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Wang R, Cong Y, Qian D, Yan C, Gong D. Structural basis for double-stranded RNA recognition by SID1. Nucleic Acids Res 2024:gkae395. [PMID: 38742627 DOI: 10.1093/nar/gkae395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
The nucleic acid transport properties of the systemic RNAi-defective (SID) 1 family make them attractive targets for developing RNA-based therapeutics and drugs. However, the molecular basis for double-stranded (ds) RNA recognition by SID1 family remains elusive. Here, we report the cryo-EM structures of Caenorhabditis elegans (c) SID1 alone and in complex with dsRNA, both at a resolution of 2.2 Å. The dimeric cSID1 interacts with two dsRNA molecules simultaneously. The dsRNA is located at the interface between β-strand rich domain (BRD)1 and BRD2 and nearly parallel to the membrane plane. In addition to extensive ionic interactions between basic residues and phosphate backbone, several hydrogen bonds are formed between 2'-hydroxyl group of dsRNA and the contact residues. Additionally, the electrostatic potential surface shows three basic regions are fitted perfectly into three major grooves of dsRNA. These structural characteristics enable cSID1 to bind dsRNA in a sequence-independent manner and to distinguish between DNA and RNA. The cSID1 exhibits no conformational changes upon binding dsRNA, with the exception of a few binding surfaces. Structural mapping of dozens of loss-of-function mutations allows potential interpretation of their diverse functional mechanisms. Our study marks an important step toward mechanistic understanding of the SID1 family-mediated dsRNA uptake.
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Affiliation(s)
- Runhao Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Ye Cong
- School of Life Sciences, Tsinghua University, Beijing, 100084, China. Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China
| | - Dandan Qian
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Chuangye Yan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China. Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China
| | - Deshun Gong
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
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2
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Cañón-Beltrán K, Cajas YN, Almpanis V, Egido SG, Gutierrez-Adan A, González EM, Rizos D. MicroRNA-148b secreted by bovine oviductal extracellular vesicles enhance embryo quality through BPM/TGF-beta pathway. Biol Res 2024; 57:11. [PMID: 38520036 PMCID: PMC10960404 DOI: 10.1186/s40659-024-00488-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: 10/30/2023] [Accepted: 02/29/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Extracellular vesicles (EVs) and their cargoes, including MicroRNAs (miRNAs) play a crucial role in cell-to-cell communication. We previously demonstrated the upregulation of bta-mir-148b in EVs from oviductal fluid of cyclic cows. This miRNA is linked to the TGF-β pathway in the cell proliferation. Our aim was to verify whether miR-148b is taken up by embryos through gymnosis, validate its target genes, and investigate the effect of miR-148b supplementation on early embryo development and quality. METHODS Zygotes were cultured in SOF + 0.3% BSA (Control) or supplemented with: 1 µM miR-148b mimics during: D1-D7 (miR148b) or D1-D4 (miR148b-OV: representing miRNA effect in the oviduct) or D4-D7 (miR148b-UT: representing miRNA effect in the uterus) or 1 µM control mimics was used during: D1-D7 (CMimic). Embryos at ≥ 16-cells and D7 blastocysts (BD7) were collected to examine the mRNA abundance of transcripts linked to the TGF-β pathway (TGFBR2, SMAD1, SMAD2, SMAD3, SMAD5, BMPR2, RPS6KB1, POU5F1, NANOG), total cell number (TC), trophectoderm (TE), and inner cell mass (ICM) were also evaluated. One-way ANOVA was used for all analyses. RESULTS We demonstrated that miR-148b can be taken up in both 16-cell embryos and BD7 by gymnosis, and we observed a decrease in SMAD5 mRNA, suggesting it's a potential target of miR-148b. Cleavage and blastocysts rates were not affected in any groups; however, supplementation of miR-148b mimics had a positive effect on TC, TE and ICM, with values of 136.4 ± 1.6, 92.5 ± 0.9, 43.9 ± 1.3 for miR148b and 135.3 ± 1.5, 92.6 ± 1.2, 42.7 ± 0.8, for miR148b-OV group. Furthermore, mRNA transcripts of SMAD1 and SMAD5 were decreased (P ≤ 0.001) in 16-cell embryos and BD7 from miR148b and miR148b-OV groups, while POU5F1 and NANOG were upregulated (P ≤ 0.001) in BD7 and TGFBR2 was only downregulated in 16-cell embryos. pSMAD1/5 levels were higher in the miR148b and miR148b-OV groups. CONCLUSIONS Our findings suggest that supplementation of bta-miR-148b mimics during the entire culture period (D1 - D7) or from D1 - D4 improves embryo quality and influences the TGF-β signaling pathway by altering the transcription of genes associated with cellular differentiation and proliferation. This highlights the importance of miR-148b on embryo quality and development.
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Affiliation(s)
- Karina Cañón-Beltrán
- Department of Biochemistry and Molecular Biology, Veterinary Faculty, Complutense University of Madrid (UCM), Madrid, Spain
- Programa de Medicina Veterinaria y Zootecnia, Corporación Universitaria del Huila (CORHUILA), Grupo Kyron, Huila, Colombia
| | - Yulia N Cajas
- Department Agrarian Production, Technical University of Madrid (UPM), Madrid, Spain
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), Loja, Ecuador
| | - Vasileios Almpanis
- Department of Animal Reproduction, National Institute for Agriculture and Food Research and Technology (CSIC-INIA), Madrid, Spain
| | - Sandra Guisado Egido
- Department of Animal Reproduction, National Institute for Agriculture and Food Research and Technology (CSIC-INIA), Madrid, Spain
| | - Alfonso Gutierrez-Adan
- Department of Animal Reproduction, National Institute for Agriculture and Food Research and Technology (CSIC-INIA), Madrid, Spain
| | - Encina M González
- Department of Anatomy and Embryology, Veterinary Faculty, Complutense University of Madrid (UCM), Madrid, Spain.
| | - Dimitrios Rizos
- Department of Animal Reproduction, National Institute for Agriculture and Food Research and Technology (CSIC-INIA), Madrid, Spain.
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3
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Zhang N, Tang W, Torres L, Wang X, Ajaj Y, Zhu L, Luan Y, Zhou H, Wang Y, Zhang D, Kurbatov V, Khan SA, Kumar P, Hidalgo A, Wu D, Lu J. Cell surface RNAs control neutrophil recruitment. Cell 2024; 187:846-860.e17. [PMID: 38262409 PMCID: PMC10922858 DOI: 10.1016/j.cell.2023.12.033] [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: 03/27/2023] [Revised: 10/30/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024]
Abstract
RNAs localizing to the outer cell surface have been recently identified in mammalian cells, including RNAs with glycan modifications known as glycoRNAs. However, the functional significance of cell surface RNAs and their production are poorly known. We report that cell surface RNAs are critical for neutrophil recruitment and that the mammalian homologs of the sid-1 RNA transporter are required for glycoRNA expression. Cell surface RNAs can be readily detected in murine neutrophils, the elimination of which substantially impairs neutrophil recruitment to inflammatory sites in vivo and reduces neutrophils' adhesion to and migration through endothelial cells. Neutrophil glycoRNAs are predominantly on cell surface, important for neutrophil-endothelial interactions, and can be recognized by P-selectin (Selp). Knockdown of the murine Sidt genes abolishes neutrophil glycoRNAs and functionally mimics the loss of cell surface RNAs. Our data demonstrate the biological importance of cell surface glycoRNAs and highlight a noncanonical dimension of RNA-mediated cellular functions.
