearing impairment (HI) in the three hearing impaired family members. The three affected individuals were compound heterozygous for both variants, and all unaffected individuals were heterozygous for one of the two variants. Both variants were absent from the genome aggregation database (gnomAD), the Single Nucleotide Polymorphism Database (dbSNP), and the UK10K and Greater Middle East (GME) databases, as well as from 122 apparently healthy controls from Cameroon. We also did not identify these pathogenic variants in 118 unrelated sporadic cases of non-syndromic hearing impairment (NSHI) from Cameroon. In silico analysis showed that the missense variant CLIC5-p.(L75P) substitutes a highly conserved amino acid residue (leucine), and is expected to alter the stability, the structure, and the function of the CLIC5 protein, while the splicing variant CLIC5-(c.63+1G>A) is predicted to disrupt a consensus donor splice site and alter the splicing of the pre-mRNA. This study is the second report, worldwide, to describe CLIC5 involvement in human hearing impairment, and thus confirms CLIC5 as a novel non-syndromic hearing impairment gene that should be included in targeted diagnostic gene panels.
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Affiliation(s)
- Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Kevin K. Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Liz M. Nouel-Saied
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Anushree Acharya
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea;
| | - Samuel M. Adadey
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra LG 54, Ghana
| | - Shaheen Mowla
- Division of Haematology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa;
| | - Suzanne M. Leal
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer’s Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA; (I.S.); (T.B.); (L.M.N.-S.); (A.A.); (S.M.L.)
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (E.W.-T.); (K.K.E.); (S.M.A.)
- Correspondence: ; Tel.: +27-21-4066-307
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17
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How Dysregulated Ion Channels and Transporters Take a Hand in Esophageal, Liver, and Colorectal Cancer. Rev Physiol Biochem Pharmacol 2020; 181:129-222. [PMID: 32875386 DOI: 10.1007/112_2020_41] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Over the last two decades, the understanding of how dysregulated ion channels and transporters are involved in carcinogenesis and tumor growth and progression, including invasiveness and metastasis, has been increasing exponentially. The present review specifies virtually all ion channels and transporters whose faulty expression or regulation contributes to esophageal, hepatocellular, and colorectal cancer. The variety reaches from Ca2+, K+, Na+, and Cl- channels over divalent metal transporters, Na+ or Cl- coupled Ca2+, HCO3- and H+ exchangers to monocarboxylate carriers and organic anion and cation transporters. In several cases, the underlying mechanisms by which these ion channels/transporters are interwoven with malignancies have been fully or at least partially unveiled. Ca2+, Akt/NF-κB, and Ca2+- or pH-dependent Wnt/β-catenin signaling emerge as cross points through which ion channels/transporters interfere with gene expression, modulate cell proliferation, trigger epithelial-to-mesenchymal transition, and promote cell motility and metastasis. Also miRs, lncRNAs, and DNA methylation represent potential links between the misexpression of genes encoding for ion channels/transporters, their malfunctioning, and cancer. The knowledge of all these molecular interactions has provided the basis for therapeutic strategies and approaches, some of which will be broached in this review.
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18
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Ferofontov A, Vankova P, Man P, Giladi M, Haitin Y. Conserved cysteine dioxidation enhances membrane interaction of human Cl - intracellular channel 5. FASEB J 2020; 34:9925-9940. [PMID: 32725932 DOI: 10.1096/fj.202000399r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/21/2020] [Accepted: 04/30/2020] [Indexed: 11/11/2022]
Abstract
The human chloride intracellular channel (hCLIC) family is thought to transition between globular and membrane-associated forms by exposure of a hydrophobic surface. However, the molecular identity of this surface, and the triggering events leading to its exposure, remain elusive. Here, by combining biochemical and structural approaches, together with mass spectrometry (MS) analyses, we show that hCLIC5 is inherently flexible. X-ray crystallography revealed the existence of a globular conformation, while small-angle X-ray scattering showed additional elongated forms consisting of exposure of the conserved hydrophobic inter-domain interface to the bulk phase. Tryptophan fluorescence measurements demonstrated that the transition to the membrane-associated form is enhanced by the presence of oxidative environment and lipids. Using MS, we identified a dose-dependent oxidation of a highly conserved cysteine residue, known to play a key role in the structurally related omega-class of glutathione-S-transferases. Hydrogen/deuterium exchange MS analysis revealed that oxidation of this cysteine facilitates the exposure of the conserved hydrophobic inter-domain interface. Together, our results pinpoint an oxidation of a specific cysteine residue as a triggering mechanism initializing the molecular commitment for membrane interaction in the CLIC family.
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Affiliation(s)
- Alisa Ferofontov
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Pavla Vankova
- Division BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Man
- Division BioCeV, Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Moshe Giladi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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19
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de Bruijn SE, Smits JJ, Liu C, Lanting CP, Beynon AJ, Blankevoort J, Oostrik J, Koole W, de Vrieze E, Cremers CWRJ, Cremers FPM, Roosing S, Yntema HG, Kunst HPM, Zhao B, Pennings RJE, Kremer H. A RIPOR2 in-frame deletion is a frequent and highly penetrant cause of adult-onset hearing loss. J Med Genet 2020; 58:jmedgenet-2020-106863. [PMID: 32631815 PMCID: PMC8120656 DOI: 10.1136/jmedgenet-2020-106863] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/25/2020] [Accepted: 04/01/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Hearing loss is one of the most prevalent disabilities worldwide, and has a significant impact on quality of life. The adult-onset type of the condition is highly heritable but the genetic causes are largely unknown, which is in contrast to childhood-onset hearing loss. METHODS Family and cohort studies included exome sequencing and characterisation of the hearing phenotype. Ex vivo protein expression addressed the functional effect of a DNA variant. RESULTS An in-frame deletion of 12 nucleotides in RIPOR2 was identified as a highly penetrant cause of adult-onset progressive hearing loss that segregated as an autosomal dominant trait in 12 families from the Netherlands. Hearing loss associated with the deletion in 63 subjects displayed variable audiometric characteristics and an average (SD) age of onset of 30.6 (14.9) years (range 0-70 years). A functional effect of the RIPOR2 variant was demonstrated by aberrant localisation of the mutant RIPOR2 in the stereocilia of cochlear hair cells and failure to rescue morphological defects in RIPOR2-deficient hair cells, in contrast to the wild-type protein. Strikingly, the RIPOR2 variant is present in 18 of 22 952 individuals not selected for hearing loss in the Southeast Netherlands. CONCLUSION Collectively, the presented data demonstrate that an inherited form of adult-onset hearing loss is relatively common, with potentially thousands of individuals at risk in the Netherlands and beyond, which makes it an attractive target for developing a (genetic) therapy.
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Affiliation(s)
- Suzanne E de Bruijn
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Jeroen J Smits
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Chang Liu
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Cornelis P Lanting
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Andy J Beynon
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | | | - Jaap Oostrik
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Wouter Koole
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
| | - Erik de Vrieze
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Cor W R J Cremers
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Henricus P M Kunst
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
- Radboud Institute for Health Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Bo Zhao
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ronald J E Pennings
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - Hannie Kremer
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
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20
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Li J, Zhang T, Ramakrishnan A, Fritzsch B, Xu J, Wong EYM, Loh YHE, Ding J, Shen L, Xu PX. Dynamic changes in cis-regulatory occupancy by Six1 and its cooperative interactions with distinct cofactors drive lineage-specific gene expression programs during progressive differentiation of the auditory sensory epithelium. Nucleic Acids Res 2020; 48:2880-2896. [PMID: 31956913 PMCID: PMC7102962 DOI: 10.1093/nar/gkaa012] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/16/2019] [Accepted: 01/17/2020] [Indexed: 12/23/2022] Open
Abstract
The transcription factor Six1 is essential for induction of sensory cell fate and formation of auditory sensory epithelium, but how it activates gene expression programs to generate distinct cell-types remains unknown. Here, we perform genome-wide characterization of Six1 binding at different stages of auditory sensory epithelium development and find that Six1-binding to cis-regulatory elements changes dramatically at cell-state transitions. Intriguingly, Six1 pre-occupies enhancers of cell-type-specific regulators and effectors before their expression. We demonstrate in-vivo cell-type-specific activity of Six1-bound novel enhancers of Pbx1, Fgf8, Dusp6, Vangl2, the hair-cell master regulator Atoh1 and a cascade of Atoh1's downstream factors, including Pou4f3 and Gfi1. A subset of Six1-bound sites carry consensus-sequences for its downstream factors, including Atoh1, Gfi1, Pou4f3, Gata3 and Pbx1, all of which physically interact with Six1. Motif analysis identifies RFX/X-box as one of the most significantly enriched motifs in Six1-bound sites, and we demonstrate that Six1-RFX proteins cooperatively regulate gene expression through binding to SIX:RFX-motifs. Six1 targets a wide range of hair-bundle regulators and late Six1 deletion disrupts hair-bundle polarity. This study provides a mechanistic understanding of how Six1 cooperates with distinct cofactors in feedforward loops to control lineage-specific gene expression programs during progressive differentiation of the auditory sensory epithelium.
