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Itahashi K, Irie T, Yuda J, Kumagai S, Tanegashima T, Lin YT, Watanabe S, Goto Y, Suzuki J, Aokage K, Tsuboi M, Minami Y, Ishii G, Ohe Y, Ise W, Kurosaki T, Suzuki Y, Koyama S, Nishikawa H. BATF epigenetically and transcriptionally controls the activation program of regulatory T cells in human tumors. Sci Immunol 2022; 7:eabk0957. [PMID: 36206353 DOI: 10.1126/sciimmunol.abk0957] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Regulatory T (Treg) cells suppress effective antitumor immunity in tumor-bearing hosts, thereby becoming promising targets in cancer immunotherapy. Despite the importance of Treg cells in tumor immunity, little is known about their differentiation process and epigenetic profiles in the tumor microenvironment (TME). Here, we showed that Treg cells in the TME of human lung cancers harbored a completely different open chromatin profile compared with CD8+ T cells, conventional CD4+ T cells in the TME, and peripheral Treg cells. The integrative sequencing analyses including ATAC, single-cell RNA, and single-cell ATAC sequencing revealed that BATF, IRF4, NF-κB, and NR4A were important transcription factors for Treg cell differentiation in the TME. In particular, BATF was identified as a key regulator, which leveraged Treg cell differentiation through epigenetically controlling activation-associated gene expression, resulting in the robustness of Treg cells in the TME. The single-cell sequencing approaches also revealed that tissue-resident and tumor-infiltrating Treg cells followed a common pathway for differentiation and activation in a BATF-dependent manner heading toward Treg cells with the most differentiated and activated phenotypes in tissues and tumors. BATF deficiency in Treg cells remarkably inhibited tumor growth, and high BATF expression was associated with poor prognosis in lung cancer, kidney cancer, and melanoma. These findings indicate one of the specific chromatin remodeling and differentiation programs of Treg cells in the TME, which can be applied in the development of Treg cell-targeted therapies.
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Affiliation(s)
- Kota Itahashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Takuma Irie
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Junichiro Yuda
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan.,Department of Hematology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Shogo Kumagai
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Tokiyoshi Tanegashima
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Yi-Tzu Lin
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Sho Watanabe
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Yasushi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Jun Suzuki
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Keiju Aokage
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Yosuke Minami
- Department of Hematology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Genichiro Ishii
- Division of Pathology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Yuichiro Ohe
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Wataru Ise
- Regulation of Host Defense Team, Division of Microbiology and Immunology, Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan.,Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan.,Division of Microbiology and Immunology, Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan.,Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Kanagawa 230-0045, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8562, Japan
| | - Shohei Koyama
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Hiroyoshi Nishikawa
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
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2
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Kaneko Y, Fukuda K, Irie T, Shimizu H, Tamura S, Kobari T, Hasegawa H, Nakajima T, Ishii H. Electrophysiological characteristics and catheter ablation of atypical fast-slow atrioventricular nodal reentrant tachycardia using an inferolateral left atrial slow pathway. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.643] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Understandings of subtypes of atypical atrioventricular nodal reentrant tachycardia (AVNRT) using variants of slow pathway (SP) are still growing. Inferolateral (inf-lat-) left atrial (LA) SP is a rare variant extending into an inf-lat-LA along the mitral annulus (MA).
Purpose
To characterize an unknown subtype of atypical fast-slow (F/S-) AVNRT using an inf-lat-LA-SP as a retrograde limb (inf-lat-LA-F/S-AVNRT).
Methods
This Japanese multicenter retrospective study enrolled 4 patients of inf-lat-LA-F/S-AVNRT that was characterized by the earliest site of atrial activation during tachycardia (EAA) between 3 and 6 o'clock along the MA. The diagnosis was made by an exclusion of AV reentrant tachycardia (AVRT) and atrial tachycardia (AT) according to the standard criteria and was confirmed by successful elimination of tachycardia and the inf-lat-LA-SP.
Results
Surface ECG during tachycardia revealed long RP appearance except one who had short RP due to a short conduction time across the inf-lat-LA-SP. During tachycardia, far-field LA activation preceding near-field activation of coronary sinus (CS) musculature was visible in the CS recording in 2. Retrograde conduction via the inf-lat-LA-SP with a decremental delay was consistently reproducible with ventricular stimulation in 2, 1 of whom had double atrial response, while it was always masked by the presence of a retrograde conduction via the fast pathway in 1 and a retrograde block at the lower common pathway in 1. An injection of a small dose of ATP transiently interrupted a retrograde conduction over the inf-lat-LA-SP, suggesting its ATP-sensitivity. Exclusion of AVRT was made by no resetting of tachycardia with left ventricular extrastimulus in 2 and VA dissociation during overdrive pacing of tachycardia in remaining 2. Exclusion of AT was made by V-A-V response after ventricular entrainment in 1 and termination without atrial capture by ventricular pacing in 2. Ablation of the right-sided SP was unsuccessful to eliminate the tachycardia, but ablation at or near the EAA by transseptal approach was successful to cure the tachycardia, associated with an elimination of a retrograde conduction over the inf-lat-LA-SP following a development of an accelerated junction rhythm in all. Low-frequency potentials preceding local atrial activation, consistent with a retrograde activation via the inf-lat-LA-SP were detected along the MA medial to the EAA in 1.
Conclusions
Differential diagnosis of tachycardia with the EAA in the inf-lat-LA and especially long RP appearance should include inf-lat-LA-F/S-AVNRT. Presumed arrhythmogenic substrate of the inf-lat-LA-SP seemed to be consistent with the remnant of embryogenic AV ring tissue in the electropharmacological and locational characteristics. Successful elimination of this AVNRT can be obtained by ablation of the inf-lat-LA-SP, but not of the right-sided SP.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- Y Kaneko
- Gunma University Graduate School of Medicine, Maebashi , Gunma , Japan
| | - K Fukuda
- International University of Health and Welfare Hospital, Department of Cardiology , Nasushiobara , Japan
| | - T Irie
- Saitama Sekishinkai Hospita, Department of Cardiology , Sayama , Japan
| | - H Shimizu
- Saiseikai Niigata Hospital, Department of Cardiology , Niigata , Japan
| | - S Tamura
- Gunma University Graduate School of Medicine, Maebashi , Gunma , Japan
| | - T Kobari
- Gunma University Graduate School of Medicine, Maebashi , Gunma , Japan
| | - H Hasegawa
- Gunma University Graduate School of Medicine, Maebashi , Gunma , Japan
| | - T Nakajima
- Gunma University Graduate School of Medicine, Maebashi , Gunma , Japan
| | - H Ishii
- Gunma University Graduate School of Medicine, Maebashi , Gunma , Japan
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3
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Itahashi K, Irie T, Nishikawa H. Regulatory T-cell development in the tumor microenvironment. Eur J Immunol 2022; 52:1216-1227. [PMID: 35879813 DOI: 10.1002/eji.202149358] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [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: 01/18/2022] [Revised: 05/01/2022] [Accepted: 06/23/2022] [Indexed: 12/20/2022]
Abstract
Regulatory T (Treg) cells are required for maintaining self-tolerance and preventing the development of autoimmune diseases. However, Treg cells are abundant in tumors and suppress antitumor immunity, contributing to tumor development and growth. Thus, the selective deletion of tumor-infiltrating Treg cells is important for successful Treg cell-targeted therapies, providing effective antitumor immunity without inducing deleterious autoimmune disorders. Advancements in sequencing technologies have exposed the diversity and heterogeneity of human Treg cells during activation and differentiation, further emphasizing the importance of understanding tumor-infiltrating Treg cells for the development of Treg cell-targeted therapies. This review provides an overview of the classification and function of Treg cells and summarizes recent knowledge on the activation and differentiation of Treg cells in the tumor microenvironment.