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Affiliation(s)
- Ningning Zhang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Wenwen Tang
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Lidiane Torres
- Department of Cell Biology and Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Xujun Wang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yasmeen Ajaj
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Li Zhu
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven CT 06511
| | - Yi Luan
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Hongyue Zhou
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Yadong Wang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cooperative Center of Excellence in Hematology, New Haven, CT 12208, USA
| | - Dingyao Zhang
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Computational Biology and Bioinformatics Graduate Program, Yale University, New Haven, CT 06520, USA
| | - Vadim Kurbatov
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Surgery, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Sajid A Khan
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven CT 06511
| | - Andres Hidalgo
- Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Dianqing Wu
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Vascular Biology and Therapeutics Program and Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06519, USA; Yale Cancer Center, New Haven, CT 06520, USA.
| | - Jun Lu
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cooperative Center of Excellence in Hematology, New Haven, CT 12208, USA; Yale Cancer Center, New Haven, CT 06520, USA; Yale Center for RNA Science and Medicine, New Haven, CT 06520, USA.
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4
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Yang T, Xiao H, Chen X, Zheng L, Guo H, Wang J, Jiang X, Zhang CY, Yang F, Ji X. Characterization of N-glycosylation and its functional role in SIDT1-Mediated RNA uptake. J Biol Chem 2024; 300:105654. [PMID: 38237680 PMCID: PMC10850970 DOI: 10.1016/j.jbc.2024.105654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/08/2024] Open
Abstract
The mammalian SID-1 transmembrane family members, SIDT1 and SIDT2, are multipass transmembrane proteins that mediate the cellular uptake and intracellular trafficking of nucleic acids, playing important roles in the immune response and tumorigenesis. Previous work has suggested that human SIDT1 and SIDT2 are N-glycosylated, but the precise site-specific N-glycosylation information and its functional contribution remain unclear. In this study, we use high-resolution liquid chromatography tandem mass spectrometry to comprehensively map the N-glycosites and quantify the N-glycosylation profiles of SIDT1 and SIDT2. Further molecular mechanistic probing elucidates the essential role of N-linked glycans in regulating cell surface expression, RNA binding, protein stability, and RNA uptake of SIDT1. Our results provide crucial information about the potential functional impact of N-glycosylation in the regulation of SIDT1-mediated RNA uptake and provide insights into the molecular mechanisms of this promising nucleic acid delivery system with potential implications for therapeutic applications.
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Affiliation(s)
- Tingting Yang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Haonan Xiao
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Le Zheng
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Hangtian Guo
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Jiaqi Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Xiaohong Jiang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Chen-Yu Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, China.
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, China; Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China; Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, Jiangsu, China.
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5
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Zheng L, Yang T, Guo H, Qi C, Lu Y, Xiao H, Gao Y, Liu Y, Yang Y, Zhou M, Nguyen HC, Zhu Y, Sun F, Zhang CY, Ji X. Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity. Cell Res 2024; 34:80-83. [PMID: 37932445 PMCID: PMC10770124 DOI: 10.1038/s41422-023-00893-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/13/2023] [Indexed: 11/08/2023] Open
Affiliation(s)
- Le Zheng
- National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China
| | - Tingting Yang
- National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China
| | - Hangtian Guo
- National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China.
| | - Chen Qi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuchi Lu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Lingang Laboratory, Shanghai, China
| | - Haonan Xiao
- National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Yue Liu
- National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China
| | - Yixuan Yang
- National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China
| | - Mengru Zhou
- National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China
| | - Henry C Nguyen
- National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China
| | - Yun Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Fei Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Chen-Yu Zhang
- National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China.
| | - Xiaoyun Ji
- National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China.
- Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, Jiangsu, China.
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6
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Song Y, Gu J, You J, Tao Y, Zhang Y, Wang L, Gao J. The functions of SID1 transmembrane family, member 2 (Sidt2). FEBS J 2023; 290:4626-4637. [PMID: 36176242 DOI: 10.1111/febs.16641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/30/2022]
Abstract
The SID1 transmembrane family, member 2, namely, Sidt2, is a highly glycosylated multichannel lysosomal transmembrane protein, but its specific physiological function remains unknown. Lysosomal membrane proteins are very important for the executive functioning of lysosomes. As an important part of the lysosomal membrane, Sidt2 can maintain the normal morphology of lysosomes and help stabilize them from the acidic pH environment within. As a receptor/transporter, it binds and transports nucleic acids and mediates the uptake and degradation of RNA and DNA by the lysosome. During glucose metabolism, deletion of Sidt2 can cause an increase in fasting blood glucose and the impairment of grape tolerance, which is closely related to the secretion of insulin. During lipid metabolism, the loss of Sidt2 can cause hepatic steatosis and lipid metabolism disorders and can also play a role in signal regulation and transport. Here, we review the function of the lysosomal membrane protein Sidt2, and focus on its role in glucose and lipid metabolism, autophagy and nucleotide (DNA/RNA) transport.
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Affiliation(s)
- Yingying Song
- Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Department of Endocrinology and Genetic Metabolism, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
| | - Jing Gu
- Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Department of Endocrinology and Genetic Metabolism, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
| | - Jingya You
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
- School of Clinical Medicine, Wannan Medical College, Wuhu, China
| | - Yiyang Tao
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
- School of Clinical Medicine, Wannan Medical College, Wuhu, China
| | - Yao Zhang
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
| | - Lizhuo Wang
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
- Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu, China
| | - Jialin Gao
- Department of Endocrinology and Genetic Metabolism, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Department of Endocrinology and Genetic Metabolism, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
- Anhui Province Key Laboratory of Biological Macro-Molecules Research, Wannan Medical College, Wuhu, China
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7
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Wang LJ, Lee YC, Chiou JT, Chen YJ, Chang LS. Effects of SIDT2 on the miR-25/NOX4/HuR axis and SIRT3 mRNA stability lead to ROS-mediated TNF-α expression in hydroquinone-treated leukemia cells. Cell Biol Toxicol 2023; 39:2207-2225. [PMID: 35302183 DOI: 10.1007/s10565-022-09705-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/28/2022] [Indexed: 11/02/2022]
Abstract
Our previous studies indicated that the benzene metabolite hydroquinone (HQ) evokes the ROS/p38 MAPK/protein phosphatase 2A/tristetraprolin axis, leading to increased TNF-α expression in human acute myeloid leukemia cell lines U937 and HL-60. In this study, we aimed to identify the upstream pathway involved in ROS-mediated TNF-α expression. HQ treatment increased SIDT2 expression, which subsequently decreased miR-25 and SIRT3 expression in U937 cells. Notably, miR-25 downregulation promoted SIDT2 expression in HQ-treated U937 cells. SIDT2 induced lysosomal degradation of SIRT3 mRNA, but inhibited miR-25 expression through a lysosome-independent pathway. MiR-25 inhibition reduced NOX4 mRNA turnover, resulting in increased NOX4 protein levels. NOX4 induces mitochondrial ROS production and HuR downregulation. Restoration of HuR expression increased SIRT3 expression, suggesting that NOX4-mediated HuR downregulation promotes SIDT2-mediated degradation of SIRT3 mRNA. Inhibition of NOX4 or SIRT3 overexpression abolished HQ-induced ROS production, thereby abolishing TNF-α upregulation. Overall, these results indicate that SIDT2 regulates the miR-25/NOX4/HuR axis and SIRT3 mRNA destabilization, leading to ROS-mediated TNF-α upregulation in HQ-treated U937 cells. HQ-induced increase in TNF-α expression in HL-60 cells was also mediated through a similar pathway.
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Affiliation(s)
- Liang-Jun Wang
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
| | - Yuan-Chin Lee
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
| | - Jing-Ting Chiou
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
| | - Ying-Jung Chen
- Department of Fragrance and Cosmetic Science, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Long-Sen Chang
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan.