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Affiliation(s)
- Jun Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ting Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aarthi Ramakrishnan
- Department of Neurosciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bernd Fritzsch
- Department of Biology, University of Iowa, Iowa, IA 52242-1324
| | - Jinshu Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elaine Y M Wong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yong-Hwee Eddie Loh
- Department of Neurosciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jianqiang Ding
- Department of Infectious Diseases, Shunde Hospital, Southern Medical University, Shunde 528308, Guangdong, China
| | - Li Shen
- Department of Neurosciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pin-Xian Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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21
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McGowen MR, Tsagkogeorga G, Williamson J, Morin PA, Rossiter ASJ. Positive Selection and Inactivation in the Vision and Hearing Genes of Cetaceans. Mol Biol Evol 2020; 37:2069-2083. [DOI: 10.1093/molbev/msaa070] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Abstract
The transition to an aquatic lifestyle in cetaceans (whales and dolphins) resulted in a radical transformation in their sensory systems. Toothed whales acquired specialized high-frequency hearing tied to the evolution of echolocation, whereas baleen whales evolved low-frequency hearing. More generally, all cetaceans show adaptations for hearing and seeing underwater. To determine the extent to which these phenotypic changes have been driven by molecular adaptation, we performed large-scale targeted sequence capture of 179 sensory genes across the Cetacea, incorporating up to 54 cetacean species from all major clades as well as their closest relatives, the hippopotamuses. We screened for positive selection in 167 loci related to vision and hearing and found that the diversification of cetaceans has been accompanied by pervasive molecular adaptations in both sets of genes, including several loci implicated in nonsyndromic hearing loss. Despite these findings, however, we found no direct evidence of positive selection at the base of odontocetes coinciding with the origin of echolocation, as found in studies examining fewer taxa. By using contingency tables incorporating taxon- and gene-based controls, we show that, although numbers of positively selected hearing and nonsyndromic hearing loss genes are disproportionately high in cetaceans, counts of vision genes do not differ significantly from expected values. Alongside these adaptive changes, we find increased evidence of pseudogenization of genes involved in cone-mediated vision in mysticetes and deep-diving odontocetes.
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Affiliation(s)
- Michael R McGowen
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Joseph Williamson
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA
| | - and Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
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22
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Mutai H, Wasano K, Momozawa Y, Kamatani Y, Miya F, Masuda S, Morimoto N, Nara K, Takahashi S, Tsunoda T, Homma K, Kubo M, Matsunaga T. Variants encoding a restricted carboxy-terminal domain of SLC12A2 cause hereditary hearing loss in humans. PLoS Genet 2020; 16:e1008643. [PMID: 32294086 PMCID: PMC7159186 DOI: 10.1371/journal.pgen.1008643] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Hereditary hearing loss is challenging to diagnose because of the heterogeneity of the causative genes. Further, some genes involved in hereditary hearing loss have yet to be identified. Using whole-exome analysis of three families with congenital, severe-to-profound hearing loss, we identified a missense variant of SLC12A2 in five affected members of one family showing a dominant inheritance mode, along with de novo splice-site and missense variants of SLC12A2 in two sporadic cases, as promising candidates associated with hearing loss. Furthermore, we detected another de novo missense variant of SLC12A2 in a sporadic case. SLC12A2 encodes Na+, K+, 2Cl− cotransporter (NKCC) 1 and plays critical roles in the homeostasis of K+-enriched endolymph. Slc12a2-deficient mice have congenital, profound deafness; however, no human variant of SLC12A2 has been reported as associated with hearing loss. All identified SLC12A2 variants mapped to exon 21 or its 3’-splice site. In vitro analysis indicated that the splice-site variant generates an exon 21-skipped SLC12A2 mRNA transcript expressed at much lower levels than the exon 21-included transcript in the cochlea, suggesting a tissue-specific role for the exon 21-encoded region in the carboy-terminal domain. In vitro functional analysis demonstrated that Cl− influx was significantly decreased in all SLC12A2 variants studied. Immunohistochemistry revealed that SLC12A2 is located on the plasma membrane of several types of cells in the cochlea, including the strial marginal cells, which are critical for endolymph homeostasis. Overall, this study suggests that variants affecting exon 21 of the SLC12A2 transcript are responsible for hereditary hearing loss in humans. Sounds are perceived by auditory sensory cells, owing to tissues surrounding them, including the cochlear lateral wall. Part of the cochlear lateral wall, the stria vascularis, is critical for production and maintenance of inner-ear fluid with a high potassium concentration, and for generating the positive voltage in the inner ear, important for sound perception, by stimulating secretion of potassium from marginal cells. The gene SLC12A2 encodes a protein involved in sodium, potassium, and chloride transport essential for proper function of specific cells in the stria vascularis; however, human variants of SLC12A2 have not previously been associated with hearing loss. By comprehensive genetic analysis of protein-coding sequences, we identified four candidate changes in SLC12A2 in four families with congenital, severe-to-profound hearing loss. Intriguingly, all four genetic variants were either within or at the 3’-splice site of the exon 21 which encodes a part of the carboxy terminal intracellular domain of SLC12A2. Experiments in cultured cells showed that skipping or mutation of exon 21 significantly decreased chloride influx mediated by the SLC12A2 protein. Overall, our results strongly indicate that mutations influencing exon 21 of SLC12A2 represent a novel mechanism underlying deafness in humans.
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Affiliation(s)
- Hideki Mutai
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro, Tokyo, Japan
| | - Koichiro Wasano
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro, Tokyo, Japan
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshidakonoecho, Kyoto, Japan
| | - Fuyuki Miya
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
| | - Sawako Masuda
- Department of Otorhinolaryngology, National Hospital Organization Mie National Hospital, Tsu, Mie, Japan
| | - Noriko Morimoto
- Department of Otorhinolaryngology, National Center for Child Health and Development, Setagaya, Tokyo, Japan
| | - Kiyomitsu Nara
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro, Tokyo, Japan
| | - Satoe Takahashi
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, Japan
- Laboratory for Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Kazuaki Homma
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, Illinois, United States of America
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Tatsuo Matsunaga
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro, Tokyo, Japan
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Meguro, Tokyo, Japan
- * E-mail:
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23
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Song J, Patterson R, Metlagel Z, Krey JF, Hao S, Wang L, Ng B, Sazzed S, Kovacs J, Wriggers W, He J, Barr-Gillespie PG, Auer M. A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1. J Struct Biol 2020; 210:107461. [PMID: 31962158 DOI: 10.1016/j.jsb.2020.107461] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/11/2020] [Accepted: 01/14/2020] [Indexed: 12/11/2022]
Abstract
Electron cryo-tomography allows for high-resolution imaging of stereocilia in their native state. Because their actin filaments have a higher degree of order, we imaged stereocilia from mice lacking the actin crosslinker plastin 1 (PLS1). We found that while stereocilia actin filaments run 13 nm apart in parallel for long distances, there were gaps of significant size that were stochastically distributed throughout the actin core. Actin crosslinkers were distributed through the stereocilium, but did not occupy all possible binding sites. At stereocilia tips, protein density extended beyond actin filaments, especially on the side of the tip where a tip link is expected to anchor. Along the shaft, repeating density was observed that corresponds to actin-to-membrane connectors. In the taper region, most actin filaments terminated near the plasma membrane. The remaining filaments twisted together to make a tighter bundle than was present in the shaft region; the spacing between them decreased from 13 nm to 9 nm, and the apparent filament diameter decreased from 6.4 to 4.8 nm. Our models illustrate detailed features of distinct structural domains that are present within the stereocilium.
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Affiliation(s)
- Junha Song
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Roma Patterson
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zoltan Metlagel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jocelyn F Krey
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, USA
| | - Samantha Hao
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Linshanshan Wang
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brian Ng
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Salim Sazzed
- Department of Computer Science, Old Dominion University, Norfolk, VA, USA
| | - Julio Kovacs
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA, USA
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA, USA
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA, USA
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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24
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Lee S, Dondzillo A, Gubbels SP, Raphael Y. Practical aspects of inner ear gene delivery for research and clinical applications. Hear Res 2020; 394:107934. [PMID: 32204962 DOI: 10.1016/j.heares.2020.107934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/24/2022]
Abstract
The application of gene therapy is widely expanding in research and continuously improving in preparation for clinical applications. The inner ear is an attractive target for gene therapy for treating environmental and genetic diseases in both the auditory and vestibular systems. With the lack of spontaneous cochlear hair cell replacement, hair cell regeneration in adult mammals is among the most important goals of gene therapy. In addition, correcting gene defects can open up a new era for treating inner ear diseases. The relative isolation and small size of the inner ear dictate local administration routes and carefully calculated small volumes of reagents. In the current review, we will cover effective timing, injection routes and types of vectors for successful gene delivery to specific target cells within the inner ear. Differences between research purposes and clinical applications are also discussed.
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Affiliation(s)
- Sungsu Lee
- Kresge Hearing Research Institute, Department of Otolaryngology, Head and Neck Surgery, Michigan Medicine, Ann Arbor, MI, USA
| | - Anna Dondzillo
- Department of Otolaryngology, Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Samuel P Gubbels
- Department of Otolaryngology, Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Yehoash Raphael
- Kresge Hearing Research Institute, Department of Otolaryngology, Head and Neck Surgery, Michigan Medicine, Ann Arbor, MI, USA.
