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Kanzaki Y, Kuramoto T, Takarabe S, Shibayama Y, Yoshikawa H, Kato T. Effect of high- and low-energy entrance surface dose allocation ratio for two-shot dual-energy subtraction imaging on low-contrast resolution. Radiography (Lond) 2023; 29:240-246. [PMID: 36608378 DOI: 10.1016/j.radi.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/08/2022] [Accepted: 11/20/2022] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Dual-energy subtraction (DES) imaging can obtain chest radiographs with high contrast between nodules and healthy lung tissue, and evaluating of chest radiography and evaluating exposure conditions is crucial to obtain a high-quality diagnostic image. This study aimed to investigate the effect of the dose allocation ratio of entrance surface dose (ESD) between high- and low-energy projection in low-contrast resolution of soft-tissue images for two-shot DES imaging in digital radiography using a contrast-detail phantom (CD phantom). METHODS A custom-made phantom mimicking a human chest that combined a CD phantom, polymethylmethacrylate square plate, and an aluminum plate (1-3 mm) was used. The tube voltage was 120 kVp (high-energy) and 60 kVp (low-energy). The ESD was changed from 0.1 to 0.5 mGy in 0.1 mGy increments. Dose allocation ratio of ESD between 120 kVp and 60 kVp projection was set at 1:1, 1:2, 1:3, and 2:1. Inverse image quality figure (IQFinv) was calculated from the custom-made phantom images. RESULTS When the total ESD and aluminum thickness were constant, no significant difference in IQFinv was observed under most conditions of varied dose allocation ratio. Similarly, when the total ESD and the dose allocation ratio were constant, there was no significant difference in IQFinv based on the aluminum plate thickness. CONCLUSION Using IQFinv to evaluate the quality of the two-shot DES image suggested that dose allocation ratio did not have a significant effect on low-contrast resolution of soft-tissue images. IMPLICATIONS FOR PRACTICE The present results provide useful information for determining exposure conditions for two-shot DES imaging.
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Affiliation(s)
- Y Kanzaki
- Division of Radiology, Department of Medical Technology, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - T Kuramoto
- Department of Radiological Technology, Faculty of Health Sciences, Kobe Tokiwa University, 2-6-2 Otanicho, Nagata-ku, Kobe 653-0838, Japan.
| | - S Takarabe
- Division of Radiology, Department of Medical Technology, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Y Shibayama
- Division of Radiology, Department of Medical Technology, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - H Yoshikawa
- Division of Radiology, Department of Medical Technology, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - T Kato
- Division of Radiology, Department of Medical Technology, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Yip CW, Hon CC, Yasuzawa K, Sivaraman DM, Ramilowski JA, Shibayama Y, Agrawal S, Prabhu AV, Parr C, Severin J, Lan YJ, Dostie J, Petri A, Nishiyori-Sueki H, Tagami M, Itoh M, López-Redondo F, Kouno T, Chang JC, Luginbühl J, Kato M, Murata M, Yip WH, Shu X, Abugessaisa I, Hasegawa A, Suzuki H, Kauppinen S, Yagi K, Okazaki Y, Kasukawa T, de Hoon M, Carninci P, Shin JW. Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types. Cell Rep 2022; 41:111893. [PMID: 36577377 DOI: 10.1016/j.celrep.2022.111893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/30/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022] Open
Abstract
Within the scope of the FANTOM6 consortium, we perform a large-scale knockdown of 200 long non-coding RNAs (lncRNAs) in human induced pluripotent stem cells (iPSCs) and systematically characterize their roles in self-renewal and pluripotency. We find 36 lncRNAs (18%) exhibiting cell growth inhibition. From the knockdown of 123 lncRNAs with transcriptome profiling, 36 lncRNAs (29.3%) show molecular phenotypes. Integrating the molecular phenotypes with chromatin-interaction assays further reveals cis- and trans-interacting partners as potential primary targets. Additionally, cell-type enrichment analysis identifies lncRNAs associated with pluripotency, while the knockdown of LINC02595, CATG00000090305.1, and RP11-148B6.2 modulates colony formation of iPSCs. We compare our results with previously published fibroblasts phenotyping data and find that 2.9% of the lncRNAs exhibit a consistent cell growth phenotype, whereas we observe 58.3% agreement in molecular phenotypes. This highlights that molecular phenotyping is more comprehensive in revealing affected pathways.
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Affiliation(s)
- Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Anika V Prabhu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Callum Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yan Jun Lan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, QC, Canada
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 2450, Denmark
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | | | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masaki Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Wing Hin Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Xufeng Shu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 2450, Denmark
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Human Technopole, via Rita Levi Montalcini 1, Milan, Italy
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore.
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3
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJ, Rackham OJ, Rizzu P, Martinez DFS, Sandelin A, Sanjana P, Semple CA, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest AR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJ, Shin JW, Carninci P. Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020. [DOI: 10.1101/gr.270330.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJF, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020; 30:1060-1072. [PMID: 32718982 PMCID: PMC7397864 DOI: 10.1101/gr.254219.119] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/24/2020] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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Affiliation(s)
- Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yari Ciani
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Mickaël Mendez
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | | | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Leonie Roos
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max Delbrük Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Ivan V Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alessandro Bonetti
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Beatrice Borsari
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Christopher JF Cameron
- School of Computer Science, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden 01062, Germany.,Center for Complex Network Intelligence (CCNI) at the Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Bioengineering, Tsinghua University, Beijing 100084, China
| | - Ryan Cardenas
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Melissa Cardon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Howard Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, California 94305, USA
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich 8093, Switzerland
| | - Alexander Favorov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Alexandre Fort
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Diego Garrido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Noa Gil
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Juliette Gimenez
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome 00179, Italy
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lusy Handoko
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki Hasegawa
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Norihito Hayatsu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Peter Heutink
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Eddie L Imada
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Bogumil Kaczkowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Aditi Kanhere
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Emily Kawabata
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Tsugumi Kawashima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - S Thomas Kelly
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Miki Kojima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Anton Kratz
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Mariola Kurowska-Stolarska
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, Scotland G12 8QQ, United Kingdom
| | - Andrew Tae Jun Kwon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jeffrey Leek
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Fernando López-Redondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shiori Maeda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Vsevolod J Makeev
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Aki Minoda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hiromi Nishiyori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuhiro R Nitta
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yukihiko Noro
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ramil Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Valerio Orlando
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Denis Paquette
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Callum J C Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Patrizia Rizzu
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | | | - Albin Sandelin
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Pillay Sanjana
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Colin A M Semple
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Martin S Taylor
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Malte Thodberg
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Supat Thongjuea
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Vidisha Tripathi
- National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roberto Verardo
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ilya E Vorontsov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Chinatsu Yamamoto
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Robert S Young
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Western Australia 6009, Australia
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia 08002, Spain
| | | | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen N-5008, Norway
| | - Claudio Schneider
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy.,Department of Medicine and Consorzio Interuniversitario Biotecnologie p.zle Kolbe 1 University of Udine, Udine 33100, Italy
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
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5
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Nakamura Y, Namikawa K, Yoshino K, Yoshikawa S, Uchi H, Goto K, Nakamura Y, Fukushima S, Kiniwa Y, Takenouchi T, Uhara H, Kawai T, Hatta N, Funakoshi T, Teramoto Y, Otsuka A, Doi H, Ogata D, Matsushita S, Isei T, Hayashi T, Shibayama Y, Yamazaki N. Anti-PD1 checkpoint inhibitor therapy in acral melanoma: a multicenter study of 193 Japanese patients. Ann Oncol 2020; 31:1198-1206. [PMID: 32522691 DOI: 10.1016/j.annonc.2020.05.031] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/04/2020] [Accepted: 05/28/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Acral melanoma (AM) is an epidemiologically and molecularly distinct entity that is underrepresented in clinical trials on immunotherapy in melanoma. We aimed to analyze the efficacy of anti-programmed cell death 1 (anti-PD-1) antibodies in advanced AM. PATIENTS AND METHODS We retrospectively evaluated unresectable stage III or stage IV AM patients treated with an anti-PD-1 antibody in any line at 21 Japanese institutions between 2014 and 2018. The clinicobiologic characteristics, objective response rate (ORR, RECIST), survival estimated using Kaplan-Meier analysis, and toxicity (Common Terminology Criteria for Adverse Events 4.0.) were analyzed to estimate the efficacy of the anti-PD-1 antibodies. RESULTS In total, 193 patients (nail apparatus, 70; palm and sole, 123) were included in the study. Anti-PD-1 antibody was used as first-line therapy in 143 patients (74.1%). Baseline lactate dehydrogenase (LDH) was within the normal concentration in 102 patients (52.8%). The ORR of all patients was 16.6% (complete response, 3.1%; partial response, 13.5%), and the median overall survival (OS) was 18.1 months. Normal LDH concentrations showed a significantly stronger association with better OS than abnormal concentrations (median OS 24.9 versus 10.7 months; P < 0.001). Although baseline characteristics were similar between the nail apparatus and the palm and sole groups, ORR was significantly lower in the nail apparatus group [6/70 patients (8.6%) versus 26/123 patients (21.1%); P = 0.026]. Moreover, the median OS in this group was significantly poorer (12.8 versus 22.3 months; P = 0.03). CONCLUSIONS Anti-PD-1 antibodies have limited efficacy in AM patients. Notably, patients with nail apparatus melanoma had poorer response and survival, making nail apparatus melanoma a strong candidate for further research on the efficacy of novel combination therapies with immune checkpoint inhibitors.