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
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8
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Chai P, Lebedenko CG, Flynn RA. RNA Crossing Membranes: Systems and Mechanisms Contextualizing Extracellular RNA and Cell Surface GlycoRNAs. Annu Rev Genomics Hum Genet 2023; 24:85-107. [PMID: 37068783 DOI: 10.1146/annurev-genom-101722-101224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The subcellular localization of a biopolymer often informs its function. RNA is traditionally confined to the cytosolic and nuclear spaces, where it plays critical and conserved roles across nearly all biochemical processes. Our recent observation of cell surface glycoRNAs may further explain the extracellular role of RNA. While cellular membranes are efficient gatekeepers of charged polymers such as RNAs, a large body of research has demonstrated the accumulation of specific RNA species outside of the cell, termed extracellular RNAs (exRNAs). Across various species and forms of life, protein pores have evolved to transport RNA across membranes, thus providing a mechanistic path for exRNAs to achieve their extracellular topology. Here, we review types of exRNAs and the pores capable of RNA transport to provide a logical and testable path toward understanding the biogenesis and regulation of cell surface glycoRNAs.
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Affiliation(s)
- Peiyuan Chai
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Charlotta G Lebedenko
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
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9
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Qian D, Cong Y, Wang R, Chen Q, Yan C, Gong D. Structural insight into the human SID1 transmembrane family member 2 reveals its lipid hydrolytic activity. Nat Commun 2023; 14:3568. [PMID: 37322007 PMCID: PMC10272179 DOI: 10.1038/s41467-023-39335-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 06/08/2023] [Indexed: 06/17/2023] Open
Abstract
The systemic RNAi-defective (SID) transmembrane family member 2 (SIDT2) is a putative nucleic acid channel or transporter that plays essential roles in nucleic acid transport and lipid metabolism. Here, we report the cryo-electron microscopy (EM) structures of human SIDT2, which forms a tightly packed dimer with extensive interactions mediated by two previously uncharacterized extracellular/luminal β-strand-rich domains and the unique transmembrane domain (TMD). The TMD of each SIDT2 protomer contains eleven transmembrane helices (TMs), and no discernible nucleic acid conduction pathway has been identified within the TMD, suggesting that it may act as a transporter. Intriguingly, TM3-6 and TM9-11 form a large cavity with a putative catalytic zinc atom coordinated by three conserved histidine residues and one aspartate residue lying approximately 6 Å from the extracellular/luminal surface of the membrane. Notably, SIDT2 can hydrolyze C18 ceramide into sphingosine and fatty acid with a slow rate. The information presented advances the understanding of the structure-function relationships in the SID1 family proteins.
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Affiliation(s)
- Dandan Qian
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, 300350, China
| | - Ye Cong
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
| | - Runhao Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, 300350, China
| | - Quan Chen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, 300350, China.
| | - Chuangye Yan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China.
| | - Deshun Gong
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, 300350, China.
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10
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Anwar S, Mir F, Yokota T. Enhancing the Effectiveness of Oligonucleotide Therapeutics Using Cell-Penetrating Peptide Conjugation, Chemical Modification, and Carrier-Based Delivery Strategies. Pharmaceutics 2023; 15:pharmaceutics15041130. [PMID: 37111616 PMCID: PMC10140998 DOI: 10.3390/pharmaceutics15041130] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Oligonucleotide-based therapies are a promising approach for treating a wide range of hard-to-treat diseases, particularly genetic and rare diseases. These therapies involve the use of short synthetic sequences of DNA or RNA that can modulate gene expression or inhibit proteins through various mechanisms. Despite the potential of these therapies, a significant barrier to their widespread use is the difficulty in ensuring their uptake by target cells/tissues. Strategies to overcome this challenge include cell-penetrating peptide conjugation, chemical modification, nanoparticle formulation, and the use of endogenous vesicles, spherical nucleic acids, and smart material-based delivery vehicles. This article provides an overview of these strategies and their potential for the efficient delivery of oligonucleotide drugs, as well as the safety and toxicity considerations, regulatory requirements, and challenges in translating these therapies from the laboratory to the clinic.
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Affiliation(s)
- Saeed Anwar
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Farin Mir
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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11
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Zhao JC, Saleh A, Crooke ST. SIDT2 Inhibits Phosphorothioate Antisense Oligonucleotide Activity by Regulating Cellular Localization of Lysosomes. Nucleic Acid Ther 2022; 33:108-116. [PMID: 36576400 DOI: 10.1089/nat.2022.0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Phosphorothioate (PS)-modified antisense oligonucleotide (ASO) drugs enter cells through endocytic pathways where a majority are entrapped within membrane-bound endosomes and lysosomes, representing a limiting step for antisense activity. While late endosomes have been identified as a major site for productive PS-ASO release, how lysosomes regulate PS-ASO activity beyond macromolecule degradation remains not fully understood. In this study, we reported that SID1 transmembrane family, member 2 (SIDT2), a lysosome transmembrane protein, can robustly regulate PS-ASO activity. We showed that SIDT2 is required for the proper colocalization between PS-ASO and lysosomes, suggesting an important role of SIDT2 in the entrapment of PS-ASOs in lysosomes. Mechanistically, we revealed that SIDT2 regulates lysosome cellular location. Lysosome location is largely determined by its movement along microtubules. Interestingly, we also observed an enrichment of proteins involved in microtubule function among SIDT2-binding proteins, suggesting that SIDT2 regulates lysosome location via its interaction with microtubule-related proteins. Overall, our data suggest that lysosome protein SIDT2 inhibits PS-ASO activity potentially through its interaction with microtubule-related proteins to place lysosomes at perinuclear regions, thus, facilitating PS-ASO's localization to lysosomes for degradation.
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Affiliation(s)
- Jing Crystal Zhao
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Aurian Saleh
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, California, USA
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12
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Bakowski K, Vogel S. Evolution of complexity in non-viral oligonucleotide delivery systems: from gymnotic delivery through bioconjugates to biomimetic nanoparticles. RNA Biol 2022; 19:1256-1275. [PMID: 36411594 PMCID: PMC9683052 DOI: 10.1080/15476286.2022.2147278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
From the early days of research on RNA biology and biochemistry, there was an interest to utilize this knowledge and RNA itself for therapeutic applications. Today, we have a series of oligonucleotide therapeutics on the market and many more in clinical trials. These drugs - exploit different chemistries of oligonucleotides, such as modified DNAs and RNAs, peptide nucleic acids (PNAs) or phosphorodiamidate morpholino oligomers (PMOs), and different mechanisms of action, such as RNA interference (RNAi), targeted RNA degradation, splicing modulation, gene expression and modification. Despite major successes e.g. mRNA vaccines developed against SARS-CoV-2 to control COVID-19 pandemic, development of therapies for other diseases is still limited by inefficient delivery of oligonucleotides to specific tissues and organs and often prohibitive costs for the final drug. This is even more critical when targeting multifactorial disorders and patient-specific biological variations. In this review, we will present the evolution of complexity of oligonucleotide delivery methods with focus on increasing complexity of formulations from gymnotic delivery to bioconjugates and to lipid nanoparticles in respect to developments that will enable application of therapeutic oligonucleotides as drugs in personalized therapies.
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Affiliation(s)
- Kamil Bakowski
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark,CONTACT Stefan Vogel Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230Odense, Denmark
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13
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Perturbing the Normal Level of SIDT1 Suppresses the Naked ASO Effect. J Nucleic Acids 2021; 2021:2458470. [PMID: 34824869 PMCID: PMC8610720 DOI: 10.1155/2021/2458470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 11/18/2022] Open
Abstract
Although antisense oligonucleotide (ASO) therapeutics can be taken up by living cells without carrier molecules, a large part of incorporated ASOs are trapped in the endosomes and do not exert therapeutic effects. To improve their therapeutic effects, it would be important to elucidate the mechanism of cellular uptake and intracellular trafficking of ASOs. In this study, we investigated how SIDT1 affects cellular uptake and intracellular trafficking of ASOs. Fluorescence microscopic analysis suggested that most of naked ASOs are trafficked to the lysosomes via the endosomes. The data obtained from flow cytometry and fluorescence microscopy together showed that although the SIDT1 level barely affects the total cellular uptake of ASOs, it appears to affect the intracellular trafficking of ASOs. We also showed that SIDT1 exists mainly in the endoplasmic reticulum and that perturbing the normal level of SIDT1 suppresses the antisense effect of the naked ASO targeting miR-16.