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Affiliation(s)
- Kota Itahashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Japan
| | - Takuma Irie
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Japan
| | - Hiroyoshi Nishikawa
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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4
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Masuhiro K, Tamiya M, Fujimoto K, Koyama S, Naito Y, Osa A, Hirai T, Suzuki H, Okamoto N, Shiroyama T, Nishino K, Adachi Y, Nii T, Kinugasa-Katayama Y, Kajihara A, Morita T, Imoto S, Uematsu S, Irie T, Okuzaki D, Aoshi T, Takeda Y, Kumagai T, Hirashima T, Kumanogoh A. Bronchoalveolar lavage fluid reveals factors contributing to the efficacy of PD-1 blockade in lung cancer. JCI Insight 2022; 7:157915. [PMID: 35389889 PMCID: PMC9090256 DOI: 10.1172/jci.insight.157915] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
Bronchoalveolar lavage is commonly performed to assess inflammation and identify responsible pathogens in lung diseases. Findings from bronchoalveolar lavage might be used to evaluate the immune profile of the lung tumor microenvironment (TME). To investigate whether bronchoalveolar lavage fluid (BALF) analysis can help identify patients with non–small cell lung cancer (NSCLC) who respond to immune checkpoint inhibitors (ICIs), BALF and blood were prospectively collected before initiating nivolumab. The secreted molecules, microbiome, and cellular profiles based on BALF and blood analysis of 12 patients were compared with regard to therapeutic effect. Compared with ICI nonresponders, responders showed significantly higher CXCL9 levels and a greater diversity of the lung microbiome profile in BALF, along with a greater frequency of the CD56+ subset in blood T cells, whereas no significant difference in PD-L1 expression was found in tumor cells. Antibiotic treatment in a preclinical lung cancer model significantly decreased CXCL9 in the lung TME, resulting in reduced sensitivity to anti–PD-1 antibody, which was reversed by CXCL9 induction in tumor cells. Thus, CXCL9 might be associated with the lung TME microbiome, and the balance of CXCL9 and lung TME microbiome could contribute to nivolumab sensitivity in patients with NSCLC. BALF analysis can help predict the efficacy of ICIs when performed along with currently approved examinations.
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Affiliation(s)
- Kentaro Masuhiro
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Motohiro Tamiya
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Kosuke Fujimoto
- Department of Immunology and Genomics, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Shohei Koyama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yujiro Naito
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Akio Osa
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takashi Hirai
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hidekazu Suzuki
- Department of Thoracic Oncology, Osaka Habikino Medical Center, Osaka, Japan
| | - Norio Okamoto
- Department of Thoracic Oncology, Osaka Habikino Medical Center, Osaka, Japan
| | - Takayuki Shiroyama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Yuichi Adachi
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yumi Kinugasa-Katayama
- Department of Cellular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Akiko Kajihara
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takayoshi Morita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Satoshi Uematsu
- Department of Immunology and Genomics, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Takuma Irie
- Division of Cancer Immunology, National Cancer Center, Tokyo, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Osaka, Japan
| | - Taiki Aoshi
- Department of Cellular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Tomonori Hirashima
- Department of Thoracic Oncology, Osaka Habikino Medical Center, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
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5
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Kumagai S, Koyama S, Itahashi K, Tanegashima T, Lin YT, Togashi Y, Kamada T, Irie T, Okumura G, Kono H, Ito D, Fujii R, Watanabe S, Sai A, Fukuoka S, Sugiyama E, Watanabe G, Owari T, Nishinakamura H, Sugiyama D, Maeda Y, Kawazoe A, Yukami H, Chida K, Ohara Y, Yoshida T, Shinno Y, Takeyasu Y, Shirasawa M, Nakama K, Aokage K, Suzuki J, Ishii G, Kuwata T, Sakamoto N, Kawazu M, Ueno T, Mori T, Yamazaki N, Tsuboi M, Yatabe Y, Kinoshita T, Doi T, Shitara K, Mano H, Nishikawa H. Lactic acid promotes PD-1 expression in regulatory T cells in highly glycolytic tumor microenvironments. Cancer Cell 2022; 40:201-218.e9. [PMID: 35090594 DOI: 10.1016/j.ccell.2022.01.001] [Citation(s) in RCA: 258] [Impact Index Per Article: 129.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/07/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
The balance of programmed death-1 (PD-1)-expressing CD8+ T cells and regulatory T (Treg) cells in the tumor microenvironment (TME) determines the clinical efficacy of PD-1 blockade therapy through the competition of their reactivation. However, factors that determine this balance remain unknown. Here, we show that Treg cells gain higher PD-1 expression than effector T cells in highly glycolytic tumors, including MYC-amplified tumors and liver tumors. Under low-glucose environments via glucose consumption by tumor cells, Treg cells actively absorbed lactic acid (LA) through monocarboxylate transporter 1 (MCT1), promoting NFAT1 translocation into the nucleus, thereby enhancing the expression of PD-1, whereas PD-1 expression by effector T cells was dampened. PD-1 blockade invigorated the PD-1-expressing Treg cells, resulting in treatment failure. We propose that LA in the highly glycolytic TME is an active checkpoint for the function of Treg cells in the TME via upregulation of PD-1 expression.