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Affiliation(s)
- Y Nakamura
- Department of Skin Oncology/Dermatology, Comprehensive Cancer Center, Saitama Medical University International Medical Center, Saitama, Japan.
| | - K Namikawa
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - K Yoshino
- Department of Dermatologic Oncology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - S Yoshikawa
- Department of Dermatology, Shizuoka Cancer Center, Shizuoka, Japan
| | - H Uchi
- Department of Dermatology, Kyushu University, Fukuoka, Japan
| | - K Goto
- Department of Dermatology, Nagoya University, Nagoya, Japan
| | - Y Nakamura
- Department of Dermatology, University of Tsukuba, Tsukuba, Japan
| | - S Fukushima
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Y Kiniwa
- Department of Dermatology, Shinshu University, Matsumoto, Japan
| | - T Takenouchi
- Department of Dermatology, Niigata Cancer Center, Niigata, Japan
| | - H Uhara
- Department of Dermatology, Sapporo Medical University, Sapporo, Japan
| | - T Kawai
- Department of Dermatology, University of Tokyo, Tokyo, Japan
| | - N Hatta
- Department of Dermatology, Toyama Prefectural Central Hospital, Toyama, Japan
| | - T Funakoshi
- Department of Dermatology, Keio University, Tokyo, Japan
| | - Y Teramoto
- Department of Skin Oncology/Dermatology, Comprehensive Cancer Center, Saitama Medical University International Medical Center, Saitama, Japan
| | - A Otsuka
- Department of Dermatology, Kyoto University, Kyoto, Japan
| | - H Doi
- Department of Dermatology, Asahikawa Medical University, Asahikawa, Japan
| | - D Ogata
- Department of Dermatology, Saitama Medical University, Saitama, Japan
| | - S Matsushita
- Department of Dermato-Oncology/Dermatology, National Hospital Organization Kagoshima Medical Center, Kagoshima, Japan
| | - T Isei
- Department of Dermatological Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - T Hayashi
- Plastic and Reconstructive Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Y Shibayama
- Department of Dermatology, Fukuoka University, Fukuoka, Japan
| | - N Yamazaki
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
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6
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Kouno T, Moody J, Kwon ATJ, Shibayama Y, Kato S, Huang Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin JW. C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nat Commun 2019; 10:360. [PMID: 30664627 PMCID: PMC6341120 DOI: 10.1038/s41467-018-08126-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 12/19/2018] [Indexed: 01/06/2023] Open
Abstract
Single-cell transcriptomic profiling is a powerful tool to explore cellular heterogeneity. However, most of these methods focus on the 3′-end of polyadenylated transcripts and provide only a partial view of the transcriptome. We introduce C1 CAGE, a method for the detection of transcript 5′-ends with an original sample multiplexing strategy in the C1TM microfluidic system. We first quantifiy the performance of C1 CAGE and find it as accurate and sensitive as other methods in the C1 system. We then use it to profile promoter and enhancer activities in the cellular response to TGF-β of lung cancer cells and discover subpopulations of cells differing in their response. We also describe enhancer RNA dynamics revealing transcriptional bursts in subsets of cells with transcripts arising from either strand in a mutually exclusive manner, validated using single molecule fluorescence in situ hybridization. Single-cell transcriptomic profiling allows the exploration of cellular heterogeneity but commonly focuses on the 3′-end of the transcript. Here the authors introduce C1 CAGE, which detects the 5′ transcript end in a multiplexed microfluidic system.
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Affiliation(s)
- Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Jonathan Moody
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Andrew Tae-Jun Kwon
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Sachi Kato
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yi Huang
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,ACT Genomics Co. Ltd., 3F., No. 345, Xinhu 2nd Rd, Neihu Dist., Taipei City, 114, Taiwan
| | - Michael Böttcher
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Efthymios Motakis
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Yong Loo Lin School of Medicine MD6, #08-01, 14 Medical Drive, National University of Singapore, Singapore, 117599, Singapore
| | - Mickaël Mendez
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Princess Margaret Cancer Research Tower 11-401, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoshi Takizawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takahiro Arakawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masaaki Furuno
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Naveen Ramalingam
- Single-Cell Research and Development, Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, 94080, CA, USA
| | - Jay West
- Single-Cell Research and Development, Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, 94080, CA, USA
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Timo Lassmann
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Telethon Kids Institute, The University of Western Australia, Perth Children's Hospital, 15 Hospital Ave, Nedlands, 6009, WA, Australia
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Charles Plessy
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. .,Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
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7
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Fanucchi S, Fok ET, Dalla E, Shibayama Y, Börner K, Chang EY, Stoychev S, Imakaev M, Grimm D, Wang KC, Li G, Sung WK, Mhlanga MM. Publisher Correction: Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments. Nat Genet 2019; 51:364. [PMID: 30647470 DOI: 10.1038/s41588-018-0341-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article initially published, '+' and '-' labels were missing from the graph keys at the bottom of Fig. 8d. The error has been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Stephanie Fanucchi
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,BTRI, CSIR Biosciences, Pretoria, South Africa
| | - Ezio T Fok
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,BTRI, CSIR Biosciences, Pretoria, South Africa
| | - Emiliano Dalla
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Youtaro Shibayama
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kathleen Börner
- Department of Infectious Diseases/Virology, BioQuant Center, Heidelberg University Hospital, Heidelberg, Germany.,Heidelberg Partner Site, German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Erin Y Chang
- Department of Dermatology, Stanford University, Stanford, CA, USA
| | - Stoyan Stoychev
- Biomedical Technologies Group, CSIR Biosciences, Pretoria, South Africa
| | - Maxim Imakaev
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Boston, MA, USA
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, BioQuant Center, Heidelberg University Hospital, Heidelberg, Germany.,Heidelberg Partner Site, German Center for Infection Research (DZIF), Heidelberg, Germany.,Cluster of Excellence CellNetworks, Heidelberg, Germany
| | - Kevin C Wang
- Department of Dermatology, Stanford University, Stanford, CA, USA
| | - Guoliang Li
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Wing-Kin Sung
- School of Computing, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Singapore, Singapore
| | - Musa M Mhlanga
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal.
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8
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Fanucchi S, Fok ET, Dalla E, Shibayama Y, Börner K, Chang EY, Stoychev S, Imakaev M, Grimm D, Wang KC, Li G, Sung WK, Mhlanga MM. Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments. Nat Genet 2018; 51:138-150. [PMID: 30531872 DOI: 10.1038/s41588-018-0298-2] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 10/30/2018] [Indexed: 12/22/2022]
Abstract
Accumulation of trimethylation of histone H3 at lysine 4 (H3K4me3) on immune-related gene promoters underlies robust transcription during trained immunity. However, the molecular basis for this remains unknown. Here we show three-dimensional chromatin topology enables immune genes to engage in chromosomal contacts with a subset of long noncoding RNAs (lncRNAs) we have defined as immune gene-priming lncRNAs (IPLs). We show that the prototypical IPL, UMLILO, acts in cis to direct the WD repeat-containing protein 5 (WDR5)-mixed lineage leukemia protein 1 (MLL1) complex across the chemokine promoters, facilitating their H3K4me3 epigenetic priming. This mechanism is shared amongst several trained immune genes. Training mediated by β-glucan epigenetically reprograms immune genes by upregulating IPLs in manner dependent on nuclear factor of activated T cells. The murine chemokine topologically associating domain lacks an IPL, and the Cxcl genes are not trained. Strikingly, the insertion of UMLILO into the chemokine topologically associating domain in mouse macrophages resulted in training of Cxcl genes. This provides strong evidence that lncRNA-mediated regulation is central to the establishment of trained immunity.