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25
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Gururaja Rao S, Patel NJ, Singh H. Intracellular Chloride Channels: Novel Biomarkers in Diseases. Front Physiol 2020; 11:96. [PMID: 32116799 PMCID: PMC7034325 DOI: 10.3389/fphys.2020.00096] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/27/2020] [Indexed: 12/27/2022] Open
Abstract
Ion channels are integral membrane proteins present on the plasma membrane as well as intracellular membranes. In the human genome, there are more than 400 known genes encoding ion channel proteins. Ion channels are known to regulate several cellular, organellar, and physiological processes. Any mutation or disruption in their function can result in pathological disorders, both common or rare. Ion channels present on the plasma membrane are widely acknowledged for their role in various biological processes, but in recent years, several studies have pointed out the importance of ion channels located in intracellular organelles. However, ion channels located in intracellular organelles are not well-understood in the context of physiological conditions, such as the generation of cellular excitability and ionic homeostasis. Due to the lack of information regarding their molecular identity and technical limitations of studying them, intracellular organelle ion channels have thus far been overlooked as potential therapeutic targets. In this review, we focus on a novel class of intracellular organelle ion channels, Chloride Intracellular Ion Channels (CLICs), mainly documented for their role in cardiovascular, neurophysiology, and tumor biology. CLICs have a single transmembrane domain, and in cells, they exist in cytosolic as well as membranous forms. They are predominantly present in intracellular organelles and have recently been shown to be localized to cardiomyocyte mitochondria as well as exosomes. In fact, a member of this family, CLIC5, is the first mitochondrial chloride channel to be identified on the molecular level in the inner mitochondrial membrane, while another member, CLIC4, is located predominantly in the outer mitochondrial membrane. In this review, we discuss this unique class of intracellular chloride channels, their role in pathologies, such as cardiovascular, cancer, and neurodegenerative diseases, and the recent developments concerning their usage as theraputic targets.
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Affiliation(s)
- Shubha Gururaja Rao
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Neel J Patel
- Department of Cardiology, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - Harpreet Singh
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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26
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Yao Q, Wang L, Mittal R, Yan D, Richmond MT, Denyer S, Requena T, Liu K, Varshney GK, Lu Z, Liu XZ. Transcriptomic Analyses of Inner Ear Sensory Epithelia in Zebrafish. Anat Rec (Hoboken) 2019; 303:527-543. [PMID: 31883312 DOI: 10.1002/ar.24331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 08/01/2019] [Accepted: 11/18/2019] [Indexed: 12/25/2022]
Abstract
Analysis of gene expression has the potential to assist in the understanding of multiple cellular processes including proliferation, cell-fate specification, senesence, and activity in both healthy and disease states. Zebrafish model has been increasingly used to understand the process of hearing and the development of the vertebrate auditory system. Within the zebrafish inner ear, there are three otolith organs, each containing a sensory macula of hair cells. The saccular macula is primarily involved in hearing, the utricular macula is primarily involved in balance and the function of the lagenar macula is not completely understood. The goal of this study is to understand the transcriptional differences in the sensory macula associated with different otolith organs with the intention of understanding the genetic mechanisms responsible for the distinct role each organ plays in sensory perception. The sensory maculae of the saccule, utricle, and lagena were dissected out of adult Et(krt4:GFP)sqet4 zebrafish expressing green fluorescent protein in hair cells for transcriptional analysis. The total RNAs of the maculae were isolated and analyzed by RNA GeneChip microarray. Several of the differentially expressed genes are known to be involved in deafness, otolith development and balance. Gene expression among these otolith organs was very well conserved with less than 10% of genes showing differential expression. Data from this study will help to elucidate which genes are involved in hearing and balance. Furthermore, the findings of this study will assist in the development of the zebrafish model for human hearing and balance disorders. Anat Rec, 303:527-543, 2020. © 2019 American Association for Anatomy.
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Affiliation(s)
- Qi Yao
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida.,Department of Biology, University of Miami, Miami, Florida
| | - Lingyu Wang
- Department of Biology, University of Miami, Miami, Florida
| | - Rahul Mittal
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Denise Yan
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
| | | | - Steven Denyer
- Department of Biology, University of Miami, Miami, Florida
| | - Teresa Requena
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Kaili Liu
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Zhongmin Lu
- Department of Biology, University of Miami, Miami, Florida
| | - Xue Zhong Liu
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida.,Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
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27
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GRXCR2 Regulates Taperin Localization Critical for Stereocilia Morphology and Hearing. Cell Rep 2019; 25:1268-1280.e4. [PMID: 30380417 PMCID: PMC6317715 DOI: 10.1016/j.celrep.2018.09.063] [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: 06/14/2018] [Revised: 09/03/2018] [Accepted: 09/19/2018] [Indexed: 12/14/2022] Open
Abstract
Mutations in human GRXCR2, which encodes a protein of undetermined function, cause hearing loss by unknown mechanisms. We found that mouse GRXCR2 localizes to the base of the stereocilia, which are actin-based mechanosensing organelles in cochlear hair cells that convert sound-induced vibrations into electrical signals. The stereocilia base also contains taperin, another protein of unknown function required for human hearing. We show that taperin and GRXCR2 form a complex and that taperin is diffused throughout the stereocilia length in Grxcr2-deficient hair cells. Stereocilia lacking GRXCR2 are longer than normal and disorganized due to the mislocalization of taperin, which could modulate the actin cytoskeleton in stereocilia. Remarkably, reducing taperin expression levels could rescue the morphological defects of stereocilia and restore the hearing of Grxcr2-deficient mice. Thus, our findings suggest that GRXCR2 is critical for the morphogenesis of stereocilia and auditory perception by restricting taperin to the stereocilia base. Liu et al. show that GRXCR2 and taperin form a complex at the base of the stereocilia in cochlear hair cells. Stereocilia lacking GRXCR2 are longer than normal and disorganized due to the mislocalization of taperin, which could modulate the actin cytoskeleton in stereocilia. Reducing taperin expression levels could rescue the morphological defects of stereocilia and restore the hearing of Grxcr2-deficient mice.
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28
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Ueno Y, Ozaki S, Umakoshi A, Yano H, Choudhury ME, Abe N, Sumida Y, Kuwabara J, Uchida R, Islam A, Ogawa K, Ishimaru K, Yorozuya T, Kunieda T, Watanabe Y, Takada Y, Tanaka J. Chloride intracellular channel protein 2 in cancer and non-cancer human tissues: relationship with tight junctions. Tissue Barriers 2019; 7:1593775. [PMID: 30929599 PMCID: PMC6592591 DOI: 10.1080/21688370.2019.1593775] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chloride intracellular channel protein 2 (CLIC2) belongs to the CLIC family of conserved metazoan proteins. Although CLICs have been identified as chloride channels, they are currently considered multifunctional proteins. CLIC2 is the least studied family member. We investigated CLIC2 expression and localization in human hepatocellular carcinoma, metastatic colorectal cancer in the liver, and colorectal cancer. Significant expression of mRNAs encoding CLIC1, 2, 4, and 5 were found in the human tissues, but only CLIC2 was predominantly expressed in non-cancer tissues surrounding cancer masses. Fibrotic or dysfunctional (aspartate aminotransferase ≥40) non-cancer liver tissues and advanced stage HCC tissues expressed low levels of CLIC2. Endothelial cells lining blood vessels but not lymphatic vessels in non-cancer tissues expressed CLIC2 as well as high levels of the tight junction proteins claudins 1 and 5, occludin, and ZO-1. Most endothelial cells in blood vessels in cancer tissues had very low expressions of CLIC2 and tight junction proteins. CD31+/CD45− endothelial cells isolated from non-cancer tissues expressed mRNAs encoding CLIC2, claudin 1, occludin and ZO-1, while similar cell fractions from cancer tissues had very low expressions of these molecules. Knockdown of CLIC2 expression in human umbilical vein endothelial cells (HUVECs) allowed human cancer cells to transmigrate through a HUVEC monolayer. These results suggest that CLIC2 may be involved in the formation and/or maintenance of tight junctions and that cancer tissue vasculature lacks CLIC2 and tight junctions, which allows the intravasation of cancer cells necessary for hematogenous metastasis.
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Affiliation(s)
- Yoshitomo Ueno
- a Department of Hepato-biliary Pancreatic Surgery and Breast Surgery, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Saya Ozaki
- b Department of Neurosurgery, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Akihiro Umakoshi
- c Department of Molecular and Cellular Physiology, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Hajime Yano
- c Department of Molecular and Cellular Physiology, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Mohammed E Choudhury
- c Department of Molecular and Cellular Physiology, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Naoki Abe
- d Department of Anesthesia and Perioperative Medicine, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Yutaro Sumida
- c Department of Molecular and Cellular Physiology, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Jun Kuwabara
- e Department of Gastrointestinal Surgery and Surgical Oncology, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Rina Uchida
- c Department of Molecular and Cellular Physiology, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Afsana Islam
- c Department of Molecular and Cellular Physiology, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Kohei Ogawa
- a Department of Hepato-biliary Pancreatic Surgery and Breast Surgery, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Kei Ishimaru
- e Department of Gastrointestinal Surgery and Surgical Oncology, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Toshihiro Yorozuya
- d Department of Anesthesia and Perioperative Medicine, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Takeharu Kunieda
- b Department of Neurosurgery, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Yuji Watanabe
- e Department of Gastrointestinal Surgery and Surgical Oncology, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Yasutsugu Takada
- a Department of Hepato-biliary Pancreatic Surgery and Breast Surgery, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
| | - Junya Tanaka
- c Department of Molecular and Cellular Physiology, Graduate School of Medicine , Ehime University , Toon , Ehime , Japan
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29
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Krey JF, Barr-Gillespie PG. Molecular Composition of Vestibular Hair Bundles. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a033209. [PMID: 29844221 DOI: 10.1101/cshperspect.a033209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The vertebrate hair bundle, responsible for transduction of mechanical signals into receptor potentials in sensory hair cells, is an evolutionary masterpiece. Composed of actin-filled stereocilia of precisely regulated length, width, and number, the structure of the hair bundle is optimized for sensing auditory and vestibular stimuli. Recent developments in identifying the lipids and proteins constituting the hair bundle, obtained through genetics, biochemistry, and imaging, now permit a description of the consensus composition of vestibular bundles of mouse, rat, and chick.