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14
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Bost JP, Barriga H, Holme MN, Gallud A, Maugeri M, Gupta D, Lehto T, Valadi H, Esbjörner EK, Stevens MM, El-Andaloussi S. Delivery of Oligonucleotide Therapeutics: Chemical Modifications, Lipid Nanoparticles, and Extracellular Vesicles. ACS NANO 2021; 15:13993-14021. [PMID: 34505766 PMCID: PMC8482762 DOI: 10.1021/acsnano.1c05099] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 05/04/2023]
Abstract
Oligonucleotides (ONs) comprise a rapidly growing class of therapeutics. In recent years, the list of FDA-approved ON therapies has rapidly expanded. ONs are small (15-30 bp) nucleotide-based therapeutics which are capable of targeting DNA and RNA as well as other biomolecules. ONs can be subdivided into several classes based on their chemical modifications and on the mechanisms of their target interactions. Historically, the largest hindrance to the widespread usage of ON therapeutics has been their inability to effectively internalize into cells and escape from endosomes to reach their molecular targets in the cytosol or nucleus. While cell uptake has been improved, "endosomal escape" remains a significant problem. There are a range of approaches to overcome this, and in this review, we focus on three: altering the chemical structure of the ONs, formulating synthetic, lipid-based nanoparticles to encapsulate the ONs, or biologically loading the ONs into extracellular vesicles. This review provides a background to the design and mode of action of existing FDA-approved ONs. It presents the most common ON classifications and chemical modifications from a fundamental scientific perspective and provides a roadmap of the cellular uptake pathways by which ONs are trafficked. Finally, this review delves into each of the above-mentioned approaches to ON delivery, highlighting the scientific principles behind each and covering recent advances.
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Affiliation(s)
- Jeremy P. Bost
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
| | - Hanna Barriga
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Margaret N. Holme
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Audrey Gallud
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg 41296, Sweden
- Advanced
Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg 43150, Sweden
| | - Marco Maugeri
- Department
of Rheumatology and Inflammation Research, Institute of Medicine,
Sahlgrenska Academy, University of Gothenburg, Gothenburg 41390, Sweden
| | - Dhanu Gupta
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
| | - Taavi Lehto
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
- Institute
of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Hadi Valadi
- Department
of Rheumatology and Inflammation Research, Institute of Medicine,
Sahlgrenska Academy, University of Gothenburg, Gothenburg 41390, Sweden
| | - Elin K. Esbjörner
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, Gothenburg 41296, Sweden
| | - Molly M. Stevens
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
- Department
of Materials, Department of Bioengineering, Institute of Biomedical
Engineering, Imperial College London, London SW7 2BU, United Kingdom
| | - Samir El-Andaloussi
- Department
of Laboratory Medicine, Karolinska Institutet, Huddinge 14152, Sweden
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15
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Bin L, Malley C, Taylor P, Preethi Boorgula M, Chavan S, Daya M, Mathias M, Shankar G, Rafaels N, Vergara C, Potee J, Campbell M, Hanifin JM, Simpson E, Schneider LC, Gallo RL, Hata T, Paller AS, De Benedetto A, Beck LA, Ong PY, Guttman‐Yassky E, Richers B, Baraghoshi D, Ruczinski I, Barnes KC, Leung DYM, Mathias RA. Whole genome sequencing identifies novel genetic mutations in patients with eczema herpeticum. Allergy 2021; 76:2510-2523. [PMID: 33548076 DOI: 10.1111/all.14762] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 12/11/2020] [Accepted: 01/04/2021] [Indexed: 12/28/2022]
Abstract
BACKGROUND Eczema herpeticum (EH) is a rare complication of atopic dermatitis (AD) caused by disseminated herpes simplex virus (HSV) infection. The role of rare and/or deleterious genetic variants in disease etiology is largely unknown. This study aimed to identify genes that harbor damaging genetic variants associated with HSV infection in AD with a history of recurrent eczema herpeticum (ADEH+). METHODS Whole genome sequencing (WGS) was performed on 49 recurrent ADEH+ (≥3 EH episodes), 491 AD without a history of eczema herpeticum (ADEH-) and 237 non-atopic control (NA) subjects. Variants were annotated, and a gene-based approach (SKAT-O) was used to identify genes harboring damaging genetic variants associated with ADEH+. Genes identified through WGS were studied for effects on HSV responses and keratinocyte differentiation. RESULTS Eight genes were identified in the comparison of recurrent ADEH+to ADEH-and NA subjects: SIDT2, CLEC7A, GSTZ1, TPSG1, SP110, RBBP8NL, TRIM15, and FRMD3. Silencing SIDT2 and RBBP8NL in normal human primary keratinocytes (NHPKs) led to significantly increased HSV-1 replication. SIDT2-silenced NHPKs had decreased gene expression of IFNk and IL1b in response to HSV-1 infection. RBBP8NL-silenced NHPKs had decreased gene expression of IFNk, but increased IL1b. Additionally, silencing SIDT2 and RBBP8NL also inhibited gene expression of keratinocyte differentiation markers keratin 10 (KRT10) and loricrin (LOR). CONCLUSION SIDT2 and RBBP8NL participate in keratinocyte's response to HSV-1 infection. SIDT2 and RBBP8NL also regulate expression of keratinocyte differentiation genes of KRT10 and LOR.
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Affiliation(s)
- Lianghua Bin
- Department of Pediatrics National Jewish Health Denver CO USA
| | - Claire Malley
- Division of Allergy and Clinical Immunology Johns Hopkins University Baltimore MD USA
| | - Patricia Taylor
- Department of Pediatrics National Jewish Health Denver CO USA
| | | | - Sameer Chavan
- Department of Medicine University of Colorado Aurora CO USA
| | - Michelle Daya
- Department of Medicine University of Colorado Aurora CO USA
| | - Malaika Mathias
- Division of Allergy and Clinical Immunology Johns Hopkins University Baltimore MD USA
| | - Gautam Shankar
- Division of Allergy and Clinical Immunology Johns Hopkins University Baltimore MD USA
| | | | | | | | | | | | - Eric Simpson
- Oregon Health & Science University Portland OR USA
| | | | - Richard L. Gallo
- Department of Dermatology University of California San Diego CA USA
| | - Tissa Hata
- Department of Dermatology University of California San Diego CA USA
| | - Amy S. Paller
- Northwestern University Feinberg School of Medicine Chicago IL USA
| | | | - Lisa A. Beck
- University of Rochester Medical Center Rochester NY USA
| | - Peck Y. Ong
- Children’s Hospital Los Angeles University of Southern California Los Angeles CA USA
| | | | | | | | - Ingo Ruczinski
- Department of Biostatistics Bloomberg School of Public Health Johns Hopkins University Baltimore MD USA
| | | | | | - Rasika A. Mathias
- Division of Allergy and Clinical Immunology Johns Hopkins University Baltimore MD USA
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16
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Lehot V, Kuhn I, Nothisen M, Erb S, Kolodych S, Cianférani S, Chaubet G, Wagner A. Non-specific interactions of antibody-oligonucleotide conjugates with living cells. Sci Rep 2021; 11:5881. [PMID: 33723336 PMCID: PMC7961061 DOI: 10.1038/s41598-021-85352-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/29/2021] [Indexed: 11/15/2022] Open
Abstract
Antibody-Oligonucleotide Conjugates (AOCs) represent an emerging class of functionalized antibodies that have already been used in a wide variety of applications. While the impact of dye and drug conjugation on antibodies' ability to bind their target has been extensively studied, little is known about the effect caused by the conjugation of hydrophilic and charged payloads such as oligonucleotides on the functions of an antibody. Previous observations of non-specific interactions of nucleic acids with untargeted cells prompted us to further investigate their impact on AOC binding abilities and cell selectivity. We synthesized a series of single- and double-stranded AOCs, as well as a human serum albumin-oligonucleotide conjugate, and studied their interactions with both targeted and non-targeted living cells using a time-resolved analysis of ligand binding assay. Our results indicate that conjugation of single strand oligonucleotides to proteins induce consistent non-specific interactions with cell surfaces while double strand oligonucleotides have little or no effect, depending on the preparation method.