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MESH Headings
- Animals
- Biomarkers, Tumor
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/pathology
- Cell Line, Tumor
- Disease Models, Animal
- Fluorescent Antibody Technique
- Gene Expression Regulation, Neoplastic/drug effects
- Glycolysis
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Immune Checkpoint Inhibitors/therapeutic use
- Immune Checkpoint Proteins/metabolism
- Immunophenotyping
- Lactic Acid/metabolism
- Lactic Acid/pharmacology
- Lymphocyte Activation
- Lymphocyte Count
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Lymphocytes, Tumor-Infiltrating/pathology
- Mice
- Molecular Targeted Therapy
- Prognosis
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Programmed Cell Death 1 Receptor/genetics
- Programmed Cell Death 1 Receptor/metabolism
- T-Lymphocytes, Regulatory/drug effects
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Treatment Outcome
- Tumor Microenvironment/drug effects
- Tumor Microenvironment/genetics
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Affiliation(s)
- Shogo Kumagai
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Shohei Koyama
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan.
| | - Kota Itahashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Tokiyoshi Tanegashima
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Yi-Tzu Lin
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Yosuke Togashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Takahiro Kamada
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Takuma Irie
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Genki Okumura
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Hidetoshi Kono
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Daisuke Ito
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Rika Fujii
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Sho Watanabe
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Atsuo Sai
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Shota Fukuoka
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Eri Sugiyama
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Go Watanabe
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Takuya Owari
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Hitomi Nishinakamura
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Daisuke Sugiyama
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Yuka Maeda
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Akihito Kawazoe
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Hiroki Yukami
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Keigo Chida
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Yuuki Ohara
- Pathology and Clinical Laboratories, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Tatsuya Yoshida
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yuki Shinno
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yuki Takeyasu
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Masayuki Shirasawa
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Kenta Nakama
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Keiju Aokage
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Jun Suzuki
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Genichiro Ishii
- Pathology and Clinical Laboratories, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Takeshi Kuwata
- Pathology and Clinical Laboratories, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Naoya Sakamoto
- Pathology and Clinical Laboratories, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Taisuke Mori
- Department of Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Naoya Yamazaki
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Yasushi Yatabe
- Department of Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Takahiro Kinoshita
- Department of Gastric Surgery, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Toshihiko Doi
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Kohei Shitara
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Hiroyoshi Nishikawa
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan.
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6
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Nagasaki J, Inozume T, Sax N, Ariyasu R, Ishikawa M, Yamashita K, Kawazu M, Ueno T, Irie T, Tanji E, Morinaga T, Honobe A, Ohnuma T, Yoshino M, Iwata T, Kawase K, Sasaki K, Hanazawa T, Kochin V, Kawamura T, Matsue H, Hino M, Mano H, Suzuki Y, Nishikawa H, Togashi Y. PD-1 blockade therapy promotes infiltration of tumor-attacking exhausted T cell clonotypes. Cell Rep 2022; 38:110331. [PMID: 35108529 DOI: 10.1016/j.celrep.2022.110331] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [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: 02/07/2021] [Revised: 10/21/2021] [Accepted: 01/11/2022] [Indexed: 12/25/2022] Open
Abstract
PD-1 blockade exerts clinical efficacy against various types of cancer by reinvigorating T cells that directly attack tumor cells (tumor-specific T cells) in the tumor microenvironment (TME), and tumor-infiltrating lymphocytes (TILs) also comprise nonspecific bystander T cells. Here, using single-cell sequencing, we show that TILs include skewed T cell clonotypes, which are characterized by exhaustion (Tex) or nonexhaustion signatures (Tnon-ex). Among skewed clonotypes, those in the Tex, but not those in the Tnon-ex, cluster respond to autologous tumor cell lines. After PD-1 blockade, non-preexisting tumor-specific clonotypes in the Tex cluster appear in the TME. Tumor-draining lymph nodes (TDLNs) without metastasis harbor a considerable number of such clonotypes, whereas these clonotypes are rarely detected in peripheral blood. We propose that tumor-infiltrating skewed T cell clonotypes with an exhausted phenotype directly attack tumor cells and that PD-1 blockade can promote infiltration of such Tex clonotypes, mainly from TDLNs.
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Affiliation(s)
- Joji Nagasaki
- Chiba Cancer Center, Research Institute, 666-2 Nitona-cho, Chuo-ku, Chiba 260-8717, Japan; Division of Cancer Immunology, National Cancer Center, Research Institute, Exploratory Oncology Research and Clinical Trial Center (EPOC), 6-5-1 Kashiwanoha, Tokyo 104-0045, Kashiwa 277-8577, Japan; Department of Hematology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Takashi Inozume
- Chiba Cancer Center, Research Institute, 666-2 Nitona-cho, Chuo-ku, Chiba 260-8717, Japan; Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan; Department of Dermatology, University of Yamanashi, Chuo, Japan
| | - Nicolas Sax
- KOTAI Biotechnologies, Inc., Osaka 565-0871, Japan
| | - Ryo Ariyasu
- Division of Cancer Immunology, National Cancer Center, Research Institute, Exploratory Oncology Research and Clinical Trial Center (EPOC), 6-5-1 Kashiwanoha, Tokyo 104-0045, Kashiwa 277-8577, Japan
| | | | | | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center, Research Institute, Tokyo 104-0045, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center, Research Institute, Tokyo 104-0045, Japan
| | - Takuma Irie
- Division of Cancer Immunology, National Cancer Center, Research Institute, Exploratory Oncology Research and Clinical Trial Center (EPOC), 6-5-1 Kashiwanoha, Tokyo 104-0045, Kashiwa 277-8577, Japan
| | - Etsuko Tanji
- Chiba Cancer Center, Research Institute, 666-2 Nitona-cho, Chuo-ku, Chiba 260-8717, Japan
| | - Takao Morinaga
- Chiba Cancer Center, Research Institute, 666-2 Nitona-cho, Chuo-ku, Chiba 260-8717, Japan
| | - Akiko Honobe
- Department of Dermatology, University of Yamanashi, Chuo, Japan
| | - Takehiro Ohnuma
- Department of Dermatology, University of Yamanashi, Chuo, Japan
| | - Mitsuru Yoshino
- Department of Thoracic Surgery, Chiba Cancer Center, Chiba 260-8717, Japan
| | - Takekazu Iwata
- Department of Thoracic Surgery, Chiba Cancer Center, Chiba 260-8717, Japan
| | - Katsushige Kawase
- Chiba Cancer Center, Research Institute, 666-2 Nitona-cho, Chuo-ku, Chiba 260-8717, Japan; Department of Head and Neck Surgery, Chiba Cancer Center, Chiba 260-8717, Japan; Department of Otolaryngology, Head and Neck Surgery, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Keita Sasaki
- Department of Head and Neck Surgery, Chiba Cancer Center, Chiba 260-8717, Japan
| | - Toyoyuki Hanazawa
- Department of Otolaryngology, Head and Neck Surgery, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Vitaly Kochin
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | | | - Hiroyuki Matsue
- Department of Dermatology, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Masayuki Hino
- Department of Hematology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center, Research Institute, Tokyo 104-0045, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan
| | - Hiroyoshi Nishikawa
- Division of Cancer Immunology, National Cancer Center, Research Institute, Exploratory Oncology Research and Clinical Trial Center (EPOC), 6-5-1 Kashiwanoha, Tokyo 104-0045, Kashiwa 277-8577, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan.
| | - Yosuke Togashi
- Chiba Cancer Center, Research Institute, 666-2 Nitona-cho, Chuo-ku, Chiba 260-8717, Japan; Division of Cancer Immunology, National Cancer Center, Research Institute, Exploratory Oncology Research and Clinical Trial Center (EPOC), 6-5-1 Kashiwanoha, Tokyo 104-0045, Kashiwa 277-8577, Japan; Department of Tumor Microenvironment, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-0932, Japan.