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Affiliation(s)
- Stephanie Fanucchi
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,BTRI, CSIR Biosciences, Pretoria, South Africa
| | - Ezio T Fok
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,BTRI, CSIR Biosciences, Pretoria, South Africa
| | - Emiliano Dalla
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Medicine, Università degli Studi di Udine, Udine, Italy
| | - Youtaro Shibayama
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kathleen Börner
- Department of Infectious Diseases/Virology, BioQuant Center, Heidelberg University Hospital, Heidelberg, Germany.,Heidelberg Partner Site, German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Erin Y Chang
- Department of Dermatology, Stanford University, Stanford, CA, USA
| | - Stoyan Stoychev
- Biomedical Technologies Group, CSIR Biosciences, Pretoria, South Africa
| | - Maxim Imakaev
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Boston, MA, USA
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, BioQuant Center, Heidelberg University Hospital, Heidelberg, Germany.,Heidelberg Partner Site, German Center for Infection Research (DZIF), Heidelberg, Germany.,Cluster of Excellence CellNetworks, Heidelberg, Germany
| | - Kevin C Wang
- Department of Dermatology, Stanford University, Stanford, CA, USA
| | - Guoliang Li
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Wing-Kin Sung
- School of Computing, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Singapore, Singapore
| | - Musa M Mhlanga
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal.
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9
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Abstract
Enhancers are principal regulators that allow spatiotemporal tissue-specific control of gene expression. While mounting evidence suggests that enhancer-derived long noncoding RNAs (long ncRNAs), including enhancer RNAs (eRNAs), are an important component of enhancer function, their expression has not been broadly analyzed at a single cell level via imaging techniques. This protocol describes a method to image eRNA in single cells by in situ hybridization followed by tyramide signal amplification (TSA). The procedure can be multiplexed to simultaneously visualize both eRNA and protein-coding transcript at the site of transcriptional elongation, thereby permitting analysis of dynamics between the two transcript species in single cells. Our approach is not limited to eRNAs, but can be implemented on other transcripts.
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Affiliation(s)
- Youtaro Shibayama
- Gene Expression and Biophysics Group, Synthetic Biology ERA, CSIR, Box 395, Pretoria, 0001, South Africa
- Division of Chemical Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Stephanie Fanucchi
- Gene Expression and Biophysics Group, Synthetic Biology ERA, CSIR, Box 395, Pretoria, 0001, South Africa
- Division of Chemical Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Musa M Mhlanga
- Gene Expression and Biophysics Group, Synthetic Biology ERA, CSIR, Box 395, Pretoria, 0001, South Africa.
- Division of Chemical Systems and Synthetic Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Unidade de Biofisica e Expressao Genetica, Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, Portugal.
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10
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Hirose T, Arimura H, Shibayama Y, Fukunaga J, Umezu Y, Oga S, Sasaki T. SU-F-T-394: Impact of PTV Margins With Taking Into Account Shape Variation On IMRT Plans For Prostate Cancer. Med Phys 2016. [DOI: 10.1118/1.4956579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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11
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Sasahara M, Arimura H, Shibayama Y, Hirose T, Ohga S, Umezu Y, Honda H, Sasaki T. SU-F-J-34: Automatic Target-Based Patient Positioning Framework for Image-Guided Radiotherapy in Prostate Cancer Treatment. Med Phys 2016. [DOI: 10.1118/1.4955942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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12
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Shibayama Y, Arimura H, Hirose T, Nakamura K, Sasaki T, Ohga S, Umezu Y, Nakamura Y, Honda H. WE-AB-207B-03: A Computational Methodology for Determination of CTV-To-PTV Margins with Inter Fractional Shape Variations Based On a Statistical Point Distribution Model for Prostate Cancer Radiation Therapy. Med Phys 2016. [DOI: 10.1118/1.4957784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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13
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Shibayama Y, Kuwata T, Yamaguchi J, Matsumoto M, Watanabe M, Nakano R, Kai K, Watanabe M, Watanabe R, Ohkuchi A, Matsubara S. Changes in standing body sway of pregnant women after long-term bed rest. J OBSTET GYNAECOL 2015; 36:479-82. [PMID: 26471310 DOI: 10.3109/01443615.2015.1086983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Pregnant women tend to fall and increased body postural instability, namely body sway, may be one of the causative factors. We had a clinical impression that pregnant women after long-term bed rest tend to fall. We hypothesised that such women may show increased body sway, which we attempted to determine. Pregnant women (n = 161) were divided into three groups: (i) women with preterm labour after 2-week bed rest, (ii) those after 4-week bed rest, and (iii) those without bed rest or preterm labour. Body sway was analysed using stabilometry, that is, computed analysis of movement of the centre of gravity. The 3 groups fundamentally showed the same stabilometric measurements. Women with oedema showed greater medial-lateral sway than those without it. Factors other than oedema yielded no differences in stabilometric parameters. Long-term bed rest fundamentally did not increase body sway to the extent that stabilometry could reveal it. It may be prudent to consider that pregnant women with oedema tend to fall.
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Affiliation(s)
- Y Shibayama
- a Department of Midwifery and Nursing , Jichi Medical University Hospital , Tochigi , Japan
| | - T Kuwata
- b Department of Obstetrics and Gynecology , Jichi Medical University , Tochigi , Japan
| | - J Yamaguchi
- a Department of Midwifery and Nursing , Jichi Medical University Hospital , Tochigi , Japan
| | - M Matsumoto
- a Department of Midwifery and Nursing , Jichi Medical University Hospital , Tochigi , Japan
| | - M Watanabe
- a Department of Midwifery and Nursing , Jichi Medical University Hospital , Tochigi , Japan
| | - R Nakano
- a Department of Midwifery and Nursing , Jichi Medical University Hospital , Tochigi , Japan
| | - K Kai
- c Department of Midwifery and Nursing , Saitama Medical Center Hospital, Jichi Medical University , Saitama , Japan
| | - M Watanabe
- a Department of Midwifery and Nursing , Jichi Medical University Hospital , Tochigi , Japan
| | - R Watanabe
- d School of Nursing, Jichi Medical University , Tochigi , Japan
| | - A Ohkuchi
- b Department of Obstetrics and Gynecology , Jichi Medical University , Tochigi , Japan.,e Support Center for Clinical Investigation, Jichi Medical University , Tochigi , Japan
| | - S Matsubara
- b Department of Obstetrics and Gynecology , Jichi Medical University , Tochigi , Japan.,e Support Center for Clinical Investigation, Jichi Medical University , Tochigi , Japan
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14
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Shibayama Y, Arimura H, Hirose T, Nakamura K, Umezu Y, Nakamura Y, Honda H, Toyofuku F. SU-E-J-177: A Computational Approach for Determination of Anisotropic PTV Margins Based On Statistical Shape Analysis for Prostate Cancer Radiotherapy. Med Phys 2015. [DOI: 10.1118/1.4924262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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15
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Abstract
Bacteriophage-encoded proteins which inhibit or modify cellular components may contribute to antibacterial drug discovery by allowing the identification of novel targets. Given their abundance and diversity, phages may have various strategies in host inhibition and therefore may possess a variety of such proteins. Using Rhodococcus equi and phage YF1, we show that a single phage possesses numerous genes that inhibit the host when introduced into the host on a plasmid. These genes mostly encode proteins of unknown function, confirming the potential that this approach may have in providing new antibacterial targets.