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Affiliation(s)
- Victor Lehot
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Isabelle Kuhn
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Marc Nothisen
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Stéphane Erb
- BioOrganicMass Spectrometry Laboratory (LSMBO), IPHC, University of Strasbourg, 25 rue Becquerel, 67087, Strasbourg, France
| | - Sergii Kolodych
- Syndivia SAS, ISIS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Sarah Cianférani
- BioOrganicMass Spectrometry Laboratory (LSMBO), IPHC, University of Strasbourg, 25 rue Becquerel, 67087, Strasbourg, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France.
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17
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Herkt M, Thum T. Pharmacokinetics and Proceedings in Clinical Application of Nucleic Acid Therapeutics. Mol Ther 2021; 29:521-539. [PMID: 33188937 PMCID: PMC7854291 DOI: 10.1016/j.ymthe.2020.11.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/27/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023] Open
Abstract
Oligonucleotide therapeutics are a novel promising class of drugs designed to specifically target either coding or non-coding RNA molecules to revolutionize treatment of various diseases. During preclinical development, investigations of the pharmacokinetic characteristics of these oligonucleotide-based drug candidates are essential. Oligonucleotides possess a long history of chemical modifications to enhance their stability and binding affinity, as well as reducing toxicity. Phosphorothioate backbone modifications of oligonucleotides were a hallmark of this development process that greatly enhanced plasma stability and protein binding of these agents. Modifications such as 2'-O-methylation further improved stability, while other modifications of the ribose, such as locked nucleic acid (LNA) modification, significantly increased binding affinity, potency, and tissue half-life. These attributes render oligonucleotide therapeutics able to regulate protein expression in both directions depending on the target RNA. Thus, a growing interest has emerged using these oligonucleotides in the treatment of neurodegenerative and cardiac disorders as well as cancer, since the deregulation of certain coding and non-coding RNAs plays a key role in the development of these diseases. Cutting edge research is being performed in the field of non-coding RNAs, identifying potential therapeutic targets, and developing novel oligonucleotide-based agents that outperform classical drugs. Some of these agents are either in clinical trials showing promising results or are already US Food and Drug Administration (FDA) approved, with more oligonucleotides being developed for therapeutic purposes. This is the advent of mechanism-based next-generation therapeutics for a wide range of diseases.
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Affiliation(s)
- Markus Herkt
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School (MHH), Hannover, Germany.
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School (MHH), Hannover, Germany; REBIRTH Center for Translational Regenerative Medicine, Hannover Medical School (MHH), Hannover, Germany; Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany.
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18
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Hase K, Contu VR, Kabuta C, Sakai R, Takahashi M, Kataoka N, Hakuno F, Takahashi SI, Fujiwara Y, Wada K, Kabuta T. Cytosolic domain of SIDT2 carries an arginine-rich motif that binds to RNA/DNA and is important for the direct transport of nucleic acids into lysosomes. Autophagy 2020; 16:1974-1988. [PMID: 31944164 PMCID: PMC7595612 DOI: 10.1080/15548627.2020.1712109] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/25/2019] [Accepted: 12/30/2019] [Indexed: 12/26/2022] Open
Abstract
RNautophagy and DNautophagy (RDA) are unconventional autophagic pathways where nucleic acids are directly transported through the lysosomal membrane, then degraded inside lysosomes. We have previously shown that bitopic protein LAMP2C and putative RNA transporter SIDT2, both lysosomal membrane proteins, mediate the direct transport of nucleic acids into lysosomes and that LAMP2C interacts with the nucleic acids and functions as a receptor during RDA. Because SIDT2-mediated RDA occurs in isolated lysosomes that lack LAMP2C, in this study, we tested the hypothesis that SIDT2 itself could also interact with the nucleic acids. Our results show that SIDT2 directly binds RNA and DNA through an arginine-rich motif (ARM) located within its main cytosolic domain, and disruption of this motif dramatically impairs SIDT2-mediated RNautophagic activity. We also found that SIDT2 interacts with exon 1 of HTT (huntingtin) transcript through the ARM in a CAG-dependent manner. Moreover, overexpression of SIDT2 promoted degradation of HTT mRNA and reduced the levels of polyglutamine-expanded HTT aggregates, hallmarks of Huntington disease. In addition, a comparative analysis of LAMP2C and SIDT2 functions at the cellular level revealed that the two proteins exert a synergistic effect on RNautophagic activity and that the ARMs which mediate the interactions of SIDT2 and LAMP2C with RNA are essential for the synergy. Together, our results point out the importance of nucleic acid-binding capacity of SIDT2 for its function in translocating nucleic acids through the lipid bilayer and suggests a potential application of RNautophagy activation to reduce the expression levels of disease-causing toxic proteins. Abbreviations: ACTB/β-actin: actin beta; ARM: arginine-rich motif; CBB: Coomassie Brilliant Blue; CD: cytosolic domain; COX4I1/COX4: cytochrome c oxidase subunit 4I1; E. coli: Escherichia coli; EGFP: enhanced green fluorescent protein; EtBr: ethidium bromide; FITC: fluorescein isothiocyanate; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GOLGA2/GM130: golgin A2; GST: glutathione S-transferase; HRP: horseradish peroxidase; HSPA5/GRP78: heat shock protein family A (Hsp70) member 5; HTT: huntingtin; HTTex1: exon 1 of the HTT gene; LAMP2: lysosomal associated membrane protein 2; LMNA: lamin A/C; PAGE: polyacrylamide gel electrophoresis; PBS: phosphate-buffered saline; PEI: polyethyleneimine; polyQ: polyglutamine; qPCR: quantitative PCR; RAB5A: RAB5A, member RAS oncogene family; RDA: RNautophagy and DNautophagy; SCARB2/LIMP2: scavenger receptor class B member 2; SDS: sodium dodecyl sulfate; SID-1: systemic RNA interference deficient-1; SIDT2: SID1 transmembrane family member 2; WT: wild type.
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Affiliation(s)
- Katsunori Hase
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
- Department of Animal Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Viorica Raluca Contu
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Chihana Kabuta
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Ryohei Sakai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Masayuki Takahashi
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Naoyuki Kataoka
- Department of Animal Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Fumihiko Hakuno
- Department of Animal Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Shin-Ichiro Takahashi
- Department of Animal Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Japan
| | - Yuuki Fujiwara
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Keiji Wada
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Tomohiro Kabuta
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
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19
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van Oostrum M, Campbell B, Seng C, Müller M, Tom Dieck S, Hammer J, Pedrioli PGA, Földy C, Tyagarajan SK, Wollscheid B. Surfaceome dynamics reveal proteostasis-independent reorganization of neuronal surface proteins during development and synaptic plasticity. Nat Commun 2020; 11:4990. [PMID: 33020478 PMCID: PMC7536423 DOI: 10.1038/s41467-020-18494-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 08/24/2020] [Indexed: 12/27/2022] Open
Abstract
Neurons are highly compartmentalized cells with tightly controlled subcellular protein organization. While brain transcriptome, connectome and global proteome maps are being generated, system-wide analysis of temporal protein dynamics at the subcellular level are currently lacking. Here, we perform a temporally-resolved surfaceome analysis of primary neuron cultures and reveal dynamic surface protein clusters that reflect the functional requirements during distinct stages of neuronal development. Direct comparison of surface and total protein pools during development and homeostatic synaptic scaling demonstrates system-wide proteostasis-independent remodeling of the neuronal surface, illustrating widespread regulation on the level of surface trafficking. Finally, quantitative analysis of the neuronal surface during chemical long-term potentiation (cLTP) reveals fast externalization of diverse classes of surface proteins beyond the AMPA receptor, providing avenues to investigate the requirement of exocytosis for LTP. Our resource (neurosurfaceome.ethz.ch) highlights the importance of subcellular resolution for systems-level understanding of cellular processes. Cell surface proteins contribute to neuronal development and activity-dependent synaptic plasticity. Here, the authors perform a time-resolved surfaceome analysis of developing primary neurons and in response to homeostatic synaptic scaling and chemical long-term potentiation (cLTP), revealing surface proteome remodeling largely independent of global proteostasis.