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7
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Maeda Y, Wada H, Sugiyama D, Saito T, Irie T, Itahashi K, Minoura K, Suzuki S, Kojima T, Kakimi K, Nakajima J, Funakoshi T, Iida S, Oka M, Shimamura T, Doi T, Doki Y, Nakayama E, Ueda R, Nishikawa H. Depletion of central memory CD8 + T cells might impede the antitumor therapeutic effect of Mogamulizumab. Nat Commun 2021; 12:7280. [PMID: 34907192 PMCID: PMC8671535 DOI: 10.1038/s41467-021-27574-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/29/2021] [Indexed: 11/09/2022] Open
Abstract
Regulatory T (Treg) cells are important negative regulators of immune homeostasis, but in cancers they tone down the anti-tumor immune response. They are distinguished by high expression levels of the chemokine receptor CCR4, hence their targeting by the anti-CCR4 monoclonal antibody mogamulizumab holds therapeutic promise. Here we show that despite a significant reduction in peripheral effector Treg cells, clinical responses are minimal in a cohort of patients with advanced CCR4-negative solid cancer in a phase Ib study (NCT01929486). Comprehensive immune-monitoring reveals that the abundance of CCR4-expressing central memory CD8+ T cells that are known to play roles in the antitumor immune response is reduced. In long survivors, characterised by lower CCR4 expression in their central memory CD8+ T cells possessed and/or NK cells with an exhausted phenotype, cell numbers are eventually maintained. Our study thus shows that mogamulizumab doses that are currently administered to patients in clinical studies may not differentiate between targeting effector Treg cells and central memory CD8+ T cells, and dosage refinement might be necessary to avoid depletion of effector components during immune therapy.
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MESH Headings
- Aged
- Aged, 80 and over
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antineoplastic Agents/therapeutic use
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/metabolism
- Dose-Response Relationship, Drug
- Female
- Humans
- Immunotherapy
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/metabolism
- Male
- Memory T Cells/drug effects
- Middle Aged
- Neoplasms/drug therapy
- Neoplasms/immunology
- Receptors, CCR4/antagonists & inhibitors
- Receptors, CCR4/metabolism
- T-Lymphocytes, Regulatory/drug effects
- T-Lymphocytes, Regulatory/metabolism
- Treatment Outcome
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Grants
- Research Activity Start-up grant no. 15H06878, for Young Scientists (B) grant no. 17K15738 from the Ministry of Education, Culture, Sports, Science and Technology of Japan.the Projects for Cancer Research by Therapeutic Evolution [P-CREATE, no. 17cm0106322h0002]
- Scientific Research (B) grant no. 19H03729 from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
- the Development of Technology for Patient Stratification Biomarker Discovery grant [no.19ae0101074s0401] from the Japan Agency for Medical Research and Development (AMED)
- Grants-in-Aid for Scientific Research (S) grant no. 17H06162, for Challenging Exploratory Research grant no. 16K15551, from the Ministry of Education, Culture, Sports, Science and Technology of Japan; the Projects for Cancer Research by Therapeutic Evolution [P-CREATE, no. 16cm0106301h0001, the Development of Technology for Patient Stratification Biomarker Discovery grant [no.19ae0101074s0401] from the Japan Agency for Medical Research and Development (AMED), the National Cancer Center Research and Development Fund [no. 28-A-7 and 31-A-7]
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Affiliation(s)
- Yuka Maeda
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, 104-0045/Chiba, 277-8577, Japan
| | - Hisashi Wada
- Department of Clinical Research in Tumor Immunology, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan.
| | - Daisuke Sugiyama
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Takuro Saito
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Takuma Irie
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, 104-0045/Chiba, 277-8577, Japan
| | - Kota Itahashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, 104-0045/Chiba, 277-8577, Japan
| | - Kodai Minoura
- Department of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Susumu Suzuki
- Department of Tumor Immunology, Aichi Medical University, Aichi, 480-1195, Japan
| | - Takashi Kojima
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, 277-8577, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, 113-8655, Japan
| | - Jun Nakajima
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Takeru Funakoshi
- Department of Dermatology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Shinsuke Iida
- Department of Hematology and Oncology, Nagoya City University Institute of Medical and Pharmaceutical Sciences, Nagoya, 467-8601, Japan
| | - Mikio Oka
- Department of Respiratory Medicine, Kawasaki Medical School, Okayama 701-0192, Japan
| | - Teppei Shimamura
- Department of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Toshihiko Doi
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, 277-8577, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Eiichi Nakayama
- Faculty of Health and Welfare, Kawasaki University of Medical Welfare, Okayama, 701-0192, Japan
| | - Ryuzo Ueda
- Department of Tumor Immunology, Aichi Medical University, Aichi, 480-1195, Japan.
| | - Hiroyoshi Nishikawa
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, 104-0045/Chiba, 277-8577, Japan.
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.