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Affiliation(s)
- Youtaro Shibayama
- School of Molecular and Cell Biology; University of the Witwatersrand; Johannesburg, South Africa
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16
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Abstract
Chromatin loops are pervasive and permit the tight compaction of DNA within the confined space of the nucleus. Looping enables distal genes and DNA elements to engage in chromosomal contact, to form multigene complexes. Advances in biochemical and imaging techniques reveal that loop-mediated contact is strongly correlated with transcription of interacting DNA. However, these approaches only provide a snapshot of events and therefore are unable to reveal the dynamics of multigene complex assembly. This highlights the necessity to develop single cell-based assays that provide single molecule resolution, and are able to functionally interrogate the role of chromosomal contact on gene regulation. To this end, high-resolution single cell imaging regimes, combined with genome editing approaches, are proving to be pivotal to advancing our understanding of loop-mediated dynamics.
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Affiliation(s)
- Stephanie Fanucchi
- Gene Expression and Biophysics Group; Synthetic Biology Emerging Research Area; Biosciences Unit; Council for Scientific and Industrial Research; Pretoria, South Africa
| | - Youtaro Shibayama
- Gene Expression and Biophysics Group; Synthetic Biology Emerging Research Area; Biosciences Unit; Council for Scientific and Industrial Research; Pretoria, South Africa
| | - Musa M Mhlanga
- Gene Expression and Biophysics Group; Synthetic Biology Emerging Research Area; Biosciences Unit; Council for Scientific and Industrial Research; Pretoria, South Africa; Unidade de Biofísica e Expressão Genética; Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Lisboa, Portugal
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17
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Shibayama Y, Fanucchi S, Magagula L, Mhlanga MM. lncRNA and gene looping: what's the connection? Transcription 2014; 5:e28658. [PMID: 25764331 PMCID: PMC4215167 DOI: 10.4161/trns.28658] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/25/2014] [Accepted: 03/25/2014] [Indexed: 12/11/2022] Open
Abstract
Recent functional studies have unveiled the significant role chromatin topology plays in gene regulation. Several lines of evidence suggest genes access necessary factors for transcription by forming chromatin loops. A clearer picture of the players involved in chromatin organization, including lncRNA, is emerging.
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Affiliation(s)
- Youtaro Shibayama
- Gene Expression and Biophysics Group, Synthetic Biology Emerging Research Area, Biosciences Unit, Council for Scientific and Industrial Research; Pretoria, Gauteng, South Africa
- These authors contributed equally to this work
| | - Stephanie Fanucchi
- Gene Expression and Biophysics Group, Synthetic Biology Emerging Research Area, Biosciences Unit, Council for Scientific and Industrial Research; Pretoria, Gauteng, South Africa
- These authors contributed equally to this work
| | - Loretta Magagula
- Gene Expression and Biophysics Group, Synthetic Biology Emerging Research Area, Biosciences Unit, Council for Scientific and Industrial Research; Pretoria, Gauteng, South Africa
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18
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Zawaira A, Shibayama Y. A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs. J Struct Funct Genomics 2012; 13:185-200. [PMID: 22956349 DOI: 10.1007/s10969-012-9141-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 08/08/2012] [Indexed: 06/01/2023]
Abstract
The study of the protein-protein interactions (PPIs) of unique ORFs is a strategy for deciphering the biological roles of unique ORFs of interest. For uniform reference, we define unique ORFs as those for which no matching protein is found after PDB-BLAST search with default parameters. The uniqueness of the ORFs generally precludes the straightforward use of structure-based approaches in the design of experiments to explore PPIs. Many open-source bioinformatics tools, from the commonly-used to the relatively esoteric, have been built and validated to perform analyses and/or predictions of sorts on proteins. How can these available tools be combined into a protocol that helps the non-expert bioinformaticist researcher to design experiments to explore the PPIs of their unique ORF? Here we define a pragmatic protocol based on accessibility of software to achieve this and we make it concrete by applying it on two proteins-the ImuB and ImuA' proteins from Mycobacterium tuberculosis. The protocol is pragmatic in that decisions are made largely based on the availability of easy-to-use freeware. We define the following basic and user-friendly software pathway to build testable PPI hypotheses for a query protein sequence: PSI-PRED → MUSTER → metaPPISP → ASAView and ConSurf. Where possible, other analytical and/or predictive tools may be included. Our protocol combines the software predictions and analyses with general bioinformatics principles to arrive at consensus, prioritised and testable PPI hypotheses.
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Affiliation(s)
- Alexander Zawaira
- Gene Expression and Biophysics Group, Synthetic Biology, ERA, CSIR Biosciences, Brummeria, Pretoria, South Africa.
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19
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Shibayama Y, Dabbs ER, Yazawa K, Mikami Y. Functional analysis of a small cryptic plasmid pYS1 from Nocardia. Plasmid 2011; 66:26-37. [DOI: 10.1016/j.plasmid.2011.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/20/2011] [Accepted: 04/22/2011] [Indexed: 11/16/2022]
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20
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Affiliation(s)
- H Kuwabara
- Department of Pathology, Osaka Medical College, Japan
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21
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22
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Nakajima H, Shimakage M, Takeda Y, Furutama D, Sugino M, Kimura F, Shibayama Y, Hanafusa T. Epstein-Barr virus-associated primary leptomeningeal lymphoma. Eur J Neurol 2006; 13:e4-6. [PMID: 17038027 DOI: 10.1111/j.1468-1331.2006.01377.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Watanabe M, Maemura K, Oki K, Shiraishi N, Shibayama Y, Katsu K. Gamma-aminobutyric acid (GABA) and cell proliferation: focus on cancer cells. Histol Histopathol 2006; 21:1135-41. [PMID: 16835836 DOI: 10.14670/hh-21.1135] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In addition to its role in the adult mammalian nervous system as an inhibitory neurotransmitter, gamma-aminobutyric acid (GABA) is involved in the proliferation, differentiation, and migration of several kinds of cells including cancer cells. GABA is synthesized predominantly from glutamate by glutamate decarboxylase and exerts its effects via ionotropic GABA(A) receptors and/or metabotropic GABA(B) receptors. In this review, the current state of knowledge regarding the role of the GABAergic system in peripheral nonneuronal cell proliferation is described, and recent advances in elucidation of the mechanisms leading to cell proliferation are discussed.
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Affiliation(s)
- M Watanabe
- Department of Anatomy and Cell Biology, Osaka Medical College, Takatsuki, Osaka, Japan.
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24
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Maemura K, Yanagawa Y, Obata K, Dohi T, Egashira Y, Shibayama Y, Watanabe M. Antigen-presenting cells expressing glutamate decarboxylase 67 were identified as epithelial cells in glutamate decarboxylase 67-GFP knock-in mouse thymus. ACTA ACUST UNITED AC 2006; 67:198-206. [PMID: 16573556 DOI: 10.1111/j.1399-0039.2006.00548.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Glutamate decarboxylase (GAD), which has two isoforms, GAD65, and GAD67, is responsible for synthesis of the major inhibitory neurotransmitter, gamma-aminobutyric acid. GAD is expressed predominantly in the central nervous system; recent reports suggest that GAD is also expressed in non-neuronal organs including the pancreas. In the pancreatic islets, GAD serves as one of the autoantigens in type I diabetes mellitus. Recent flow cytometric analyses have shown that a variety of self-antigens, including GAD, are ectopically transcribed and expressed in particular cell populations of the thymus, although consensus concerning the cellular phenotype has not been obtained. The aim of this study was to clarify the localization and cellular phenotype of GAD67-expressing cells in the thymus at a cellular level with a novel approach using GAD67-green fluorescent protein (GFP) knock-in mice, in which GFP is expressed specifically in GAD67-positive cells. GFP-positive cells were detected in the thymic medulla and were identified as epithelial cells by immunohistochemistry. Almost all GFP-positive cells were positive for major histocompatibility complex (MHC) class II antigen staining and were positive for both cytokeratin and Ulex Europaeus Agglutinin I, markers of medullary thymic epithelial cells, but were negative for CD11c, Gr-1, and CD45, markers of dendritic cells, macrophages, and B-lymphocytes, respectively.