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Affiliation(s)
- Jocelyn F Krey
- Oregon Hearing Research Center and Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center and Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239
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30
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Men Y, Li X, Tu H, Zhang A, Fu X, Wang Z, Jin Y, Hou C, Zhang T, Zhang S, Zhou Y, Li B, Li J, Sun X, Wang H, Gao J. Tprn is essential for the integrity of stereociliary rootlet in cochlear hair cells in mice. Front Med 2018; 13:690-704. [PMID: 30159668 DOI: 10.1007/s11684-018-0638-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 01/27/2018] [Indexed: 11/24/2022]
Abstract
Tprn encodes the taperin protein, which is concentrated in the tapered region of hair cell stereocilia in the inner ear. In humans, TPRN mutations cause autosomal recessive nonsyndromic deafness (DFNB79) by an unknown mechanism. To determine the role of Tprn in hearing, we generated Tprn-null mice by clustered regularly interspaced short palindromic repeat/Cas9 genome-editing technology from a CBA/CaJ background. We observed significant hearing loss and progressive degeneration of stereocilia in the outer hair cells of Tprn-null mice starting from postnatal day 30. Transmission electron microscopy images of stereociliary bundles in the mutant mice showed some stereociliary rootlets with curved shafts. The central cores of the stereociliary rootlets possessed hollow structures with surrounding loose peripheral dense rings. Radixin, a protein expressed at stereocilia tapering, was abnormally dispersed along the stereocilia shafts in Tprn-null mice. The expression levels of radixin and β-actin significantly decreased.We propose that Tprn is critical to the retention of the integrity of the stereociliary rootlet. Loss of Tprn in Tprn-null mice caused the disruption of the stereociliary rootlet, which resulted in damage to stereociliary bundles and hearing impairments. The generated Tprn-null mice are ideal models of human hereditary deafness DFNB79.
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Affiliation(s)
- Yuqin Men
- School of Life Science, Shandong University, Jinan, 250100, China
| | - Xiujuan Li
- Rizhao Polytechnic, Rizhao, 276826, China
| | - Hailong Tu
- School of Life Science, Shandong University, Jinan, 250100, China
| | - Aizhen Zhang
- School of Life Science, Shandong University, Jinan, 250100, China
| | - Xiaolong Fu
- School of Life Science, Shandong University, Jinan, 250100, China
| | - Zhishuo Wang
- School of Life Science, Shandong University, Jinan, 250100, China
| | - Yecheng Jin
- School of Life Science, Shandong University, Jinan, 250100, China
| | - Congzhe Hou
- The Second Hospital of Shandong University, Jinan, 250033, China
| | - Tingting Zhang
- School of Life Science, Shandong University, Jinan, 250100, China
| | - Sen Zhang
- School of Life Science, Shandong University, Jinan, 250100, China
| | - Yichen Zhou
- School of Life Science, Shandong University, Jinan, 250100, China
| | - Boqin Li
- Electron Microscopy Laboratory, Shandong Institute of Otolaryngology, Jinan, 250022, China.,Laboratory of Electron Microscopy, Jinan WEI-YA Biotech Company, Jinan, 250100, China
| | - Jianfeng Li
- Department of Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated to Shandong University, Jinan, 250021, China
| | - Xiaoyang Sun
- School of Life Science, Shandong University, Jinan, 250100, China.
| | - Haibo Wang
- Department of Otolaryngology-Head and Neck Surgery, Provincial Hospital Affiliated to Shandong University, Jinan, 250021, China.
| | - Jiangang Gao
- School of Life Science, Shandong University, Jinan, 250100, China.
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31
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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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32
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Ferofontov A, Strulovich R, Marom M, Giladi M, Haitin Y. Inherent flexibility of CLIC6 revealed by crystallographic and solution studies. Sci Rep 2018; 8:6882. [PMID: 29720717 PMCID: PMC5931990 DOI: 10.1038/s41598-018-25231-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/16/2018] [Indexed: 12/22/2022] Open
Abstract
Chloride intracellular channels (CLICs) are a family of unique proteins, that were suggested to adopt both soluble and membrane-associated forms. Moreover, following this unusual metamorphic change, CLICs were shown to incorporate into membranes and mediate ion conduction in vitro, suggesting multimerization upon membrane insertion. Here, we present a 1.8 Å resolution crystal structure of the CLIC domain of mouse CLIC6 (mCLIC6). The structure reveals a monomeric arrangement and shows a high degree of structural conservation with other CLICs. Small-angle X-ray scattering (SAXS) analysis of mCLIC6 demonstrated that the overall solution structure is similar to the crystallographic conformation. Strikingly, further analysis of the SAXS data using ensemble optimization method unveiled additional elongated conformations, elucidating high structural plasticity as an inherent property of the protein. Moreover, structure-guided perturbation of the inter-domain interface by mutagenesis resulted in a population shift towards elongated conformations of mCLIC6. Additionally, we demonstrate that oxidative conditions induce an increase in mCLIC6 hydrophobicity along with mild oligomerization, which was enhanced by the presence of membrane mimetics. Together, these results provide mechanistic insights into the metamorphic nature of mCLIC6.
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Affiliation(s)
- Alisa Ferofontov
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | - Roi Strulovich
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | - Milit Marom
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | - Moshe Giladi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, 6997801, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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33
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Fan J, Lerner J, Wyatt MK, Cai P, Peterson K, Dong L, Wistow G. The klotho-related protein KLPH (lctl) has preferred expression in lens and is essential for expression of clic5 and normal lens suture formation. Exp Eye Res 2018; 169:111-121. [PMID: 29425878 PMCID: PMC5878992 DOI: 10.1016/j.exer.2018.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/24/2018] [Accepted: 02/02/2018] [Indexed: 10/18/2022]
Abstract
KLPH/lctl belongs to the Klotho family of proteins. Expressed sequence tag analyses unexpectedly revealed that KLPH is highly expressed in the eye lens while northern blots showed that expression is much higher in the eye than in other tissues. In situ hybridization in mouse localized mRNA to the lens, particularly in the equatorial epithelium. Immunofluorescence detected KLPH in lens epithelial cells with highest levels in the germinative/differentiation zone. The gene for KLPH in mouse was deleted by homologous recombination. Littermate knockout (KO) and wild type (WT) mice were compared in a wide panel of pathology examinations and were all grossly normal, showing no systemic effects of the deletion. However, the lens, while superficially normal at young ages, had focusing defects and exhibited age-related cortical cataract by slit lamp examination. Whole-lens imaging showed that KO mice had disorganized lens sutures, forming a loose double-y or x instead of the tight y formation of WT. RNA-seq profiles for KO and WT littermates confirmed the absence of KLPH mRNA in KO lens and also showed complete absence of transcripts for Clic5, a protein associated with cilium/basal body related auditory defects in a mouse model. Immunofluorescence of lens epithelial flat mounts showed that Clic5 localized to cilia/centrosomes. Mice mutant for Clic5 (jitterbug) also had defective sutures. These results suggest that KLPH is required for lens-specific expression of Clic5 and that Clic5 has an important role in the machinery that controls lens fiber cell extension and organization.