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Affiliation(s)
- Marc van Oostrum
- Neuroscience Center Zurich, Zurich, Switzerland.,Institute of Translational Medicine (ITM), Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Benjamin Campbell
- Neuroscience Center Zurich, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Charlotte Seng
- Neuroscience Center Zurich, Zurich, Switzerland.,Laboratory of Neural Connectivity, Faculties of Medicine and Natural Sciences, Brain Research Institute, University of Zurich, Zürich, 8057, Switzerland
| | - Maik Müller
- Institute of Translational Medicine (ITM), Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | | | - Jacqueline Hammer
- Institute of Translational Medicine (ITM), Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland
| | - Patrick G A Pedrioli
- Institute of Translational Medicine (ITM), Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Csaba Földy
- Neuroscience Center Zurich, Zurich, Switzerland.,Laboratory of Neural Connectivity, Faculties of Medicine and Natural Sciences, Brain Research Institute, University of Zurich, Zürich, 8057, Switzerland
| | - Shiva K Tyagarajan
- Neuroscience Center Zurich, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Bernd Wollscheid
- Neuroscience Center Zurich, Zurich, Switzerland. .,Institute of Translational Medicine (ITM), Department of Health Sciences and Technology, ETH Zurich, 8093, Zurich, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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20
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Deprey K, Batistatou N, Kritzer JA. A critical analysis of methods used to investigate the cellular uptake and subcellular localization of RNA therapeutics. Nucleic Acids Res 2020; 48:7623-7639. [PMID: 32644123 PMCID: PMC7430645 DOI: 10.1093/nar/gkaa576] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022] Open
Abstract
RNA therapeutics are a promising strategy to treat genetic diseases caused by the overexpression or aberrant splicing of a specific protein. The field has seen major strides in the clinical efficacy of this class of molecules, largely due to chemical modifications and delivery strategies that improve nuclease resistance and enhance cell penetration. However, a major obstacle in the development of RNA therapeutics continues to be the imprecise, difficult, and often problematic nature of most methods used to measure cell penetration. Here, we review these methods and clearly distinguish between those that measure total cellular uptake of RNA therapeutics, which includes both productive and non-productive uptake, and those that measure cytosolic/nuclear penetration, which represents only productive uptake. We critically analyze the benefits and drawbacks of each method. Finally, we use key examples to illustrate how, despite rigorous experimentation and proper controls, our understanding of the mechanism of gymnotic uptake of RNA therapeutics remains limited by the methods commonly used to analyze RNA delivery.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Nefeli Batistatou
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
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21
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Abstract
Small RNAs (sRNAs), including microRNAs (miRNAs), are noncoding RNA (ncRNA) molecules involved in gene regulation. sRNAs play important roles in development; however, their significance in nutritional control and as metabolic modulators is still emerging. The mechanisms by which diet impacts metabolic genes through miRNAs remain an important area of inquiry. Recent work has established how miRNAs are transported in body fluids often within exosomes, which are small cell-derived vesicles that function in intercellular communication. The abundance of other recently identified ncRNAs and new insights regarding ncRNAs as dietary bioactive compounds could remodel our understanding about how foods impact gene expression. Although controversial, some groups have shown that dietary RNAs from plants and animals (i.e., milk) are functional in consumers. In the future, regulating sRNAs either directly through dietary delivery or indirectly by altered expression of endogenous sRNA may be part of nutritional interventions for regulating metabolism.
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Affiliation(s)
- Elizabeth M McNeill
- Department of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011, USA
| | - Kendal D Hirschi
- Departments of Pediatrics and Human and Molecular Genetics, Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas 77030, USA;
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22
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Lazar S, Wurtzel JGT, Chen X, Ma P, Goldfinger LE. High-efficiency unassisted transfection of platelets with naked double-stranded miRNAs modulates signal-activated translation and platelet function. Platelets 2020; 32:794-806. [PMID: 32838617 DOI: 10.1080/09537104.2020.1809642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We sought novel approaches to improve transfection efficiencies of microRNAs (miRNAs) in platelets, and to apply these approaches to investigate the roles of miRNAs in regulating signal-activated protein translation and functional effects. We found that ex vivo human platelets support gymnosis---internalization of ectopic miRNAs following co-incubation in the absence of conventional transfection reagents or schemes---and subsequently incorporate transfected miRNA into ARGONAUTE2 (AGO2)-based RNA-induced silencing complexes (RISC). Thrombin/fibrinogen stimulation activated translation of miR-223-3p target SEPTIN2, which was suppressed by miR-223-3p transfection in an AGO2/RISC-dependent manner. Thrombin/fibrinogen-induced exosome and microvesicle generation was inhibited by miR-223-3p transfection, and this effect was reversed with a RISC inhibitor. Platelet gymnosis of naked miRNAs appeared to be mediated in part by endocytic pathways including clathrin-dependent and fluid-phase endocytosis and caveolae. These results demonstrate the ability of ex vivo platelets to internalize ectopic miRNAs by unassisted transfection, and utilize them to modulate signal-activated translation and platelet function. Our results identify new roles for miR-223-3p in extracellular vesicle generation in stimulated platelets. High-efficiency gymnotic transfection of miRNAs in ex vivo platelets may be a broadly useful tool for exploring molecular genetic regulation of platelet function.
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Affiliation(s)
- Sophia Lazar
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jeremy G T Wurtzel
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Xi Chen
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Peisong Ma
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Lawrence E Goldfinger
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
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23
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Richbourg HA, Hu DP, Xu Y, Barczak AJ, Marcucio RS. miR-199 family contributes to regulation of sonic hedgehog expression during craniofacial development. Dev Dyn 2020; 249:1062-1076. [PMID: 32391617 DOI: 10.1002/dvdy.191] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The frontonasal ectodermal zone (FEZ) is a signaling center that regulates patterned development of the upper jaw, and Sonic hedgehog (SHH) mediates FEZ activity. Induction of SHH expression in the FEZ results from SHH-dependent signals from the brain and neural crest cells. Given the role of miRNAs in modulating gene expression, we investigated the extent to which miRNAs regulate SHH expression and FEZ signaling. RESULTS In the FEZ, the miR-199 family appears to be regulated by SHH-dependent signals from the brain; expression of this family increased from HH18 to HH22, and upon activation of SHH signaling in the brain. However, the miR-199 family is more broadly expressed in the mesenchyme of the frontonasal process and adjacent neuroepithelium. Downregulating the miR-199 genes expanded SHH expression in the FEZ, resulting in wider faces, while upregulating miR-199 genes resulted in decreased SHH expression and narrow faces. Hypoxia inducible factor 1 alpha (HIF1A) and mitogen-activated protein kinase kinase kinase 4 (MAP3K4) appear to be potential targets of miR-199b. Reduction of MAP3K4 altered beak development but increased apoptosis, while reducing HIF1A reduced expression of SHH in the FEZ and produced malformations independent of apoptosis. CONCLUSIONS Our results demonstrate that this miRNA family appears to participate in regulating SHH expression in the FEZ; however, specific molecular mechanisms remain unknown.