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Affiliation(s)
- K Maemura
- Department of Anatomy, Osaka Medical College, Japan
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25
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Yamamoto K, Nakashima H, Shibayama Y, Shirahama K. Anomalous suppression of superfluidity in 4He confined in a nanoporous glass. Phys Rev Lett 2004; 93:075302. [PMID: 15324246 DOI: 10.1103/physrevlett.93.075302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Revised: 03/18/2004] [Indexed: 05/24/2023]
Abstract
We explore the superfluidity of 4He confined in a porous glass, which has nanopores of 2.5 nm in diameter, at pressures up to 5 MPa. With increasing pressure, the superfluidity is drastically suppressed, and the superfluid transition temperature approaches 0 K at some critical pressure, Pc approximately 3.4 MPa. The feature suggests that the extreme confinement of 4He into the nanopores induces a quantum phase transition from a superfluid to a nonsuperfluid at 0 K and at Pc.
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Affiliation(s)
- K Yamamoto
- Department of Physics, Keio University, Yokohama 223-8522, Japan
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26
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Shibayama Y, Ikeda R, Motoya T, Yamada K. St. John's Wort (Hypericum perforatum) induces overexpression of multidrug resistance protein 2 (MRP2) in rats: a 30-day ingestion study. Food Chem Toxicol 2004; 42:995-1002. [PMID: 15110109 DOI: 10.1016/j.fct.2004.02.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2002] [Accepted: 02/16/2004] [Indexed: 11/27/2022]
Abstract
St. John's Wort (Hypericum perforatum, SJW) has been used as a herbal medicine for the treatment of depression in oral doses of 900-1050 mg/day in humans. However, the ingestion of SJW was reported to cause interactions with drugs. In the present study, we examined the effects of SJW treatment on the induction of drug transporters and enzymes in rats. An immunoblot analysis was performed to quantify the expression of the transporters and enzymes. SJW was given at a dose of 400 mg/kg/day, since it was reported that 400 mg/kg/day is antidepressant effective dose in rats. When SJW was administered for 10 days, the amounts of multidrug resistance protein 2 (MRP2), glutathione S-transferase-P (GST-P) and cytochrome P450 1A2 (CYP1A2) in the liver were increased to 304%, 252% and 357% of controls, respectively, although the amounts of P-glycoprotein and multidrug resistance protein 1 were not changed. Under the same conditions, an increase of MRP2 in the kidney was not observed. The increase in the levels of each protein was maximal at 10 days after SJW treatment and lasted for at least 30 consecutive days. These results suggest that SJW induces hepatic MRP2, GST-P and CYP1A2 overexpressions, and thus, it could affect drug metabolism, conjugation and disposition.
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Affiliation(s)
- Y Shibayama
- Department of Clinical Pharmacy and Pharmacology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8520, Japan
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27
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Egashira Y, Yoshida T, Hirata I, Hamamoto N, Akutagawa H, Takeshita A, Noda N, Kurisu Y, Shibayama Y. Analysis of pathological risk factors for lymph node metastasis of submucosal invasive colon cancer. Mod Pathol 2004; 17:503-11. [PMID: 15001992 DOI: 10.1038/modpathol.3800030] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
There are currently no universally accepted indications and criteria for additional surgical resection of the colorectum after endoscopic resection of the submucosal invasive cancer. The purpose of the present study is to establish accurate indications and criteria for additional surgical resection of the colorectum, based on the prediction of lymph node metastasis, after endoscopic resection of the submucosal invasive cancer. We investigated 140 submucosal invasive colorectal cancers and analyzed the pathologic factors of lymph node metastasis. The tumors were evaluated for pathologic factors in the invasive area of the submucosal carcinoma and were compared between the cases with lymph node metastasis and those without lymph node metastasis. Lymph node metastasis was observed in 13 cases (9%). Univariate logistic regression analysis showed that the depth of invasion, cribriform-type structural atypia, absence of lymphoid infiltration, lymphatic permeation, and venous permeation were statistically significant as risk factors for lymph node metastasis. Multivariate logistic regression analysis showed that the important risk factors included, in decreasing order, lymphatic permeation, absence of lymphoid infiltration, cribriform-type structural atypia, venous permeation, and depth of invasion. Submucosal invasion of 2 mm or more, and/or, depth of lymphatic permeation of 2 mm or more are risk factors for lymph node metastasis. The pathologic criteria based on our results for additional colectomy enables greater accuracy selection of patients who will undergo further surgical treatment after endoscopic resection.
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Affiliation(s)
- Y Egashira
- Department of Pathology, Osaka Medical College, Takatsuki city, Osaka, Japan.
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28
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Kaplan AP, Joseph K, Shibayama Y, Reddigari S, Ghebrehiwet B. Activation of the plasma kinin forming cascade along cell surfaces. Int Arch Allergy Immunol 2001; 124:339-42. [PMID: 11307009 DOI: 10.1159/000053751] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Proteins of the plasma kinin-forming cascade bind to endothelial cells and activation of the cascade can be initiated along the surface. The light chain of high molecular weight kininogen (HK) (domain 5) and factor XII bind to gC1qR, the heavy chain of HK (domain 3) binds to cytokeratin 1 and the interactions are zinc dependent. Prekallikrein binds to domain 6 of HK. Antisera to gC1qR and cytokeratin 1 inhibit binding and activation. Incubation of normal plasma with endothelial cells leads to gradual conversion of prekallikrein to kallikrein, while plasma deficient in factor XII or HK are inactive within a 2-hour time frame. Thus factor XII is critical for activation to proceed. Augmentation of these reactions may occur when C1 inhibitor is functionally deficient or with ACE inhibitors which also inhibit kininases.
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Affiliation(s)
- A P Kaplan
- Department of Medicine, Division of Pulmonary and Critical Care, Allergy and Clinical Immunology and the Konishi-MUSC Institute for Inflammation Research, Medical University of South Carolina, Charleston 29425, USA.
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29
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Joseph K, Shibayama Y, Ghebrehiwet B, Kaplan AP. Factor XII-dependent contact activation on endothelial cells and binding proteins gC1qR and cytokeratin 1. Thromb Haemost 2001; 85:119-24. [PMID: 11204562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Although proteins of the kinin-forming pathway are bound along the surface of endothelial cells, the mechanism of activation of this proteolytic cascade is unclear. Endothelial cell surface proteins, gC1qR and cytokeratin 1, are capable of binding Factor XII and high molecular weight kininogen (HK) in a zinc-dependent reaction thus we considered the possibility that these proteins might catalyze initiation of the cascade. Incubation of Factor XII, prekallikrein, and HK with gC1qR or cytokeratin 1 leads to a zinc-dependent and Factor XII-dependent conversion of prekallikrein to kallikrein. We also demonstrate that normal plasma is capable of activating upon interaction with the cells whereas plasma deficient in Factor XII, prekallikrein and HK do not activate. Normal plasma activation was inhibitable by antibody to gC1qR and cytokeratin 1. Thus, gC1qR and cytokeratin 1, represent potential initiating surfaces for activation of the plasma kinin-forming cascade and may do so as a result of their expression along cell surfaces.
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Affiliation(s)
- K Joseph
- Department of Medicine and Konishi-MUSC Institute for Inflammation Research, Medical University of South Carolina, Charleston 29425, USA
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30
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Shibayama Y, Sato H, Enoki T, Endo M. Disordered magnetism at the metal-insulator threshold in nano-graphite-based carbon materials. Phys Rev Lett 2000; 84:1744-1747. [PMID: 11017615 DOI: 10.1103/physrevlett.84.1744] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/1999] [Indexed: 05/23/2023]
Abstract
The magnetism of activated carbon fibers composed of a disorder network of nanographites was investigated, where each nanographite has about 1 edge-inherited localized spin. The susceptibility, for samples situated around the metal-insulator threshold, shows a cusp around 4-7 K in addition to the presence of a field-cooling effect. These behaviors are explained in terms of disordered magnetism caused by random strengths of inter-nano-graphite antiferromagnetic interactions mediated by pi-conduction carriers.