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8
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Takeuchi Y, Tanegashima T, Sato E, Irie T, Sai A, Itahashi K, Kumagai S, Tada Y, Togashi Y, Koyama S, Akbay EA, Karasaki T, Kataoka K, Funaki S, Shintani Y, Nagatomo I, Kida H, Ishii G, Miyoshi T, Aokage K, Kakimi K, Ogawa S, Okumura M, Eto M, Kumanogoh A, Tsuboi M, Nishikawa H. Highly immunogenic cancer cells require activation of the WNT pathway for immunological escape. Sci Immunol 2021; 6:eabc6424. [PMID: 34767457 DOI: 10.1126/sciimmunol.abc6424] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Yoshiko Takeuchi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan.,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Tokiyoshi Tanegashima
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan.,Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Eiichi Sato
- Department of Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Takuma Irie
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan
| | - Atsuo Sai
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan
| | - Kota Itahashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan
| | - Shogo Kumagai
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuko Tada
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan
| | - Yosuke Togashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan
| | - Shohei Koyama
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan.,Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Esra A Akbay
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas TX, USA
| | - Takahiro Karasaki
- Department of Immunotherapeutics, University of Tokyo Hospital, Tokyo, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, Research Institute, National Cancer Center, Tokyo, Japan.,Department of Pathology and Tumor Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Soichiro Funaki
- Department of General Thoracic Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yasushi Shintani
- Department of General Thoracic Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Izumi Nagatomo
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hiroshi Kida
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Genichiro Ishii
- Division of Pathology, National Cancer Center Hospital East, Chiba, Japan
| | - Tomohiro Miyoshi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba, Japan
| | - Keiju Aokage
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba, Japan
| | - Kazuhiro Kakimi
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas TX, USA
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Meinoshin Okumura
- Department of General Thoracic Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba, Japan
| | - Hiroyoshi Nishikawa
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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9
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Inamori K, Togashi Y, Fukuoka S, Akagi K, Ogasawara K, Irie T, Motooka D, Kobayashi Y, Sugiyama D, Kojima M, Shiiya N, Nakamura S, Maruyama S, Suzuki Y, Ito M, Nishikawa H. Importance of lymph node immune responses in MSI-H/dMMR colorectal cancer. JCI Insight 2021; 6:137365. [PMID: 33755600 PMCID: PMC8262295 DOI: 10.1172/jci.insight.137365] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/18/2021] [Indexed: 01/21/2023] Open
Abstract
Patients with colorectal cancers (CRCs) generally exhibit improved survival through intensive lymph node (LN) dissection. However, recent progress in cancer immunotherapy revisits the potential importance of regional LNs, where T cells are primed to attack tumor cells. To elucidate the role of regional LN, we investigated the immunological status of nonmetastatic regional LN lymphocytes (LNLs) in comparison with those of the tumor microenvironment (tumor-infiltrating lymphocytes; TILs) using flow cytometry and next-generation sequencing. LNLs comprised an intermediate level of the effector T cell population between peripheral blood lymphocytes (PBLs) and TILs. Significant overlap of the T cell receptor (TCR) repertoire was observed in microsatellite instability–high/mismatch repair–deficient (MSI-H/dMMR) CRCs with high tumor mutation burden (TMB), although limited TCRs were shared between nonmetastatic LNs and primary tumors in microsatellite stable/MMR proficient (MSS/pMMR) CRC patients with low TMB. In line with the overlap of the TCR repertoire, an excessive LN dissection did not provide a positive impact on long-term prognosis in our MSI-H/dMMR CRC cohort (n = 130). We propose that regional LNs play an important role in antitumor immunity, particularly in MSI-H/dMMR CRCs with high TMB, requiring care to be taken regarding excessive nonmetastatic LN dissection in MSI-H/dMMR CRC patients.
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Affiliation(s)
- Koji Inamori
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan.,Department of Colorectal Surgery, National Cancer Center Hospital East (NCCHE), Chiba, Japan.,Surgery 1, Divisions of cardiovascular, Thoracic, General Endoscopic and Breast Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yosuke Togashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan
| | - Shota Fukuoka
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center (SCC), Saitama, Japan
| | - Kouetsu Ogasawara
- Department of Immunobiology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Takuma Irie
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yoichi Kobayashi
- Department of Immunology and.,Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | | | - Norihiko Shiiya
- Surgery 1, Divisions of cardiovascular, Thoracic, General Endoscopic and Breast Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shoichi Maruyama
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Masaaki Ito
- Department of Colorectal Surgery, National Cancer Center Hospital East (NCCHE), Chiba, Japan
| | - Hiroyoshi Nishikawa
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan.,Department of Immunology and
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10
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Kumagai S, Togashi Y, Kamada T, Sugiyama E, Nishinakamura H, Takeuchi Y, Vitaly K, Itahashi K, Maeda Y, Matsui S, Shibahara T, Yamashita Y, Irie T, Tsuge A, Fukuoka S, Kawazoe A, Udagawa H, Kirita K, Aokage K, Ishii G, Kuwata T, Nakama K, Kawazu M, Ueno T, Yamazaki N, Goto K, Tsuboi M, Mano H, Doi T, Shitara K, Nishikawa H. The PD-1 expression balance between effector and regulatory T cells predicts the clinical efficacy of PD-1 blockade therapies. Nat Immunol 2020. [PMID: 32868929 DOI: 10.1038/s41590-020-0769-3.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Immune checkpoint blockade has provided a paradigm shift in cancer therapy, but the success of this approach is very variable; therefore, biomarkers predictive of clinical efficacy are urgently required. Here, we show that the frequency of PD-1+CD8+ T cells relative to that of PD-1+ regulatory T (Treg) cells in the tumor microenvironment can predict the clinical efficacy of programmed cell death protein 1 (PD-1) blockade therapies and is superior to other predictors, including PD ligand 1 (PD-L1) expression or tumor mutational burden. PD-1 expression by CD8+ T cells and Treg cells negatively impacts effector and immunosuppressive functions, respectively. PD-1 blockade induces both recovery of dysfunctional PD-1+CD8+ T cells and enhanced PD-1+ Treg cell-mediated immunosuppression. A profound reactivation of effector PD-1+CD8+ T cells rather than PD-1+ Treg cells by PD-1 blockade is necessary for tumor regression. These findings provide a promising predictive biomarker for PD-1 blockade therapies.