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Affiliation(s)
- Heather A Richbourg
- Department of Orthopaedic Surgery, San Francisco General Hospital, University of California, San Francisco, San Francisco, California, USA
| | - Diane P Hu
- Department of Orthopaedic Surgery, San Francisco General Hospital, University of California, San Francisco, San Francisco, California, USA
| | - Yanhua Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Zhejiang University Life Sciences Institute, Hangzhou, China
| | - Andrea J Barczak
- Functional Genomics Core, University of California, San Francisco, San Francisco, California, USA
| | - Ralph S Marcucio
- Department of Orthopaedic Surgery, San Francisco General Hospital, University of California, San Francisco, San Francisco, California, USA
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24
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Metelev VG, Bogdanov AA. Synthesis and applications of theranostic oligonucleotides carrying multiple fluorine atoms. Theranostics 2020; 10:1391-1414. [PMID: 31938071 PMCID: PMC6956824 DOI: 10.7150/thno.37936] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022] Open
Abstract
The use of various oligonucleotide (ON) syntheses and post-synthetic strategies for targeted chemical modification enables improving their efficacy as potent modulators of gene expression levels in eukaryotic cells. However, the search still continues for new approaches designed for increasing internalization, lysosomal escape, and tissue specific delivery of ON. In this review we emphasized all aspects related to the synthesis and properties of ON derivatives carrying multifluorinated (MF) groups. These MF groups have unique physico-chemical properties because of their simultaneous hydrophobicity and lipophobicity. Such unusual combination of properties results in the overall modification of ON mode of interaction with the cells and making multi-fluorination highly relevant to the goal of improving potency of ON as components of new therapies. The accumulated evidence so far is pointing to high potential of ON probes, RNAi components and ON imaging beacons carrying single or multiple MF groups for improving the stability, specificity of interaction with biological targets and delivery of ONs in vitro and potentially in vivo.
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Affiliation(s)
- Valeriy G. Metelev
- Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School, Worcester MA, USA
- Department of Chemistry, Moscow State University, Moscow, Russian Federation
| | - Alexei A. Bogdanov
- Laboratory of Molecular Imaging Probes, Department of Radiology, University of Massachusetts Medical School, Worcester MA, USA
- Laboratory of Molecular Imaging, A.N. Bakh Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow
- Department of Bioengineering and Bioinformatics, Moscow State University, Moscow
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25
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Buntz A, Killian T, Schmid D, Seul H, Brinkmann U, Ravn J, Lindholm M, Knoetgen H, Haucke V, Mundigl O. Quantitative fluorescence imaging determines the absolute number of locked nucleic acid oligonucleotides needed for suppression of target gene expression. Nucleic Acids Res 2019; 47:953-969. [PMID: 30462278 PMCID: PMC6344898 DOI: 10.1093/nar/gky1158] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/05/2018] [Indexed: 11/16/2022] Open
Abstract
Locked nucleic acid based antisense oligonucleotides (LNA-ASOs) can reach their intracellular RNA targets without delivery modules. Functional cellular uptake involves vesicular accumulation followed by translocation to the cytosol and nucleus. However, it is yet unknown how many LNA-ASO molecules need to be delivered to achieve target knock down. Here we show by quantitative fluorescence imaging combined with LNA-ASO microinjection into the cytosol or unassisted uptake that ∼105 molecules produce >50% knock down of their targets, indicating that a substantial amount of LNA-ASO escapes from endosomes. Microinjected LNA-ASOs redistributed within minutes from the cytosol to the nucleus and remained bound to nuclear components. Together with the fact that RNA levels for a given target are several orders of magnitude lower than the amounts of LNA-ASO, our data indicate that only a minor fraction is available for RNase H1 mediated reduction of target RNA. When non-specific binding sites were blocked by co-administration of non-related LNA-ASOs, the amount of target LNA-ASO required was reduced by an order of magnitude. Therefore, dynamic processes within the nucleus appear to influence the distribution and activity of LNA-ASOs and may represent important parameters for improving their efficacy and potency.
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Affiliation(s)
- Annette Buntz
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Tobias Killian
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Daniela Schmid
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Heike Seul
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Ulrich Brinkmann
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
| | - Jacob Ravn
- Roche Innovation Center Copenhagen, Roche Pharma Research and Early Development, Hørsholm 2970, Denmark
| | - Marie Lindholm
- Roche Innovation Center Copenhagen, Roche Pharma Research and Early Development, Hørsholm 2970, Denmark
| | - Hendrik Knoetgen
- Roche Innovation Center Basel, Roche Pharma Research and Early Development, Basel 4070, Switzerland
| | - Volker Haucke
- Department of Molecular Pharmacology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin 13125, Germany
| | - Olaf Mundigl
- Roche Innovation Center Munich, Roche Pharma Research and Early Development, Penzberg 82377, Germany
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26
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Zhang S, Sang X, Hou D, Chen J, Gu H, Zhang Y, Li J, Yang D, Zhu H, Yang X, Wang F, Zhang C, Chen X, Zen K, Zhang CY, Hong Z. Plant-derived RNAi therapeutics: A strategic inhibitor of HBsAg. Biomaterials 2019; 210:83-93. [PMID: 31078314 DOI: 10.1016/j.biomaterials.2019.04.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023]
Abstract
Chronic infection with hepatitis B virus (HBV) is a major public health problem. Recently, RNA interfering-based strategy has shown great potential to eradicate HBV infection. In current study, we report the experimental observation of plant-derived artificial microRNAs (amiRNAs) acting as therapeutics in HBsAg-/+ transgenic mice. Two pieces of small silencing RNA sequences, siR471 and siR519, against HBV surface antigen gene (HBsAg) were designed and expressed in lettuce using plant endogenous microRNA biogenesis machinery. Administration of amiRNAs-containing lettuce decoction specifically inhibited the HBsAg gene expression. In long term treatments, the liver injury in HBsAg-/+ transgenic mice were alleviated and no toxicological effects were observed. Compared with synthetic siRNA, feeding amiRNAs at a lower level achieved a similar inhibitory effect on HBsAg expression in mice. These results strongly suggest that employing plant endogenous miRNA biogenesis machinery to generate medicinal siRNAs is a novel way to solve the problems of siRNA stability and reduce the potential side effects of RNAi therapy.
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Affiliation(s)
- Shuo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Xiaolin Sang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Dongxia Hou
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Jinmei Chen
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Hongwei Gu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Yujing Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Jing Li
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Darong Yang
- Department of Molecular Medicine of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China Research Center of Cancer Prevention and Treatment, Translational Medicine Research Center of Liver Cancer, Hunan Provincial Tumor Hospital (Affiliated Tumor Hospital of Xiangya Medical School of Central South University), Changsha, 410022, China
| | - Haizhen Zhu
- Department of Molecular Medicine of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China Research Center of Cancer Prevention and Treatment, Translational Medicine Research Center of Liver Cancer, Hunan Provincial Tumor Hospital (Affiliated Tumor Hospital of Xiangya Medical School of Central South University), Changsha, 410022, China
| | - Xiao Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Fangyu Wang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China; Department of Gastroenterology and Hepatology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, 210002, China
| | - Chunni Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China; Department of Clinical Laboratory, Jinling Hospital, School of Life Sciences, Nanjing University, Nanjing, 210002, China
| | - Xi Chen
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Ke Zen
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Chen-Yu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China.
| | - Zhi Hong
- State Key Laboratory of Pharmaceutical Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China.
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27
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Chernikov IV, Vlassov VV, Chernolovskaya EL. Current Development of siRNA Bioconjugates: From Research to the Clinic. Front Pharmacol 2019; 10:444. [PMID: 31105570 PMCID: PMC6498891 DOI: 10.3389/fphar.2019.00444] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
Small interfering RNAs (siRNAs) acting via RNA interference mechanisms are able to recognize a homologous mRNA sequence in the cell and induce its degradation. The main problems in the development of siRNA-based drugs for therapeutic use are the low efficiency of siRNA delivery to target cells and the degradation of siRNAs by nucleases in biological fluids. Various approaches have been proposed to solve the problem of siRNA delivery in vivo (e.g., viruses, cationic lipids, polymers, nanoparticles), but all have limitations for therapeutic use. One of the most promising approaches to solve the problem of siRNA delivery to target cells is bioconjugation; i.e., the covalent connection of siRNAs with biogenic molecules (lipophilic molecules, antibodies, aptamers, ligands, peptides, or polymers). Bioconjugates are "ideal nanoparticles" since they do not need a positive charge to form complexes, are less toxic, and are less effectively recognized by components of the immune system because of their small size. This review is focused on strategies and principles for constructing siRNA bioconjugates for in vivo use.