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Affiliation(s)
- Y Shibayama
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
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31
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Abstract
This study was undertaken to assess the effect of knee immobilization on the treatment of Achilles tendon rupture. After their Achilles tendons were severed, rabbits were divided into 2 groups. In Group A, only the ankle joint was immobilized. In Group B, both the knee and ankle joints were immobilized. At 4 weeks after surgery, both the ultimate tensile force and stiffness of the severed tendons were significantly greater in Group A than in Group B. In Group A, dense collagen fibers were seen in the repaired tendons, and the bundles of collagen fibers were parallel to one another along the axis of the tendons. In contrast, in Group B, dilated veins and capillaries were seen in the repaired tendons, and the proliferation of connective tissue containing collagen fibers was severely reduced around these veins and capillaries and was in general irregular and uneven. These results suggest that knee immobilization retards the healing of a ruptured Achilles tendon without suture, due to congestion and tension deprivation produced by keeping the tendon static.
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Affiliation(s)
- T Yasuda
- Department of Orthopedic Surgery, Osaka Medical College, Takatsuki, Japan
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32
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Joseph K, Shibayama Y, Nakazawa Y, Peerschke EI, Ghebrehiwet B, Kaplan AP. Interaction of factor XII and high molecular weight kininogen with cytokeratin 1 and gC1qR of vascular endothelial cells and with aggregated Abeta protein of Alzheimer's disease. Immunopharmacology 1999; 43:203-10. [PMID: 10596854 DOI: 10.1016/s0162-3109(99)00136-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
High molecular weight kininogen (HK) attaches to endothelial cells at separate sites on the heavy and light chains by a process which requires 15-50 microM zinc. Previously identified binding proteins include gClqR, cytokeratin 1, and the urokinase plasminogen activator receptor (U-par), however, their relative contribution to binding are not yet clarified. We have purified the binding proteins by affinity chromatography, in the presence of zinc ion, and identified cytokeratin 1 and gC1qR by amino acid sequencing of an internal peptide and by immunoblot as heavy chain and light chain binding proteins, respectively. Antibody to cytokeratin 1 inhibited HK binding to endothelial cells by 30%, antibody to gClqR inhibited HK binding to endothelial cells by 72%, and a mixture of both inhibited binding by 86%. The binding and activation of the proteins of the kinin-forming cascade along the cell surface is zinc-dependent. Similarly, proteins of the plasma kinin-forming cascade can be activated by binding to aggregated A(beta) protein of Alzheimer's disease. Activation of the cascade using purified proteins or upon addition of Abeta to plasma requires aggregation of A(beta) and the reactions are zinc-dependent. In plasma, HK is cleaved and bradykinin is liberated. The data demonstrate that aggregated A(beta) can bind and activate proenzymes of the plasma kinin-forming cascade to release bradykinin and these reactions are dependent on zinc ion.
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Affiliation(s)
- K Joseph
- Department of Medicine, Medical University of South Carolina, Charleston 29425, USA
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33
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Fukunishi K, Kurokawa T, Takeshita A, Nariyama K, Egashira Y, Shibayama Y, Kamei K, Oue T, Hashimoto S, Fukuda Y, Min KY, Ohsawa N. [Acute myelocytic leukemia and plasmacytoma secondary to chemotherapy and radiotherapy in a long-term survivor of small cell lung cancer]. Nihon Kokyuki Gakkai Zasshi 1999; 37:415-9. [PMID: 10410546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
A 68-year-old man was given a diagnosis of lung cancer of the right upper lobe (small cell carcinoma, T 4 N 2 M 0, stage IIIB) in February 1991. The tumor diminished after chemotherapy and radiotherapy. In February 1992, a partial resection of the lower lobe of the right lung was performed because of the appearance of a metastatic tumor. In September 1994, squamous cell carcinoma developed in the lower part of the esophagus, but disappeared after radiotherapy. In February 1998, a diagnosis of myelodysplastic syndrome was made. Two months later, the patient had an attack of acute myelocytic leukemia and died of cardiac tamponade. An autopsy determined that both the lung cancer and esophageal cancer had disappeared. Acute myelocytic leukemia and plasmacytoma of lymph nodes in the irradiated area were confirmed. These were regarded as secondary malignancies induced by chemotherapy and radiotherapy.
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Affiliation(s)
- K Fukunishi
- Department of Pathology, Osaka Medical College, Japan
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34
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Shibayama Y, Joseph K, Nakazawa Y, Ghebreihiwet B, Peerschke EI, Kaplan AP. Zinc-dependent activation of the plasma kinin-forming cascade by aggregated beta amyloid protein. Clin Immunol 1999; 90:89-99. [PMID: 9884356 DOI: 10.1006/clim.1998.4621] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Beta Amyloid proteins (Abeta) of 38, 40, and 42 amino acids long were assessed for their ability to activate the plasma kinin-forming cascade in vitro. Incubation with a mixture of Factor XII (Hageman Factor), prekallikrein, and high-molecular-weight kininogen (HK) led to conversion of prekallikrein to kallikrein that was dependent on zinc ion. No activation occurred if Factor XII was omitted. There was rapid generation of bradykinin equal to the molar HK input indicating complete cleavage. Incubation of aggregated Abeta with diluted human plasma also led to prekallikrein activation and HK cleavage. Activation of the cascade by Abeta (1-38) was dependent upon its preincubation time in buffer, suggesting that aggregation of Abeta is required, and studies with Abeta (1-40) revealed time-dependent aggregation by microscopy and augmented zinc-dependent binding of both Factor XII and HK to aggregated Abeta. These data demonstrate that aggregated Abeta can bind and activate proenzymes of the plasma kinin-forming cascade in a zinc-dependent reaction to release bradykinin and is of sufficient potency to do so at physiologic concentrations of each protein and in the presence of naturally occurring protease inhibitors.
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Affiliation(s)
- Y Shibayama
- The Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Charleston, South Carolina, 29425, USA
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Kurihara A, Shibayama Y, Kasuya A, Ikeda M, Hisaoka M. Species variation in pharmacokinetics and opsonization of palmitoyl rhizoxin (RS-1541) incorporated in lipid emulsions. J Drug Target 1998; 5:491-505. [PMID: 9783680 DOI: 10.3109/10611869808997875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Highly lipophilic antitumor agent, palmitoyl rhizoxin (RS-1541), was incorporated into stable lipid emulsions about 100-1000nm in mean diameter consisting of triglyceride ODO and surfactant HCO-60. The pharmacokinetics of RS-1541 were studied after i.v. injection in mice, rats, rabbits, and dogs. Dog showed characteristic pharmacokinetics of RS-1541, compared with other species. RS-1541 was much more rapidly eliminated from plasma with emulsion particles in dogs than in mice, rats, and rabbits. Most amounts of injected RS-1541 were recovered in the liver six hours after administration to dogs, while less than 20% recoveries were observed for mice and rats. To clarify this species variation, opsonization of emulsion particles were evaluated. When emulsions (about 200nm in size) were opsonized by dog plasma, and intravenously injected to rats, total clearance and liver uptake of RS-1541 were increased to 1.8 fold and 2.7 fold of control values, respectively. In contrasts, emulsions opsonized by mouse, rabbit and human plasma did not show such drastic changes in pharmacokinetics of RS-1541 in rats. Furthermore, total clearance of RS-1541 for emulsions opsonized by dog plasma was increased to 1.9 fold of controls after injection to rabbits. These results indicate that opsonizing activities of dog plasma for RS-1541 emulsions are high, compared with other species. This species variation in opsonizing process probably caused the species variation in the pharmacokinetics of RS-1541 incorporated in lipid emulsions.
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Affiliation(s)
- A Kurihara
- Analytical and Metabolic Research Laboratories, Sankyo Co., Ltd, Tokyo, Japan.