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Affiliation(s)
- Jianguo Fan
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joshua Lerner
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - M Keith Wyatt
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Phillip Cai
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katherine Peterson
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lijin Dong
- Genetic Engineering Facility, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Graeme Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
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34
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Gururaja Rao S, Ponnalagu D, Patel NJ, Singh H. Three Decades of Chloride Intracellular Channel Proteins: From Organelle to Organ Physiology. CURRENT PROTOCOLS IN PHARMACOLOGY 2018; 80:11.21.1-11.21.17. [PMID: 30040212 PMCID: PMC6060641 DOI: 10.1002/cpph.36] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intracellular organelles are membranous structures central for maintaining cellular physiology and the overall health of the cell. To maintain cellular function, intracellular organelles are required to tightly regulate their ionic homeostasis. Any imbalance in ionic concentrations can disrupt energy production (mitochondria), protein degradation (lysosomes), DNA replication (nucleus), or cellular signaling (endoplasmic reticulum). Ionic homeostasis is also important for volume regulation of intracellular organelles and is maintained by cation and anion channels as well as transporters. One of the major classes of ion channels predominantly localized to intracellular membranes is chloride intracellular channel proteins (CLICs). They are non-canonical ion channels with six homologs in mammals, existing as either soluble or integral membrane protein forms, with dual functions as enzymes and channels. Provided in this overview is a brief introduction to CLICs, and a summary of recent information on their localization, biophysical properties, and physiological roles. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Shubha Gururaja Rao
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Devasena Ponnalagu
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Neel J Patel
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Harpreet Singh
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania
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35
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Toyoda Y, Cattin CJ, Stewart MP, Poser I, Theis M, Kurzchalia TV, Buchholz F, Hyman AA, Müller DJ. Genome-scale single-cell mechanical phenotyping reveals disease-related genes involved in mitotic rounding. Nat Commun 2017; 8:1266. [PMID: 29097687 PMCID: PMC5668354 DOI: 10.1038/s41467-017-01147-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/22/2017] [Indexed: 01/01/2023] Open
Abstract
To divide, most animal cells drastically change shape and round up against extracellular confinement. Mitotic cells facilitate this process by generating intracellular pressure, which the contractile actomyosin cortex directs into shape. Here, we introduce a genome-scale microcantilever- and RNAi-based approach to phenotype the contribution of > 1000 genes to the rounding of single mitotic cells against confinement. Our screen analyzes the rounding force, pressure and volume of mitotic cells and localizes selected proteins. We identify 49 genes relevant for mitotic rounding, a large portion of which have not previously been linked to mitosis or cell mechanics. Among these, depleting the endoplasmic reticulum-localized protein FAM134A impairs mitotic progression by affecting metaphase plate alignment and pressure generation by delocalizing cortical myosin II. Furthermore, silencing the DJ-1 gene uncovers a link between mitochondria-associated Parkinson's disease and mitotic pressure. We conclude that mechanical phenotyping is a powerful approach to study the mechanisms governing cell shape.
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Affiliation(s)
- Yusuke Toyoda
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.,Division of Cell Biology, Life Science Institute, Kurume University, Hyakunen-Kohen 1-1, Kurume, Fukuoka, 839-0864, Japan
| | - Cedric J Cattin
- Department of Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin P Stewart
- Department of Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Department of Chemical Engineering, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139-4307, USA.,The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02139-4307, USA
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Mirko Theis
- UCC, Medical System biology, Medical Faculty Carl Gustav Carus, University of Technology Dresden, Am Tatzberg 47/49, 01307, Dresden, Germany
| | - Teymuras V Kurzchalia
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Frank Buchholz
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.,UCC, Medical System biology, Medical Faculty Carl Gustav Carus, University of Technology Dresden, Am Tatzberg 47/49, 01307, Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
| | - Daniel J Müller
- Department of Biosystems Science and Engineering (D-BSSE), Eidgenössische Technische Hochschule (ETH) Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.
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36
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Seki Y, Miyasaka Y, Suzuki S, Wada K, Yasuda SP, Matsuoka K, Ohshiba Y, Endo K, Ishii R, Shitara H, Kitajiri SI, Nakagata N, Takebayashi H, Kikkawa Y. A novel splice site mutation of myosin VI in mice leads to stereociliary fusion caused by disruption of actin networks in the apical region of inner ear hair cells. PLoS One 2017; 12:e0183477. [PMID: 28832620 PMCID: PMC5568226 DOI: 10.1371/journal.pone.0183477] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/04/2017] [Indexed: 01/03/2023] Open
Abstract
An unconventional myosin encoded by the myosin VI gene (MYO6) contributes to hearing loss in humans. Homozygous mutations of MYO6 result in nonsyndromic profound congenital hearing loss, DFNB37. Kumamoto shaker/waltzer (ksv) mice harbor spontaneous mutations, and homozygous mutants exhibit congenital defects in balance and hearing caused by fusion of the stereocilia. We identified a Myo6c.1381G>A mutation that was found to be a p.E461K mutation leading to alternative splicing errors in Myo6 mRNA in ksv mutants. An analysis of the mRNA and protein expression in animals harboring this mutation suggested that most of the abnormal alternatively spliced isoforms of MYO6 are degraded in ksv mice. In the hair cells of ksv/ksv homozygotes, the MYO6 protein levels were significantly decreased in the cytoplasm, including in the cuticular plates. MYO6 and stereociliary taper-specific proteins were mislocalized along the entire length of the stereocilia of ksv/ksv mice, thus suggesting that MYO6 attached to taper-specific proteins at the stereociliary base. Histological analysis of the cochlear hair cells showed that the stereociliary fusion in the ksv/ksv mutants, developed through fusion between stereociliary bundles, raised cuticular plate membranes in the cochlear hair cells and resulted in incorporation of the bundles into the sheaths of the cuticular plates. Interestingly, the expression of the stereociliary rootlet-specific TRIO and F-actin binding protein (TRIOBP) was altered in ksv/ksv mice. The abnormal expression of TRIOBP suggested that the rootlets in the hair cells of ksv/ksv mice had excessive growth. Hence, these data indicated that decreased MYO6 levels in ksv/ksv mutants disrupt actin networks in the apical region of hair cells, thereby maintaining the normal structure of the cuticular plates and rootlets, and additionally provided a cellular basis for stereociliary fusion in Myo6 mutants.
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Affiliation(s)
- Yuta Seki
- Mammalian Genetics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yuki Miyasaka
- Mammalian Genetics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Division of Experimental Animals, Center for Promotion of Medical Research and Education, Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Sari Suzuki
- Mammalian Genetics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kenta Wada
- Mammalian Genetics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Laboratory of Animal Biotechnology, Department of Bioproduction, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, Japan
| | - Shumpei P Yasuda
- Mammalian Genetics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kunie Matsuoka
- Mammalian Genetics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yasuhiro Ohshiba
- Mammalian Genetics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kentaro Endo
- Histology Laboratory, Advanced Technical Support Department, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Rie Ishii
- Laboratory for Transgenic Technology, Animal Research Division, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hiroshi Shitara
- Laboratory for Transgenic Technology, Animal Research Division, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Shin-Ichiro Kitajiri
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naomi Nakagata
- Division of Reproductive Engineering, Center for Animal Resources and Development (CARD), Kumamoto University, Kumamoto, Japan
| | - Hirohide Takebayashi
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Yoshiaki Kikkawa
- Mammalian Genetics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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37
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Argenzio E, Moolenaar WH. Emerging biological roles of Cl- intracellular channel proteins. J Cell Sci 2017; 129:4165-4174. [PMID: 27852828 DOI: 10.1242/jcs.189795] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cl- intracellular channels (CLICs) are a family of six evolutionary conserved cytosolic proteins that exist in both soluble and membrane-associated forms; however, their functions have long been elusive. Soluble CLICs adopt a glutathione S-transferase (GST)-fold, can induce ion currents in artificial membranes and show oxidoreductase activity in vitro, but there is no convincing evidence of CLICs having such activities in vivo. Recent studies have revealed a role for CLIC proteins in Rho-regulated cortical actin dynamics as well as vesicular trafficking and integrin recycling, the latter of which are under the control of Rab GTPases. In this Commentary, we discuss the emerging roles of CLIC proteins in these processes and the lessons learned from gene-targeting studies. We also highlight outstanding questions regarding the molecular function(s) of these important but still poorly understood proteins.
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Affiliation(s)
- Elisabetta Argenzio
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Wouter H Moolenaar
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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38
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Ji H, Pai AV, West CA, Wu X, Speth RC, Sandberg K. Loss of Resistance to Angiotensin II-Induced Hypertension in the Jackson Laboratory Recombination-Activating Gene Null Mouse on the C57BL/6J Background. Hypertension 2017; 69:1121-1127. [PMID: 28438904 DOI: 10.1161/hypertensionaha.117.09063] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 01/27/2017] [Accepted: 03/13/2017] [Indexed: 01/11/2023]
Abstract
Resistance to angiotensin II (Ang II)-induced hypertension in T-cell-deficient male mice with a targeted mutation in the recombination-activating gene-1 (Rag1) on the C57BL/6J background (B6.Rag1-/- -M), which was reported by 5 independent laboratories including ours before 2015, has been lost. In mice purchased from Jackson Laboratory in 2015 and 2016, the time course and magnitude increase in mean arterial pressure induced by 2 weeks of Ang II infusion at 490 ng/kg per minute was identical between B6.Rag1-/- -M and male wild-type littermates. Moreover, there were no differences in the time course or magnitude increase in mean arterial pressure at the lowest dose of Ang II (200 ng/kg per minute) that increased mean arterial pressure. This loss in Ang II resistance is independent of T cells. Angiotensin type 1-receptor binding was 1.4-fold higher in glomeruli isolated from recently purchased B6.Rag1-/- -M suggesting an increase in renal angiotensin type 1-receptor activity masks the blood pressure protection afforded by the lack of T cells. The phenotypic change in B6.Rag1-/- -M has implications for investigators using this strain to study mechanisms of T-cell modulation of Ang II-dependent blood pressure control. These findings also serve as a reminder that the universal drive for genetic variation occurs in all animals including inbred mouse strains and that spontaneous mutations leading to phenotypic change can compromise experimental reproducibility over time and place. Finally, these observations illustrate the importance of including experimental details about the location and time period over which animals are bred in publications involving animal studies to promote rigor and reproducibility in the scientific literature.