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Affiliation(s)
- Ivan V Chernikov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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28
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Cron MA, Maillard S, Truffault F, Gualeni AV, Gloghini A, Fadel E, Guihaire J, Behin A, Berrih-Aknin S, Le Panse R. Causes and Consequences of miR-150-5p Dysregulation in Myasthenia Gravis. Front Immunol 2019; 10:539. [PMID: 30984166 PMCID: PMC6450174 DOI: 10.3389/fimmu.2019.00539] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/27/2019] [Indexed: 12/31/2022] Open
Abstract
Autoimmune Myasthenia gravis (MG) is a chronic neuromuscular disease mainly due to antibodies against the acetylcholine receptor (AChR) at the neuromuscular junction that induce invalidating muscle weaknesses. In early-onset MG, the thymus is the effector organ and is often characterized by B-cell infiltrations leading to ectopic germinal center (GC) development. The microRNA miR-150-5p has been previously characterized as a biomarker in MG due to its increase in the serum of patients and its decrease after thymectomy, correlated with an improvement of symptoms. Here, we investigated the causes and consequences of the miR-150 increase in the serum of early-onset MG patients. We observed that miR-150 expression was upregulated in MG thymuses in correlation with the presence of thymic B cells and showed by in situ hybridization experiments, that miR-150 was mainly expressed by cells of the mantle zone of GCs. However, we did not observe any correlation between the degree of thymic hyperplasia and the serum levels in MG patients. In parallel, we also investigated the expression of miR-150 in peripheral blood mononuclear cells (PBMCs) from MG patients. We observed that miR-150 was down-regulated, especially in CD4+ T cells compared to controls. These results suggest that the increased serum levels of miR-150 could result from a release from activated peripheral CD4+ T cells. Next, we demonstrated that the in vitro treatment of PBMCs with miR-150 or antimiR-150 oligonucleotides, respectively, decreased or increased the expression of one of its major target gene: the proto-oncogene MYB, a well-known actor of hematopoiesis. These results revealed that increased serum levels of miR-150 in MG patients could have a functional effect on PBMCs. We also showed that antimiR-150 caused increased cellular death of CD4+ and CD8+ T cells, along with the overexpression of pro-apoptotic genes targeted by miR-150 suggesting that miR-150 controlled the survival of these cells. Altogether, these results showed that miR-150 could play a role in MG both at the thymic level and in periphery by modulating the expression of target genes and peripheral cell survival.
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Affiliation(s)
- Mélanie A Cron
- Center of Research in Myology, Sorbonne University, INSERM, Association Institute of Myology - UMRS 974, Paris, France
| | - Solène Maillard
- Center of Research in Myology, Sorbonne University, INSERM, Association Institute of Myology - UMRS 974, Paris, France
| | - Frédérique Truffault
- Center of Research in Myology, Sorbonne University, INSERM, Association Institute of Myology - UMRS 974, Paris, France
| | - Ambra Vittoria Gualeni
- Department of Pathology and Laboratory Medicine, Istituto Nazionale dei Tumori, Milan, Italy
| | - Annunziata Gloghini
- Department of Pathology and Laboratory Medicine, Istituto Nazionale dei Tumori, Milan, Italy
| | - Elie Fadel
- Marie Lannelongue Hospital, Paris-Sud University, Le Plessis-Robinson, France
| | - Julien Guihaire
- Marie Lannelongue Hospital, Paris-Sud University, Le Plessis-Robinson, France
| | - Anthony Behin
- Neuromuscular Disease Center, AIM, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Sonia Berrih-Aknin
- Center of Research in Myology, Sorbonne University, INSERM, Association Institute of Myology - UMRS 974, Paris, France
| | - Rozen Le Panse
- Center of Research in Myology, Sorbonne University, INSERM, Association Institute of Myology - UMRS 974, Paris, France
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29
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Tatematsu M, Funami K, Seya T, Matsumoto M. Extracellular RNA Sensing by Pattern Recognition Receptors. J Innate Immun 2018; 10:398-406. [PMID: 30404092 PMCID: PMC6784046 DOI: 10.1159/000494034] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 12/11/2022] Open
Abstract
RNA works as a genome and messenger in RNA viruses, and it sends messages in most of the creatures of the Earth, including viruses, bacteria, fungi, plants, and animals. The human innate immune system has evolved to detect single- and double-stranded RNA molecules from microbes by pattern recognition receptors and induce defense reactions against infections such as the production of type I interferons and inflammatory cytokines. To avoid cytokine toxicity causing chronic inflammation or autoimmunity by sensing self-RNA, the activation of RNA sensors is strictly regulated. All of the Toll-like receptors that recognize RNA are localized to endosomes/lysosomes, which require internalization of RNA for sensing through an endocytic pathway. RIG-I-like receptors sense RNA in cytosol. These receptors are expressed in a cell type-specific fashion, enabling sensing of RNA for a wide range of microbial invasions. At the same time, both endosomal and cytoplasmic receptors have strategies to respond only to RNA of pathogenic microorganisms or dying cells. RNA are potential vaccine adjuvants for immune enhancement against cancer and provide a benefit for vaccinations. Understanding the detailed molecular mechanisms of the RNA-sensing system will help us to broaden the clinical utility of RNA adjuvants for patients with incurable diseases.
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Affiliation(s)
- Megumi Tatematsu
- Department of Vaccine Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
| | - Kenji Funami
- Department of Vaccine Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Tsukasa Seya
- Department of Vaccine Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Misako Matsumoto
- Department of Vaccine Immunology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
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30
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Contu VR, Hase K, Kozuka-Hata H, Oyama M, Fujiwara Y, Kabuta C, Takahashi M, Hakuno F, Takahashi SI, Wada K, Kabuta T. Lysosomal targeting of SIDT2 via multiple YXXΦ motifs is required for SIDT2 function in the process of RNautophagy. J Cell Sci 2017; 130:2843-2853. [DOI: 10.1242/jcs.202481] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/10/2017] [Indexed: 01/13/2023] Open
Abstract
RNA degradation is an essential process for maintaining cellular homeostasis. Previously, we have discovered a novel RNA degradation system, RNautophagy, during which direct import of RNA into lysosomes in an ATP-dependent manner followed by degradation takes place. The putative nucleic acids transporter, SID-1 transmembrane family member 2 (SIDT2), predominantly localizes to lysosomes and mediates the translocation of RNA into lysosomes during RNautophagy. However, little is known about the mechanisms of sorting SIDT2 to lysosomes. Here, we showed that three cytosolic YXXΦ motifs are required for the lysosomal localization of SIDT2 and that SIDT2 interacts with adaptor protein complexes AP-1 and AP-2. We also found that localization to lysosomes by these three motifs is necessary for SIDT2 function in the process of RNautophagy, and that SIDT2 strikingly increases endogenous RNA degradation at the cellular level. To our knowledge, this is the first study to report an endogenous intracellular protein of which overexpression substantially boosted intracellular RNA degradation. This study provides new insight into lysosomal targeting of proteins and intracellular RNA degradation, and further confirms the critical function of SIDT2 in RNautophagy.
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Affiliation(s)
- Viorica Raluca Contu
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
- Department of Neurology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Katsunori Hase
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
- Department of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yuuki Fujiwara
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Chihana Kabuta
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Masayuki Takahashi
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Fumihiko Hakuno
- Department of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shin-Ichiro Takahashi
- Department of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Keiji Wada
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Tomohiro Kabuta
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
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