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Affiliation(s)
- Shogo Kumagai
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yosuke Togashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan
| | - Takahiro Kamada
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Eri Sugiyama
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hitomi Nishinakamura
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan
| | - Yoshiko Takeuchi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan
| | - Kochin Vitaly
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kota Itahashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan
| | - Yuka Maeda
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan
| | - Shigeyuki Matsui
- Department of Biostatics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | | | - Takuma Irie
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan
| | - Ayaka Tsuge
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shota Fukuoka
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan
| | - Akihito Kawazoe
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Hibiki Udagawa
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Keisuke Kirita
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Keiju Aokage
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba, Japan
| | - Genichiro Ishii
- Pathology and Clinical Laboratories, National Cancer Center Hospital East, Chiba, Japan
| | - Takeshi Kuwata
- Pathology and Clinical Laboratories, National Cancer Center Hospital East, Chiba, Japan
| | - Kenta Nakama
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoya Yamazaki
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshihiko Doi
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Kohei Shitara
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba, Japan
| | - Hiroyoshi Nishikawa
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo, Chiba, Japan. .,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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11
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Morota T, Sugita S, Cho Y, Kanamaru M, Tatsumi E, Sakatani N, Honda R, Hirata N, Kikuchi H, Yamada M, Yokota Y, Kameda S, Matsuoka M, Sawada H, Honda C, Kouyama T, Ogawa K, Suzuki H, Yoshioka K, Hayakawa M, Hirata N, Hirabayashi M, Miyamoto H, Michikami T, Hiroi T, Hemmi R, Barnouin OS, Ernst CM, Kitazato K, Nakamura T, Riu L, Senshu H, Kobayashi H, Sasaki S, Komatsu G, Tanabe N, Fujii Y, Irie T, Suemitsu M, Takaki N, Sugimoto C, Yumoto K, Ishida M, Kato H, Moroi K, Domingue D, Michel P, Pilorget C, Iwata T, Abe M, Ohtake M, Nakauchi Y, Tsumura K, Yabuta H, Ishihara Y, Noguchi R, Matsumoto K, Miura A, Namiki N, Tachibana S, Arakawa M, Ikeda H, Wada K, Mizuno T, Hirose C, Hosoda S, Mori O, Shimada T, Soldini S, Tsukizaki R, Yano H, Ozaki M, Takeuchi H, Yamamoto Y, Okada T, Shimaki Y, Shirai K, Iijima Y, Noda H, Kikuchi S, Yamaguchi T, Ogawa N, Ono G, Mimasu Y, Yoshikawa K, Takahashi T, Takei Y, Fujii A, Nakazawa S, Terui F, Tanaka S, Yoshikawa M, Saiki T, Watanabe S, Tsuda Y. Sample collection from asteroid (162173) Ryugu by Hayabusa2: Implications for surface evolution. Science 2020; 368:654-659. [DOI: 10.1126/science.aaz6306] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/02/2020] [Indexed: 11/02/2022]
Affiliation(s)
- T. Morota
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
- Departments of Earth and Environmental Sciences and Physics, Nagoya University, Nagoya 464-8601, Japan
| | - S. Sugita
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - Y. Cho
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - M. Kanamaru
- Department of Earth and Space Science, Osaka University, Toyonaka 560-0043, Japan
| | - E. Tatsumi
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
- Departamento de Astrofísica, Universidad de La Laguna, 38206 La Laguna, Tenerife, Spain
- Instituto de Astrofísica de Canarias, 38205 La Laguna, Tenerife, Spain
| | - N. Sakatani
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - R. Honda
- Department of Information Science, Kochi University, Kochi 780-8520, Japan
| | - N. Hirata
- Department of Planetology, Kobe University, Kobe 657-8501, Japan
| | - H. Kikuchi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - M. Yamada
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - Y. Yokota
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Department of Information Science, Kochi University, Kochi 780-8520, Japan
| | - S. Kameda
- Department of Physics, Rikkyo University, Tokyo 171-8501, Japan
| | - M. Matsuoka
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - H. Sawada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - C. Honda
- School of Computer Science and Engineering, University of Aizu, Aizu-Wakamatsu 965-8580, Japan
| | - T. Kouyama
- National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064 Japan
| | - K. Ogawa
- Department of Planetology, Kobe University, Kobe 657-8501, Japan
- JAXA Space Exploration Center, Japan Aerospace Exploration Agency, Sagamihara 252-5210, Japan
| | - H. Suzuki
- Department of Physics, Meiji University, Kawasaki 214-8571, Japan
| | - K. Yoshioka
- Department of Complexity Science and Engineering, The University of Tokyo, Kashiwa 277-8561, Japan
| | - M. Hayakawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - N. Hirata
- School of Computer Science and Engineering, University of Aizu, Aizu-Wakamatsu 965-8580, Japan
| | - M. Hirabayashi
- Department of Aerospace Engineering, Auburn University, Auburn, AL 36849, USA
| | - H. Miyamoto
- Department of Systems Innovation, The University of Tokyo, Tokyo 113-8656, Japan
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - T. Michikami
- Faculty of Engineering, Kindai University, Higashi-Hiroshima 739-2116, Japan
| | - T. Hiroi
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI 02912, USA
| | - R. Hemmi
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan
| | - O. S. Barnouin
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - C. M. Ernst
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - K. Kitazato
- School of Computer Science and Engineering, University of Aizu, Aizu-Wakamatsu 965-8580, Japan
| | - T. Nakamura
- Department of Earth Science, Tohoku University, Sendai 980-8578, Japan
| | - L. Riu
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - H. Senshu
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - H. Kobayashi
- Departments of Earth and Environmental Sciences and Physics, Nagoya University, Nagoya 464-8601, Japan
| | - S. Sasaki
- Department of Earth and Space Science, Osaka University, Toyonaka 560-0043, Japan
| | - G. Komatsu
- International Research School of Planetary Sciences, Università d’Annunzio, 65127 Pescara, Italy
| | - N. Tanabe
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Y. Fujii
- Department of Information Science, Kochi University, Kochi 780-8520, Japan
| | - T. Irie
- Departments of Earth and Environmental Sciences and Physics, Nagoya University, Nagoya 464-8601, Japan
| | - M. Suemitsu
- Departments of Earth and Environmental Sciences and Physics, Nagoya University, Nagoya 464-8601, Japan
| | - N. Takaki
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - C. Sugimoto
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K. Yumoto
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - M. Ishida
- Department of Physics, Rikkyo University, Tokyo 171-8501, Japan
| | - H. Kato
- Department of Physics, Rikkyo University, Tokyo 171-8501, Japan
| | - K. Moroi
- Department of Physics, Rikkyo University, Tokyo 171-8501, Japan
| | - D. Domingue
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - P. Michel
- Université Côte d’Azur, Observatoire de la Côte d’Azur, Centre National de le Recherche Scientifique, Laboratoire Lagrange, 06304 Nice, France
| | - C. Pilorget
- Institut d’Astrophysique Spatiale, Université Paris-Sud, 91405 Orsay, France
| | - T. Iwata
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
| | - M. Abe
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
| | - M. Ohtake
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- School of Computer Science and Engineering, University of Aizu, Aizu-Wakamatsu 965-8580, Japan
| | - Y. Nakauchi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K. Tsumura
- Department of Natural Science, Faculty of Science and Engineering, Tokyo City University, Tokyo 158-8557, Japan
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8578, Japan
| | - H. Yabuta
- Department of Earth and Planetary Systems Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Y. Ishihara
- National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - R. Noguchi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K. Matsumoto
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
- National Astronomical Observatory of Japan, Mitaka 181-8588, Japan
| | - A. Miura
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
| | - N. Namiki
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
- National Astronomical Observatory of Japan, Mitaka 181-8588, Japan
| | - S. Tachibana
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - M. Arakawa
- Department of Planetology, Kobe University, Kobe 657-8501, Japan
| | - H. Ikeda
- Research and Development Directorate, JAXA, Sagamihara 252-5210, Japan
| | - K. Wada
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - T. Mizuno
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
| | - C. Hirose
- Research and Development Directorate, JAXA, Sagamihara 252-5210, Japan
| | - S. Hosoda
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - O. Mori