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Affiliation(s)
- Hong Ji
- From the Department of Medicine (H.J., C.A.W., X.W., K.S.), Department of Biochemistry and Molecular and Cell Biology (A.V.P., K.S.), and Center for the Study of Sex Differences in Health, Aging and Disease (H.J., A.V.P., C.A.W., X.W., K.S.), Georgetown University, Washington, DC; and Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, FL (R.C.S.)
| | - Amrita V Pai
- From the Department of Medicine (H.J., C.A.W., X.W., K.S.), Department of Biochemistry and Molecular and Cell Biology (A.V.P., K.S.), and Center for the Study of Sex Differences in Health, Aging and Disease (H.J., A.V.P., C.A.W., X.W., K.S.), Georgetown University, Washington, DC; and Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, FL (R.C.S.)
| | - Crystal A West
- From the Department of Medicine (H.J., C.A.W., X.W., K.S.), Department of Biochemistry and Molecular and Cell Biology (A.V.P., K.S.), and Center for the Study of Sex Differences in Health, Aging and Disease (H.J., A.V.P., C.A.W., X.W., K.S.), Georgetown University, Washington, DC; and Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, FL (R.C.S.)
| | - Xie Wu
- From the Department of Medicine (H.J., C.A.W., X.W., K.S.), Department of Biochemistry and Molecular and Cell Biology (A.V.P., K.S.), and Center for the Study of Sex Differences in Health, Aging and Disease (H.J., A.V.P., C.A.W., X.W., K.S.), Georgetown University, Washington, DC; and Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, FL (R.C.S.)
| | - Robert C Speth
- From the Department of Medicine (H.J., C.A.W., X.W., K.S.), Department of Biochemistry and Molecular and Cell Biology (A.V.P., K.S.), and Center for the Study of Sex Differences in Health, Aging and Disease (H.J., A.V.P., C.A.W., X.W., K.S.), Georgetown University, Washington, DC; and Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, FL (R.C.S.)
| | - Kathryn Sandberg
- From the Department of Medicine (H.J., C.A.W., X.W., K.S.), Department of Biochemistry and Molecular and Cell Biology (A.V.P., K.S.), and Center for the Study of Sex Differences in Health, Aging and Disease (H.J., A.V.P., C.A.W., X.W., K.S.), Georgetown University, Washington, DC; and Department of Pharmaceutical Sciences, Nova Southeastern University, Fort Lauderdale, FL (R.C.S.).
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Bird JE, Barzik M, Drummond MC, Sutton DC, Goodman SM, Morozko EL, Cole SM, Boukhvalova AK, Skidmore J, Syam D, Wilson EA, Fitzgerald T, Rehman AU, Martin DM, Boger ET, Belyantseva IA, Friedman TB. Harnessing molecular motors for nanoscale pulldown in live cells. Mol Biol Cell 2016; 28:463-475. [PMID: 27932498 PMCID: PMC5341729 DOI: 10.1091/mbc.e16-08-0583] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/08/2016] [Accepted: 11/29/2016] [Indexed: 11/13/2022] Open
Abstract
Nanoscale pulldown (NanoSPD) miniaturizes the concept of affinity pulldown to detect protein–protein interactions in live cells. NanoSPD hijacks the myosin-based intracellular trafficking machinery to assess interactions under physiological buffer conditions and is microscopy-based, allowing for sensitive detection and quantification. Protein–protein interactions (PPIs) regulate assembly of macromolecular complexes, yet remain challenging to study within the native cytoplasm where they normally exert their biological effect. Here we miniaturize the concept of affinity pulldown, a gold-standard in vitro PPI interrogation technique, to perform nanoscale pulldowns (NanoSPDs) within living cells. NanoSPD hijacks the normal process of intracellular trafficking by myosin motors to forcibly pull fluorescently tagged protein complexes along filopodial actin filaments. Using dual-color total internal reflection fluorescence microscopy, we demonstrate complex formation by showing that bait and prey molecules are simultaneously trafficked and actively concentrated into a nanoscopic volume at the tips of filopodia. The resulting molecular traffic jams at filopodial tips amplify fluorescence intensities and allow PPIs to be interrogated using standard epifluorescence microscopy. A rigorous quantification framework and software tool are provided to statistically evaluate NanoSPD data sets. We demonstrate the capabilities of NanoSPD for a range of nuclear and cytoplasmic PPIs implicated in human deafness, in addition to dissecting these interactions using domain mapping and mutagenesis experiments. The NanoSPD methodology is extensible for use with other fluorescent molecules, in addition to proteins, and the platform can be easily scaled for high-throughput applications.
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Affiliation(s)
- Jonathan E Bird
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Melanie Barzik
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Meghan C Drummond
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Daniel C Sutton
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Spencer M Goodman
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Eva L Morozko
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Stacey M Cole
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | | | - Jennifer Skidmore
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109
| | - Diana Syam
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109
| | - Elizabeth A Wilson
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Tracy Fitzgerald
- Mouse Auditory Testing Core Facility, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20814
| | - Atteeq U Rehman
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Donna M Martin
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109.,Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Erich T Boger
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20814
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Tavasoli M, Al-Momany A, Wang X, Li L, Edwards JC, Ballermann BJ. Both CLIC4 and CLIC5A activate ERM proteins in glomerular endothelium. Am J Physiol Renal Physiol 2016; 311:F945-F957. [PMID: 27582103 DOI: 10.1152/ajprenal.00353.2016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/25/2016] [Indexed: 01/17/2023] Open
Abstract
The chloride intracellular channel (CLIC) 5A is expressed at very high levels in renal glomeruli, in both endothelial cells (EC) and podocytes. CLIC5A stimulates Rac1- and phosphatidylinositol (4,5)-bisphosphate-dependent ERM (ezrin, radixin, moesin) activation. ERM proteins, in turn, function in lumen formation and in the development of actin-based cellular projections. In mice lacking CLIC5A, ERM phosphorylation is profoundly reduced in podocytes, but preserved in glomerular EC. Since glomerular EC also express CLIC4, we reasoned that, if CLIC4 activates ERM proteins like CLIC5A, then CLIC4 could compensate for the CLIC5A loss in glomerular EC. In glomeruli of CLIC5-deficient mice, CLIC4 expression was upregulated and colocalized with moesin and ezrin in glomerular EC, but not in podocytes. In cultured glomerular EC, CLIC4 silencing reduced ERM phosphorylation and cytoskeletal association, and expression of exogenous CLIC4 or CLIC5A rescued ERM de-phosphorylation due to CLIC4 silencing. In mice lacking either CLIC4 or CLIC5, ERM phosphorylation was retained in glomerular EC, but, in mice lacking both CLIC4 and CLIC5, glomerular EC ERM phosphorylation was profoundly reduced. Although glomerular EC fenestrae developed normally in dual CLIC4/CLIC5-deficient mice, the density of fenestrae declined substantially by 8 mo of age, along with the deposition of subendothelial electron-lucent material. The dual CLIC4/CLIC5-deficient mice developed spontaneous proteinuria, glomerular cell proliferation, and matrix deposition. Thus CLIC4 stimulates ERM activation and can compensate for CLIC5A in glomerular EC. The findings indicate that CLIC4/CLIC5A-mediated ERM activation is required for maintenance of the glomerular capillary architecture.
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Affiliation(s)
- Mahtab Tavasoli
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Abass Al-Momany
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; and
| | - Xin Wang
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Laiji Li
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - John C Edwards
- Department of Internal Medicine, St. Louis University, St. Louis, Missouri
| | - Barbara J Ballermann
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; .,Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; and
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Genetics of vestibular disorders: pathophysiological insights. J Neurol 2016; 263 Suppl 1:S45-53. [PMID: 27083884 PMCID: PMC4833787 DOI: 10.1007/s00415-015-7988-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/01/2015] [Accepted: 11/29/2015] [Indexed: 01/09/2023]
Abstract
The two most common vestibular disorders are motion sickness and vestibular migraine, affecting 30 and 1–2 % of the population respectively. Both are related to migraine and show a familial trend. Bilateral vestibular hypofunction is a rare condition, and some of patients also present cerebellar ataxia and neuropathy. We present recent advances in the genetics of vestibular disorders with familial aggregation. The clinical heterogeneity observed in different relatives of the same families suggests a variable penetrance and the interaction of several genes in each family. Some Mendelian sensorineural hearing loss also exhibits vestibular dysfunction, including DFNA9, DFNA11, DFNA15 and DFNA28. However, the most relevant finding during the past years is the familial clustering observed in Meniere’s disease. By using whole exome sequencing and combining bioinformatics tools, novel variants in DTNA and FAM136A genes have been identified in familial Meniere’s disease, and this genomic strategy will facilitate the discovery of the genetic basis of familial vestibular disorders.
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Tavasoli M, Li L, Al-Momany A, Zhu LF, Adam BA, Wang Z, Ballermann BJ. The chloride intracellular channel 5A stimulates podocyte Rac1, protecting against hypertension-induced glomerular injury. Kidney Int 2016; 89:833-47. [PMID: 26924049 DOI: 10.1016/j.kint.2016.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/02/2015] [Accepted: 10/15/2015] [Indexed: 11/16/2022]
Abstract
Glomerular capillary hypertension elicits podocyte remodeling and is a risk factor for the progression of glomerular disease. Ezrin, which links podocalyxin to actin in podocytes, is activated through the chloride intracellular channel 5A (CLIC5A)-dependent phosphatidylinositol 4,5 bisphosphate (PI[4,5]P2) accumulation. Because Rac1 is involved in podocyte actin remodeling and can promote PI[4,5]P2 production we determined whether CLIC5A-dependent PI[4,5]P2 generation and ezrin activation are mediated by Rac1. In COS7 cells, CLIC5A expression stimulated Rac1 but not Cdc42 or Rho activity. CLIC5A also stimulated phosphorylation of the Rac1 effector Pak1 in COS7 cells and in cultured mouse podocytes. CLIC5A-induced PI[4,5]P2 accumulation and Pak1 and ezrin phosphorylation were all Rac1 dependent. In DOCA/Salt hypertension, phosphorylated Pak increased in podocytes of wild-type, but not CLIC5-deficient mice. In DOCA/salt hypertensive mice lacking CLIC5, glomerular capillary microaneurysms were more frequent and albuminuria was greater than in wild-type mice. Thus, augmented hypertension-induced glomerular capillary injury in mice lacking CLIC5 results from abrogation of Rac1-dependent Pak and ezrin activation, perhaps reducing the tensile strength of the podocyte actin cytoskeleton.