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Omata F, Itoh T, Shibayama Y, Ide H, Takahashi H, Ueno F, Saubermann LJ, Matsuzaki S. Duodenal variceal bleeding treated with a combination of endoscopic ligation and sclerotherapy. Endoscopy 1998; 30:S62-3. [PMID: 9693913 DOI: 10.1055/s-2007-1001329] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- F Omata
- Dept. of Medicine, Tokai University Oiso Hospital, Kanagawa, Japan
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Oda K, Shibayama Y, Abe M, Onomura T. Morphogenesis of vertebral deformities in involutional osteoporosis. Age-related, three-dimensional trabecular structure. Spine (Phila Pa 1976) 1998; 23:1050-5, discussion 1056. [PMID: 9589545 DOI: 10.1097/00007632-199805010-00016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
STUDY DESIGN The relation between the semiquantitative data of alteration in three-dimensional trabecular structure and deformities of the vertebral body was analyzed to clarify the morphogenesis of vertebral deformities in involutional osteoporosis. OBJECTIVES To evaluate semiquantitatively the age-related alterations of the three-dimensional structure of trabeculae of the vertebral body and to clarify their relation to vertebral deformities in involutional osteoporosis. SUMMARY OF BACKGROUND DATA Recent studies have shown that bone fractures and deformities in osteoporosis do not depend only on a reduced amount of bone tissue. There is no previous study on the relation between bone deformity and the alterations of the three-dimensional structure of trabeculae. METHODS The second lumbar vertebrae were removed at autopsy from 25 patients who had no disease predisposing them to secondary osteoporosis and no severe vertebral deformities. The sections of the vertebral body were immersed in sodium hypochlorite solution to corrode the bone marrow. Atrophy of trabeculae and increased spacing between trabeculae were evaluated semiquantitatively under stereoscopic microscopy. The authors examined the relation between the semiquantitative data found in the autopsy vertebrae and the patterns and frequencies of each deformity of the second lumbar vertebrae in 99 patients with involutional osteoporosis. RESULTS The most frequent vertebral deformity was wedge-shaped vertebrae with compression of the anterosuperior portion, and the alterations of the trabecular structure of the anterosuperior portion were severe and closely related to aging. Severe trabecular alterations with no relation to aging did not necessarily cause vertebral deformity. CONCLUSIONS Trabecular abnormality, which is significantly correlated with aging, may be the necessary and sufficient condition for vertebral deformities in involutional osteoporosis.
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Affiliation(s)
- K Oda
- Department of Pathology, Osaka Medical College, Japan
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38
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Shibayama Y, Reddigari SR, Teruya M, Nakamura K, Fukunaga Y, Ienaga K, Nishikawa K, Suehiro S, Kaplan AP. Effect of neurotropin on the binding of high molecular weight kininogen and Hageman factor to human umbilical vein endothelial cells and the autoactivation of bound Hageman factor. Biochem Pharmacol 1998; 55:1175-80. [PMID: 9719471 DOI: 10.1016/s0006-2952(97)00577-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bradykinin is generated by activation of the plasma kallikrein-kinin (K-K) cascade and contributes to the symptoms of allergic reactions and the perception of pain. Neurotropin is a biological material obtained from inflamed rabbit skin inoculated with vaccinia virus, which is widely used clinically in Japan as an effective agent for these disorders. Factor XII (FXII) and high molecular weight kininogen (HK), two critical constituents of the plasma K-K cascade, bind to endothelial cells, and bound FXII is autoactivated in the presence of zinc ions. We have investigated the effects of Neurotropin on the interactions of FXII and HK with endothelial cells. Neurotropin inhibited the binding of both proteins to cultured human umbilical vein endothelial cells (HUVEC) and inhibited autoactivation of FXII upon HUVEC in a concentration-dependent manner. These data suggest that the ameliorating effects of Neurotropin in allergic disorders and pain syndromes may be related to this ability to inhibit activation of the K-K cascade and, consequently, the formation of bradykinin.
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Affiliation(s)
- Y Shibayama
- Department of Medicine, The State University of New York at Stony Brook, 11794, USA
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Kaplan AP, Joseph K, Shibayama Y, Nakazawa Y, Ghebrehiwet B, Reddigari S, Silverberg M. Bradykinin formation. Plasma and tissue pathways and cellular interactions. Clin Rev Allergy Immunol 1998; 16:403-29. [PMID: 9926288 DOI: 10.1007/bf02737659] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- A P Kaplan
- Division of Pulmonary and Critical Care Medicine, Allergy and Clinical Immunology, Medical University of South Carolina, Charleston 29425-2220, USA.
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Kaplan AP, Joseph K, Shibayama Y, Reddigari S, Ghebrehiwet B, Silverberg M. The intrinsic coagulation/kinin-forming cascade: assembly in plasma and cell surfaces in inflammation. Adv Immunol 1997; 66:225-72. [PMID: 9328643 DOI: 10.1016/s0065-2776(08)60599-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- A P Kaplan
- Department of Medicine, State University of New York, Stony Brook 11794-8161, USA
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41
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Kataoka K, Shibayama Y, Ohuchi M, Yokokawa S. Laser printer optics with use of slant scanning of multiple beams. Appl Opt 1997; 36:6294-6307. [PMID: 18259481 DOI: 10.1364/ao.36.006294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Simultaneous scanning of multiple beams in an array is an effective method to realize high-speed and high-resolution printers. The arrayed multiple beams can be generated by devices such as grating, Wollaston prism, fiber array, and laser diode array. In any of these devices, the focused spots in an array have a period several tens of times larger than the spot diameter. We propose a simultaneous scanning method suitable for these devices in which the arrayed multiple beams are arranged in a slant angle to the scanning direction to produce consecutive scan lines. Laser print experiments with two or four beams were carried out, and high-performance printing of a 431.8-mm print width, 23.6 dot/mm (i.e., 600 dot/in.) resolution, and of 541-mm/s speed were realized.
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MESH Headings
- Amino Acid Sequence
- Binding, Competitive
- Blood Proteins/metabolism
- Carrier Proteins
- Cell Membrane/metabolism
- Cells, Cultured
- Complement C1q/metabolism
- Cysteine Proteinase Inhibitors/chemistry
- Cysteine Proteinase Inhibitors/metabolism
- Electrophoresis, Polyacrylamide Gel
- Endothelium, Vascular/cytology
- Endothelium, Vascular/drug effects
- Endothelium, Vascular/metabolism
- Factor XII/chemistry
- Factor XII/metabolism
- Humans
- Hyaluronan Receptors
- Kininogens/chemistry
- Kininogens/metabolism
- Membrane Glycoproteins
- Mitochondrial Proteins
- Molecular Weight
- Prekallikrein/metabolism
- Receptors, Complement/chemistry
- Receptors, Complement/metabolism
- Receptors, Peptide/chemistry
- Receptors, Peptide/isolation & purification
- Receptors, Peptide/metabolism
- Recombinant Proteins/metabolism
- Umbilical Veins/cytology
- Umbilical Veins/drug effects
- Umbilical Veins/metabolism
- Zinc/blood
- Zinc/pharmacology
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Affiliation(s)
- A P Kaplan
- Department of Medicine, SUNY-Stony Brook, Health Sciences Center 11794, USA
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43
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Brunnée T, Reddigari SR, Shibayama Y, Kaplan AP, Silverberg M. Mast cell derived heparin activates the contact system: a link to kinin generation in allergic reactions. Clin Exp Allergy 1997; 27:653-63. [PMID: 9208186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Contact activation occurs when plasma comes in contact with negatively charged manmade surfaces but no substance that initiates contact activation in vivo has been identified. We have isolated a mast cell heparin proteoglycan (MC-HepPG) from a Furth mouse mastocytoma-derived cell line that is analogous to human tissue-type mast cell HepPG. This material and other glycosaminoglycans (GAGs) were tested for their ability to accelerate the reciprocal activation of factor XII and prekallikrein and the autoactivation of factor XII. Quantitative analysis showed the MC-HepPG to be as active as dextran sulfate on a weight basis; hog intestine heparin, dermatan sulfate, keratan polysulfate and chondroitin sulfate C were less active, other sulfated polysaccharides were essentially inactive. Incubation of MC-HepPG in 1:4 diluted plasma resulted in complete cleavage of high molecular weight kininogen in a factor XII-dependent reaction. All of the MC-HepPG dependent reactions described above were inhibited by preincubation of MC-HepPG with heparinase I and II but not by pretreatment with heparitinase, chondroitinase ABC or the serine protease inhibitor aPMSF thus indicating that heparin proteoglycan is indeed acting as an initiating 'surface'. We analysed the proteoglycan preparation by HPLC gel filtration. Fractions spanning a molecular weight range of > 400000-8000 were active initiators. Comparison of the chromatograms obtained before and after cleavage of GAG side chains from the protein core suggested that dissociated GAGs in the MW range 69000-17000 are the most active species rather than the complete proteoglycan. MC-HepPG GAGs therefore represent a physiologic macromolecule with activity comparable to non-physiological surfaces in a purified system and with the capability to induce activation of the contact system in diluted plasma. Its ability to promote kinin generation links cellular and humoral inflammatory responses in the perivasculature and provides a possible explanation for the elevated kinin levels observed after allergen exposure.