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - T. Shimada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - S. Soldini
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Department of Mechanical, Materials and Aerospace Engineering, University of Liverpool, Liverpool L69 3BX, UK
| | - R. Tsukizaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - H. Yano
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
| | - M. Ozaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
| | - H. Takeuchi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
| | - Y. Yamamoto
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
| | - T. Okada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
| | - Y. Shimaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K. Shirai
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - Y. Iijima
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - H. Noda
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
- National Astronomical Observatory of Japan, Mitaka 181-8588, Japan
| | - S. Kikuchi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - T. Yamaguchi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - N. Ogawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - G. Ono
- Research and Development Directorate, JAXA, Sagamihara 252-5210, Japan
| | - Y. Mimasu
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K. Yoshikawa
- Research and Development Directorate, JAXA, Sagamihara 252-5210, Japan
| | - T. Takahashi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - Y. Takei
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Research and Development Directorate, JAXA, Sagamihara 252-5210, Japan
| | - A. Fujii
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - S. Nakazawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - F. Terui
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - S. Tanaka
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
| | - M. Yoshikawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
| | - T. Saiki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - S. Watanabe
- Departments of Earth and Environmental Sciences and Physics, Nagoya University, Nagoya 464-8601, Japan
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - Y. Tsuda
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
- Departments of Space and Astronautical Science and Astronomical Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama 240-0193, Japan
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Kirita K, Sugiyama E, Togashi Y, Udagawa H, Irie T, Iida S, Nakamoto M, Nomura S, Ikeda T, Zenke Y, Matsumoto S, Yoh K, Niho S, Sato A, Nishikawa H, Goto K. Clinical utility of precision immunoprofiling and monitoring of the tumour microenvironment using flow cytometry and CyTOF in patients with advanced NSCLC treated with atezolizumab: Results from a phase II study for biomarker analysis (EPOC1702). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz253.068] [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: 11/12/2022] Open
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Irie T, Sugawara Y, Narita Y, Ibuki S, Shimata K, Yamamoto H, Hibi T. Single-center Experience of Living-donor Liver Transplantation in Patients Receiving Maintenance Renal Replacement Therapy. Transplant Proc 2019; 51:1520-1521. [PMID: 31155186 DOI: 10.1016/j.transproceed.2019.01.121] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/28/2019] [Indexed: 11/18/2022]
Abstract
BACKGROUND For most patients with liver failure receiving maintenance renal replacement therapy (RRT), treatment with living-donor liver transplantation (LDLT) alone is indicated in Japan. MATERIAL AND METHODS We retrospectively reviewed patients who underwent LDLT while receiving RRT in our hospital. RESULTS Three of the 5 patients who underwent LDLT while on RRT died during the first year after transplantation. CONCLUSIONS The indications for liver transplantation in patients on RRT require careful examination.
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Affiliation(s)
- T Irie
- Department of Pediatric Surgery and Transplantation, Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan
| | - Y Sugawara
- Department of Pediatric Surgery and Transplantation, Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan.
| | - Y Narita
- Department of Pediatric Surgery and Transplantation, Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan
| | - S Ibuki
- Department of Pediatric Surgery and Transplantation, Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan
| | - K Shimata
- Department of Pediatric Surgery and Transplantation, Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan
| | - H Yamamoto
- Department of Pediatric Surgery and Transplantation, Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan
| | - T Hibi
- Department of Pediatric Surgery and Transplantation, Kumamoto University Graduate School of Medical Sciences, Kumamoto, Japan
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Narita Y, Sugawara Y, Ibuki S, Irie T, Shimata K, Yamamoto H, Hibi T. Portal Vein Stent Placement in Living-donor Liver Transplantation: A Single-center Experience. Transplant Proc 2019; 51:1522-1524. [DOI: 10.1016/j.transproceed.2019.01.123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/28/2019] [Indexed: 01/02/2023]
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Tanegashima T, Togashi Y, Azuma K, Kawahara A, Ideguchi K, Sugiyama D, Kinoshita F, Akiba J, Kashiwagi E, Takeuchi A, Irie T, Tatsugami K, Hoshino T, Eto M, Nishikawa H. Immune Suppression by PD-L2 against Spontaneous and Treatment-Related Antitumor Immunity. Clin Cancer Res 2019; 25:4808-4819. [DOI: 10.1158/1078-0432.ccr-18-3991] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/08/2019] [Accepted: 05/07/2019] [Indexed: 11/16/2022]
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Nakajima T, Ono Y, Kaneko Y, Saito A, Imai M, Iizuka T, Irie T, Funada R, Takama N, Kasama S, Nakamura K, Niwamae N, Tange S, Kurabayashi M. P799The clinical and genetic predispositions to ventricular tachyarrhythmias associated with vasospastic angina. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx501.p799] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Liu Y, Irie T, Yada T, Suzuki Y. A new computational method to predict transcriptional activity of a DNA sequence from diverse datasets of massively parallel reporter assays. Nucleic Acids Res 2017; 45:e124. [PMID: 28531296 PMCID: PMC5737609 DOI: 10.1093/nar/gkx396] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 04/17/2017] [Accepted: 05/18/2017] [Indexed: 11/15/2022] Open
Abstract
In recent years, the dramatic increase in the number of applications for massively parallel reporter assay (MPRA) technology has produced a large body of data for various purposes. However, a computational model that can be applied to decipher regulatory codes for diverse MPRAs does not exist yet. Here, we propose a new computational method to predict the transcriptional activity of MPRAs, as well as luciferase reporter assays, based on the TRANScription FACtor database. We employed regression trees and multivariate adaptive regression splines to obtain these predictions and considered a feature redundancy-dependent formula for conventional regression trees to enable adaptation to diverse data. The developed method was applicable to various MPRAs despite the use of different types of transfected cells, sequence lengths, construct numbers and sequence types. We demonstrate that this method can predict the transcriptional activity of promoters in HEK293 cells through predictive functions that were estimated by independent assays in eight tumor cell lines. The prediction was generally good (Pearson's r = 0.68) which suggested that common active transcription factor binding sites across different cell types make greater contributions to transcriptional activity and that known promoter activity could confer transcriptional activity of unknown promoters in some instances, regardless of cell type.
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Affiliation(s)
- Ying Liu
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
| | - Takuma Irie
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
| | - Tetsushi Yada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
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Watahiki J, Yamaguchi T, Irie T, Nakano H, Maki K, Tachikawa T. Gene Expression Profiling of Mouse Condylar Cartilage during Mastication by Means of Laser Microdissection and cDNA Array. J Dent Res 2016; 83:245-9. [PMID: 14981128 DOI: 10.1177/154405910408300312] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 11/16/2022] Open
Abstract
Little is known about the mechanisms of mandibular condylar growth. In this study, gene expression in the mandibular condylar cartilage of young post-natal mice was monitored by means of a cDNA microarray, real-time PCR, and laser microdissection before and after the initiation of mastication (newborn, 7 days, 21 days, initiation of mastication, and 35 days). Insulin-like growth factor-1 (IGF-I), transforming-growth-factor-beta-2 (TGFbeta2), and aggrecan mRNAs were clearly expressed at 21 days, while the expression of osteopontin mRNAs was most clear at 35 days. Parathyroid-hormone-related protein (PTHrP), Indian-hedgehog (Ihh), and insulin-like growth factor-2 (IGF-2) mRNAs were clearly expressed during lactation (newborn and 7 days). Heat-shock-protein 84 (HSP-84) and heat-shock-protein 86 (HSP-86) were clearly expressed at 35 days. These results revealed that gene expression changed during mandibular condylar cartilage growth, and that, interestingly, these changes coincided with the initiation of mastication.