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Affiliation(s)
- Mahtab Tavasoli
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Laiji Li
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Abass Al-Momany
- Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Lin-Fu Zhu
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Benjamin A Adam
- Department of Pathology and Laboratory Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Zhixiang Wang
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Barbara J Ballermann
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada; Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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Ponnalagu D, Gururaja Rao S, Farber J, Xin W, Hussain AT, Shah K, Tanda S, Berryman M, Edwards JC, Singh H. Molecular identity of cardiac mitochondrial chloride intracellular channel proteins. Mitochondrion 2016; 27:6-14. [PMID: 26777142 DOI: 10.1016/j.mito.2016.01.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 12/08/2015] [Accepted: 01/07/2016] [Indexed: 01/08/2023]
Abstract
Emerging evidences demonstrate significance of chloride channels in cardiac function and cardioprotection from ischemia-reperfusion (IR) injury. Unlike mitochondrial potassium channels sensitive to calcium (BKCa) and ATP (KATP), molecular identity of majority of cardiac mitochondrial chloride channels located at the inner membrane is not known. In this study, we report the presence of unique dimorphic chloride intracellular channel (CLIC) proteins namely CLIC1, CLIC4 and CLIC5 as abundant CLICs in the rodent heart. Further, CLIC4, CLIC5, and an ortholog present in Drosophila (DmCLIC) localize to adult cardiac mitochondria. We found that CLIC4 is enriched in the outer mitochondrial membrane, whereas CLIC5 is present in the inner mitochondrial membrane. Also, CLIC5 plays a direct role in regulating mitochondrial reactive oxygen species (ROS) generation. Our study highlights that CLIC5 is localized to the cardiac mitochondria and directly modulates mitochondrial function.
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Affiliation(s)
- Devasena Ponnalagu
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, United States
| | - Shubha Gururaja Rao
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, United States
| | - Jason Farber
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, United States
| | - Wenyu Xin
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, United States
| | - Ahmed Tafsirul Hussain
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, United States
| | - Kajol Shah
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, United States
| | - Soichi Tanda
- Department of Biological Sciences, Ohio University, Athens, OH 45701, United States
| | - Mark Berryman
- Department of Biomedical Sciences, Ohio University, Athens, OH 45701, United States
| | - John C Edwards
- Division of Nephrology, St. Louis University, St. Louis, MO 63110, United States
| | - Harpreet Singh
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, United States.
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Helios(®) Gene Gun-Mediated Transfection of the Inner Ear Sensory Epithelium: Recent Updates. Methods Mol Biol 2016; 1427:3-26. [PMID: 27259918 DOI: 10.1007/978-1-4939-3615-1_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The transfection of vertebrate inner ear hair cells has proven to be challenging. Therefore, many laboratories attempt to use and improve different transfection methods. Each method has its own advantages and disadvantages. A particular researcher's skills in addition to available equipment and the type of experiment (in vivo or in vitro) likely determine the transfection method of choice. Biolistic delivery of exogenous DNA, mRNA, or siRNA, also known as Helios(®) Gene Gun-mediated transfection, uses the mechanical energy of compressed helium gas to bombard tissue with micron- or submicron-sized DNA or RNA-coated gold particles, which can penetrate and transfect cells in vitro or in vivo. Helios(®) Gene Gun-mediated transfection has several advantages: (1) it is simple enough to learn in a short time; (2) it is designed to overcome cell barriers even as tough as plant cell membrane or stratum corneum in the epidermis; (3) it can transfect cells deep inside a tissue such as specific neurons within a brain slice; (4) it can accommodate mRNA, siRNA, or DNA practically of any size to be delivered; and (5) it works well with various cell types including non-dividing, terminally differentiated cells that are difficult to transfect, such as neurons or mammalian inner ear sensory hair cells. The latter advantage is particularly important for inner ear research. The disadvantages of this method are: (1) low efficiency of transfection due to many variables that have to be adjusted and (2) potential mechanical damage of the tissue if the biolistic shot parameters are not optimal. This chapter provides a step-by-step protocol and critical evaluation of the Bio-Rad Helios(®) Gene Gun transfection method used to deliver green fluorescent protein (GFP)-tagged full-length cDNAs of myosin 15a, whirlin, β-actin, and Clic5 into rodent hair cells of the postnatal inner ear sensory epithelia in culture.
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Alawieh A, Mondello S, Kobeissy F, Shibbani K, Bassim M. Proteomics studies in inner ear disorders: pathophysiology and biomarkers. Expert Rev Proteomics 2015; 12:185-96. [PMID: 25795149 DOI: 10.1586/14789450.2015.1024228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although proteomics has been exploited in a wide range of diseases for identification of biomarkers and pathophysiological mechanisms, there are still biomedical disciplines such as otology where proteomics platforms are underused due to technical challenges and/or complex features of the disease. Thus, in the past few years, healthcare and scientific agencies have advocated the development and adoption of proteomic technologies in otological research. However, few studies have been conducted and limited literature is available in this area. Here, we present the state of the art of proteomics in otology, discussing the substantial evidence from recent experimental models and clinical studies in inner-ear conditions. We also delineate a series of critical issues including minute size of the inner ear, delicacy and poor accessibility of tissue that researchers face while undertaking otology proteomics research. Furthermore, we provide perspective to enhance the impact and lead to the clinical implementation of these proteomics-based strategies.
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Affiliation(s)
- Ali Alawieh
- Department of Neurosciences, Medical University of South Carolina, Charleston, SC 29425, USA
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Flores-Téllez TNJ, Lopez TV, Vásquez Garzón VR, Villa-Treviño S. Co-Expression of Ezrin-CLIC5-Podocalyxin Is Associated with Migration and Invasiveness in Hepatocellular Carcinoma. PLoS One 2015; 10:e0131605. [PMID: 26135398 PMCID: PMC4489913 DOI: 10.1371/journal.pone.0131605] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/03/2015] [Indexed: 11/18/2022] Open
Abstract
Background and Aim Prognostic markers are important for predicting the progression and staging of hepatocellular carcinoma (HCC). Ezrin (EZR) and Podocalyxin (PODXL) are proteins associated with invasion, migration and poor prognosis in various types of cancer. Recently, it has been observed that chloride intracellular channel 5 (CLIC5) forms a complex with EZR and PODXL and that it is required for podocyte structure and function. In this study, we evaluated the overexpression of EZR, PODXL and CLIC5 in HCC. Methods The modified resistant hepatocyte model (MRHR), human biopsies and HCC cell lines (HepG2, Huh7 and SNU387) were used in this study. Gene and protein expression levels were evaluated in the MRHR by qRT-PCR, Western blot and immunohistochemistry analyses, and protein expression in the human biopsies was evaluated by immunohistochemistry. Protein expression in the HCC cell lines was evaluated by immunofluorescence and Western blot, also the migration and invasive abilities of Huh7 cells were evaluated using shRNA-mediated inhibition. Results Our results indicated that these genes and proteins were overexpressed in HCC. Moreover, when the expression of CLIC5 and PODXL was inhibited in Huh7 cells, we observed decreased migration and invasion. Conclusion This study suggested that EZR, CLIC5 and PODXL could be biological markers to predict the prognosis of HCC and that these proteins participate in migration and invasion processes.
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Affiliation(s)
- Teresita N. J. Flores-Téllez
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN No. 2508 Col. San Pedro Zacatenco, México 14, CP 07360, México, Distrito Federal
| | - Tania V. Lopez
- Instituto Nacional De Medicina Genómica (INMEGEN), Periférico Sur 4809, Arenal Tepepan, Tlalpan, 14610 Ciudad de México, Distrito Federal
- * E-mail: (TVL); (SVT)
| | - Verónica Rocío Vásquez Garzón
- Facultad de Medicina y Cirugía, Universidad Benito Juárez de Oaxaca. Av Universidad S/N, Col. 5 Señores. C.P. 68120, México, Oaxaca
| | - Saúl Villa-Treviño
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN No. 2508 Col. San Pedro Zacatenco, México 14, CP 07360, México, Distrito Federal
- * E-mail: (TVL); (SVT)
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Nishio SY, Hattori M, Moteki H, Tsukada K, Miyagawa M, Naito T, Yoshimura H, Iwasa YI, Mori K, Shima Y, Sakuma N, Usami SI. Gene expression profiles of the cochlea and vestibular endorgans: localization and function of genes causing deafness. Ann Otol Rhinol Laryngol 2015; 124 Suppl 1:6S-48S. [PMID: 25814645 DOI: 10.1177/0003489415575549] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OBJECTIVES We sought to elucidate the gene expression profiles of the causative genes as well as the localization of the encoded proteins involved in hereditary hearing loss. METHODS Relevant articles (as of September 2014) were searched in PubMed databases, and the gene symbols of the genes reported to be associated with deafness were located on the Hereditary Hearing Loss Homepage using localization, expression, and distribution as keywords. RESULTS Our review of the literature allowed us to systematize the gene expression profiles for genetic deafness in the inner ear, clarifying the unique functions and specific expression patterns of these genes in the cochlea and vestibular endorgans. CONCLUSIONS The coordinated actions of various encoded molecules are essential for the normal development and maintenance of auditory and vestibular function.