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Affiliation(s)
- T Brunnée
- Department of Clinical Immunology and Asthma OPD, Humboldt-University, Berlin, Germany
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44
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Kataoka K, Shibayama Y. Optics for modulating multiple beams using an asymmetric multilevel phase grating and a multichannel acousto-optic modulator. Appl Opt 1997; 36:853-861. [PMID: 18250749 DOI: 10.1364/ao.36.000853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Asymmetric multilevel phase gratings for generating even numbered beams have been designed, assuming that their phase patterns are formed by overlapping plural binary-phase patterns, each of which has an arbitrary phase height. The grating for four beams, which produces uniform and high intense diffraction orders of the minus first to the plus second order, is fabricated. The efficiency is 75.5%, although the theoretical efficiency is 79.9%. It is also demonstrated that the optics in which the beams from the grating are fed into a multichannel acousto-optic modulator through a Fourier-transform lens makes their successful modulation possible for pulse signals of 20-ns pulse duration.
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Affiliation(s)
- K Kataoka
- Katsuta Research Laboratory, Hitachi Koki Corporation, Ltd., 1060 Takeda, Hitachi-Naka City, Ibaraki Prefecture 312, Japan
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45
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Omata F, Ide H, Ito T, Shibayama Y, Takahashi H, Ueno F. Interferon therapy for fulminant hepatitis associated with precore region mutation in hepatitis B virus carrier. Am J Gastroenterol 1996; 91:1673-5. [PMID: 8759701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Shibayama Y, Skoner D, Suehiro S, Konishi JE, Fireman P, Kaplan AP. Bradykinin levels during experimental nasal infection with rhinovirus and attenuated influenza virus. Immunopharmacology 1996; 33:311-3. [PMID: 8856172 DOI: 10.1016/0162-3109(96)00051-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Abstract
The present study was undertaken in rats to clarify the role of sinusoidal circulatory disturbances due to fibrin thrombi in the development of focal and random hepatocellular necrosis in endotoxemia. Sinusoidal circulation was examined microscopically in vivo in rats injected with endotoxin or heparin, or both. The sinusoids in places were occluded by adherent fibrin and neutrophils soon after endotoxin injection, and subsequently the sinusoidal blood flow stagnated, reversed, or detoured. Most of these sinusoidal circulatory disturbances recovered in a few hours. However, when the sinusoidal occlusion developed simultaneously in clusters of adjacent sinusoids, the sinusoidal circulatory disturbance persisted and induced ischemic foci and then hepatocellular coagulative necrosis. Pretreatment with heparin definitely prevented the adherence of fibrin and neutrophils to the sinusoidal walls, and focal hepatocellular necrosis did not appear. These results suggest that focal and random hepatocellular necrosis in endotoxemia is caused by circulatory disturbances due to fibrin thrombi in clusters of adjacent sinusoids.
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Affiliation(s)
- S Asaka
- Department of Pathology, Osaka Medical College, Japan
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48
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Affiliation(s)
- Y Shibayama
- Department of Medicine, SUNY-Stony Brook, Health Sciences Center 11794, USA
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49
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Kurihara A, Shibayama Y, Yasuno A, Ikeda M, Hisaoka M. Lipid emulsions of palmitoylrhizoxin: effects of particle size on blood dispositions of emulsion lipid and incorporated compound in rats. Biopharm Drug Dispos 1996; 17:343-53. [PMID: 8743405 DOI: 10.1002/(sici)1099-081x(199605)17:4<343::aid-bdd958>3.0.co;2-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Emulsion formulations of various particle sizes for the highly lipophilic antitumour agent, RS-1541 (13-O-palmitoylrhizoxin), were prepared using dioctanoyldecanoylglycerol (ODO) as lipids and polyoxyethylene-(60)-hydrogenated castor oil (HCO-60) as a surfactant. These emulsions were evaluated as injectable drug carriers and compared with a colloidal solution. Both in vitro and in vivo after i.v. administration, RS-1541 was distributed into lipoproteins from the colloidal solution. When applied as emulsions of various particle sizes (124-419 nm) in vitro, RS-1541 was retained and stabilized within the emulsions. In the in vivo study, however, retention of RS-1541 in the emulsions after i.v. injection depended on their size. The small-particle emulsions (94-112 nm) resulted in long retention, and the large-particle emulsions (415-474 nm) led to short retention. Lipolysis rates of emulsion particles by lipoprotein lipase also depended on their size, indicating rapid lipolysis for small-particle emulsions (133 nm). However, the lipolysis was not such an extensive one, showing 10-30% release of capric acid from ODO within 6 h. Blood dispositions of capric acids approximately paralleled those of RS-1541 after i.v. injection of various particle size emulsions (130-368 nm) to rats, although relatively rapid eliminations of capric acids compared with RS-1541 were observed for the small-particle size emulsions (130 nm). These results suggest that when injected as emulsion formulations, the highly lipophilic antitumour agent, RS-1541, has behaviour similar to that of the emulsion particles in the body, which is dependent on the size of the latter. Thus, by properly selecting the particle size, lipid emulsions consisting of ODO and HCO-60 are expected to be effective and useful DDS carriers for RS-1541.
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Affiliation(s)
- A Kurihara
- Analytical and Metabolic Research Laboratories, Sankyo Co Ltd., Tokyo, Japan
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50
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Kurihara A, Shibayama Y, Mizota A, Yasuno A, Ikeda M, Sasagawa K, Kobayashi T, Hisaoka M. Lipid emulsions of palmitoylrhizoxin: effects of composition on lipolysis and biodistribution. Biopharm Drug Dispos 1996; 17:331-42. [PMID: 8743404 DOI: 10.1002/(sici)1099-081x(199605)17:4<331::aid-bdd959>3.0.co;2-b] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Four types of lipid emulsion for highly lipophilic antitumour agent RS-1541 (13-O-palmitoylrhizoxin) with mean particle diameters of 200-260 nm were prepared using soybean oil (SOY) or dioctanoyldecanoylglycerol (ODO) for the oil phase and lecithin (LEC) or polyoxyethylene-(60)-hydrogenated castor oil (HCO-60) for surfactants. The lipolysis rate of HCO-60-emulsified emulsions by lipoprotein lipase was much slower than that of LEC-emulsified emulsions. Particle sizes of emulsions incubated in plasma with the lipase for six hours were 75%, 79%, 101%, and 93% of initial values for SOY/LEC, ODO/LEC, SOY/HCO-60, and ODO/HCO-60 emulsions, respectively, showing an apparent size decrease for LEC-emulsified emulsions. In rats, uptake clearance values of SOY/LEC and ODO/LEC emulsions of RS-1541 in the reticuloendothelial system (RES) were 81.2 and 135.3 mL h(-1), respectively, and AUC values were 4.0 and 1.3 microg h mL(-1), respectively. In contrast, RES uptake clearances of HCO-60 emulsions of RS-1541 were considerably lower (4.2 mL h(-1) for SOY/HCO-60; 2.2 mL h(-1) for ODO/HCO-60), resulting in high AUC values (35.4 microg h mL(-1) for SOY/ HCO-60; 63.9 microg h mL(-1) for ODO/HCO-60). The concentrations of RS-1541 in tumour tissues after an intravenous administration of ODO/HCO-60 emulsions of RS-1541 to mice bearing solid tumour M5076 sarcoma were about ten times higher than those after the administration of SOY/LEC emulsions. These results indicate that HCO-60 emulsions, compared with conventional LEC emulsions, are more stable to lipoprotein lipase and show low uptakes by RES organs, long circulations in the plasma, and high distributions in tumours. Thus, these sterically stabilized emulsions could show potential as effective carriers for highly lipophilic antitumour agents to enhance the drug delivery in tumours.
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Affiliation(s)
- A Kurihara
- Analytical and Metabolic Research Laboratories, Sankyo Co., Ltd., Tokyo, Japan
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