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Affiliation(s)
- Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Mitsuru Hattori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hideaki Moteki
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Keita Tsukada
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Maiko Miyagawa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Takehiko Naito
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hidekane Yoshimura
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yoh-Ichiro Iwasa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kentaro Mori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yutaka Shima
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Naoko Sakuma
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Otorhinolaryngology and Head and Neck Surgery, Yokohama City University School of Medicine, Yokohama, Japan
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
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Al Khamici H, Brown LJ, Hossain KR, Hudson AL, Sinclair-Burton AA, Ng JPM, Daniel EL, Hare JE, Cornell BA, Curmi PMG, Davey MW, Valenzuela SM. Members of the chloride intracellular ion channel protein family demonstrate glutaredoxin-like enzymatic activity. PLoS One 2015; 10:e115699. [PMID: 25581026 PMCID: PMC4291220 DOI: 10.1371/journal.pone.0115699] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 11/26/2014] [Indexed: 01/07/2023] Open
Abstract
The Chloride Intracellular Ion Channel (CLIC) family consists of six evolutionarily conserved proteins in humans. Members of this family are unusual, existing as both monomeric soluble proteins and as integral membrane proteins where they function as chloride selective ion channels, however no function has previously been assigned to their soluble form. Structural studies have shown that in the soluble form, CLIC proteins adopt a glutathione S-transferase (GST) fold, however, they have an active site with a conserved glutaredoxin monothiol motif, similar to the omega class GSTs. We demonstrate that CLIC proteins have glutaredoxin-like glutathione-dependent oxidoreductase enzymatic activity. CLICs 1, 2 and 4 demonstrate typical glutaredoxin-like activity using 2-hydroxyethyl disulfide as a substrate. Mutagenesis experiments identify cysteine 24 as the catalytic cysteine residue in CLIC1, which is consistent with its structure. CLIC1 was shown to reduce sodium selenite and dehydroascorbate in a glutathione-dependent manner. Previous electrophysiological studies have shown that the drugs IAA-94 and A9C specifically block CLIC channel activity. These same compounds inhibit CLIC1 oxidoreductase activity. This work for the first time assigns a functional activity to the soluble form of the CLIC proteins. Our results demonstrate that the soluble form of the CLIC proteins has an enzymatic activity that is distinct from the channel activity of their integral membrane form. This CLIC enzymatic activity may be important for protecting the intracellular environment against oxidation. It is also likely that this enzymatic activity regulates the CLIC ion channel function.
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Affiliation(s)
- Heba Al Khamici
- School of Medical and Molecular Biosciences, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Louise J. Brown
- Department of Chemistry and Bimolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Khondker R. Hossain
- School of Medical and Molecular Biosciences, University of Technology Sydney, Sydney, New South Wales 2007, Australia
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Sydney, New South Wales 2234, Australia
| | - Amanda L. Hudson
- School of Medical and Molecular Biosciences, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Alxcia A. Sinclair-Burton
- School of Medical and Molecular Biosciences, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Jane Phui Mun Ng
- School of Medical and Molecular Biosciences, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Elizabeth L. Daniel
- Department of Chemistry and Bimolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Joanna E. Hare
- Department of Chemistry and Bimolecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Bruce A. Cornell
- Surgical Diagnostics, Roseville, Sydney, New South Wales 2069, Australia
| | - Paul M. G. Curmi
- School of Physics, University of New South Wales, Sydney, New South Wales 2052, Australia
- Centre for Applied Medical Research, St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Mary W. Davey
- School of Medical and Molecular Biosciences, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Stella M. Valenzuela
- School of Medical and Molecular Biosciences, University of Technology Sydney, Sydney, New South Wales 2007, Australia
- Centre for Health Technologies, University of Technology Sydney, Sydney, New South Wales 2007, Australia
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Al-Momany A, Li L, Alexander RT, Ballermann BJ. Clustered PI(4,5)P₂ accumulation and ezrin phosphorylation in response to CLIC5A. J Cell Sci 2014; 127:5164-78. [PMID: 25344252 DOI: 10.1242/jcs.147744] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
CLIC5A (encoded by CLIC5) is a component of the ezrin-NHERF2-podocalyxin complex in renal glomerular podocyte foot processes. We explored the mechanism(s) by which CLIC5A regulates ezrin function. In COS-7 cells, CLIC5A augmented ezrin phosphorylation without changing ezrin abundance, increased the association of ezrin with the cytoskeletal fraction and enhanced actin polymerization and the formation of cell surface projections. CLIC5A caused the phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] reporter RFP-PH-PLC to translocate from the cytosol to discrete plasma membrane clusters at the cell surface, where it colocalized with CLIC5A. Transiently expressed HA-PIP5Kα colocalized with GFP-CLIC5A and was pulled from cell lysates by GST-CLIC5A, and silencing of endogenous PIP5Kα abrogated CLIC5A-dependent ERM phosphorylation. N- and C-terminal deletion mutants of CLIC5A, which failed to associate with the plasma membrane, failed to colocalize with PIP5Kα, did not alter the abundance of PI(4,5)P2 plasma membrane clusters and failed to enhance ezrin phosphorylation. Relative to wild-type mice, in CLIC5-deficient mice, the phosphorylation of glomerular ezrin was diminished and the cytoskeletal association of both ezrin and NHERF2 was reduced. Therefore, the mechanism of CLIC5A action involves clustered plasma membrane PI(4,5)P2 accumulation through an interaction of CLIC5A with PI(4,5)P2-generating kinases, in turn facilitating ezrin activation and actin-dependent cell surface remodeling.
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Affiliation(s)
- Abass Al-Momany
- Department of Physiology, University of Alberta, Edmonton, AL T6G 2V2, Canada
| | - Laiji Li
- Department of Medicine (Nephrology), University of Alberta, Edmonton, AL T6G 2V2, Canada
| | - R Todd Alexander
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AL T6G 2V2, Canada
| | - Barbara J Ballermann
- Department of Physiology, University of Alberta, Edmonton, AL T6G 2V2, Canada Department of Medicine (Nephrology), University of Alberta, Edmonton, AL T6G 2V2, Canada
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Tsai WT, Hassan A, Sarkar P, Correa J, Metlagel Z, Jorgens DM, Auer M. From voxels to knowledge: a practical guide to the segmentation of complex electron microscopy 3D-data. J Vis Exp 2014:e51673. [PMID: 25145678 PMCID: PMC4448944 DOI: 10.3791/51673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Modern 3D electron microscopy approaches have recently allowed unprecedented insight into the 3D ultrastructural organization of cells and tissues, enabling the visualization of large macromolecular machines, such as adhesion complexes, as well as higher-order structures, such as the cytoskeleton and cellular organelles in their respective cell and tissue context. Given the inherent complexity of cellular volumes, it is essential to first extract the features of interest in order to allow visualization, quantification, and therefore comprehension of their 3D organization. Each data set is defined by distinct characteristics, e.g., signal-to-noise ratio, crispness (sharpness) of the data, heterogeneity of its features, crowdedness of features, presence or absence of characteristic shapes that allow for easy identification, and the percentage of the entire volume that a specific region of interest occupies. All these characteristics need to be considered when deciding on which approach to take for segmentation. The six different 3D ultrastructural data sets presented were obtained by three different imaging approaches: resin embedded stained electron tomography, focused ion beam- and serial block face- scanning electron microscopy (FIB-SEM, SBF-SEM) of mildly stained and heavily stained samples, respectively. For these data sets, four different segmentation approaches have been applied: (1) fully manual model building followed solely by visualization of the model, (2) manual tracing segmentation of the data followed by surface rendering, (3) semi-automated approaches followed by surface rendering, or (4) automated custom-designed segmentation algorithms followed by surface rendering and quantitative analysis. Depending on the combination of data set characteristics, it was found that typically one of these four categorical approaches outperforms the others, but depending on the exact sequence of criteria, more than one approach may be successful. Based on these data, we propose a triage scheme that categorizes both objective data set characteristics and subjective personal criteria for the analysis of the different data sets.
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Affiliation(s)
- Wen-Ting Tsai
- Life Sciences Division, Lawrence Berkeley National Laboratory
| | - Ahmed Hassan
- Life Sciences Division, Lawrence Berkeley National Laboratory
| | - Purbasha Sarkar
- Joint Bioenergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory
| | - Joaquin Correa
- Life Sciences Division, Lawrence Berkeley National Laboratory; National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory
| | - Zoltan Metlagel
- Life Sciences Division, Lawrence Berkeley National Laboratory
| | | | - Manfred Auer
- Life Sciences Division, Lawrence Berkeley National Laboratory; Joint Bioenergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory;
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