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Affiliation(s)
- J Watahiki
- Department of Orthodontics and Department of Oral Pathology, School of Dentistry, Showa University, 2-1-2 Kitasenzoku, Ohta-ku, Tokyo 145-8515, Japan.
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Irie T, Takeshita K, Makita K, Yamauchi T, Kusano S. A One-Stage Method for Obtaining CT during Arterial Portography and Hepatic Arteriography. Acta Radiol 2016. [DOI: 10.1177/028418519403500206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We describe a new technique for performing CT during arterial portography (CTAP) and during hepatic arteriography (CTHA) in a one-stage procedure, using a coaxial balloon catheter system and slip-ring CT equipment. This technique was employed in 10 patients with liver neoplasms. Both CTAP and CTHA images were obtained in all patients.
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Abstract
A technique for the prediction of the time to peak hepatic enhancement to optimize contrast-enhanced spiral CT has been developed. The procedures are (a) to inject a small amount of contrast medium rapidly via the antecubital vein and measure aortic transit time (ATT) of the bolus by single slice dynamic CT; (b) to inject contrast medium at a high rate, expecting peak hepatic enhancement to occur at ATT plus 8 seconds after the end of injection; (c) to perform spiral scanning of the liver using thin collimation and caudo-cranial table movement beginning at ATT after the end of contrast medium injection.
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Abstract
We have developed an embolizing material consisting of Y-shaped silicone particles for partial splenic embolization. Wide spaces for blood flow are left around the particles when these are lodged in arterial branches. We embolized one kidney in each of 3 dogs with the particles and observed a slowly induced occlusion of renal arterial branches during one month. The particles were also used for partial splenic embolization in 14 patients. The average portion of infarcted spleen tissue 7 days after embolization was 51% calculated from CT images. In 6 patients who had CT both 2 and 7 days after embolization, the average rate of splenic infarction increased from 29% at 2 days to 60% at 7 days. Our patients required analgesics for only 2.3 days on average. The Y-shaped silicone particles by slowly occluding splenic arterial branches produce ischemia in a gradual fashion which may minimize the pain after embolization.
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Saito M, Masutani M, Mabe K, Izumiyama K, Mori A, Irie T, Tanaka M, Morioka M, Tanino M. Regression of gastric de novo diffuse large B-cell lymphoma following Helicobacter pylori eradication: a case report. Acta Gastroenterol Belg 2016; 79:367-369. [PMID: 27821034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report a case of primary gastric diffuse large B-cell lymphoma (DLBCL), de novo DLBCL without the features of mucosa-associated lymphoid tissue (MALT) lymphoma, which regressed after Helicobacter pylori (HP) eradication. A 27-year-old Japanese female with epigastralgia was revealed to have ulcerated lesions in the angle and antral regions on gastroscopy. Biopsy specimen was consistent with a diagnosis of DLBCL without MALT lymphoma component, indicating de novo development. Her clinical staging on the Lugano system was Stage I. HP was positive on a rapid urease test, and she received HP eradication therapy twice, because the first therapy was not successful. On gastroscopy performed 1 month after the second HP eradication therapy, no ulcerated lesion was noted, and the lymphoma cells had regressed histopathologically. (Acta gastro-enterol. belg., 2016, 79, 367-369A).
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Shimada H, Hirano S, Sinotoh H, Ota T, Tanaka N, Sato K, Yamada M, Fukushi K, Irie T, Zhang MR, Higuchi M, Kuwabara S, Suhara T. Dementia with Lewy bodies can be well-differentiated from Alzheimer's disease by measurement of brain acetylcholinesterase activity-a [11C]MP4A PET study. Int J Geriatr Psychiatry 2015; 30:1105-13. [PMID: 26280153 DOI: 10.1002/gps.4338] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 07/07/2015] [Accepted: 07/08/2015] [Indexed: 11/12/2022]
Abstract
OBJECTIVE To investigate the diagnostic performance of brain acetylcholinesterase (AChE) activity measurement using N-[(11) C]-methyl-4-piperidyl acetate (MP4A) and PET in patients with dementia with Lewy bodies (DLB) and Alzheimer's disease (AD). METHODS Participants were 14 DLB patients, 25 AD patients and 18 age-matched healthy controls (HC). All subjects underwent PET scans and MP4A to measure regional brain AChE activity. We performed anatomical standardization of each brain image, and k3 values, an index of AChE activity, in each voxel were estimated by nonlinear least squares analysis. Volumes of interest (VOIs) were identified on parametric k3 images in frontal, temporal, parietal and occipital cortices, and in anterior and posterior cingulate gyri (ACG and PCG). In each VOI, the differential diagnostic performance between AD and DLB of k3 values was assessed by area under the curve (AUC) of the receiver-operating characteristic. Voxel-based statistical analyses were also performed. RESULTS Mean cortical AChE activities in AD patients (-8.2% compared with normal mean) and DLB patients (-27.8%) were lower than HCs (p < 0.05, p < 0.001, respectively). There was a significant difference in mean cortical AChE activities between AD and DLB patients (p < 0.001). All regional brain AChE activities of defined VOIs except ACG were able to well discriminate DLB from AD, and notably performance was the most significant in PCG (AUC = 0.989, 95% CI: 0.965-1.000). CONCLUSIONS Brain cholinergic deficit is consistently prominent in DLB compared with AD. PET measurement of brain AChE activity may be useful for the differential diagnosis between DLB and AD.
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Affiliation(s)
- H Shimada
- Molecular Neuroimaging Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan
| | - S Hirano
- Molecular Neuroimaging Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan.,Department of Neurology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba, Japan
| | - H Sinotoh
- Molecular Neuroimaging Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan.,Neurology Chiba Clinic, Chiba-shi, Chiba, Japan
| | - T Ota
- Molecular Neuroimaging Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan.,Department of Psychiatry, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - N Tanaka
- Molecular Neuroimaging Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan
| | - K Sato
- Molecular Neuroimaging Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan.,Department of Psychiatry, Teikyo University Chiba Medical Center, Ichihara-shi, Chiba, Japan
| | - M Yamada
- Molecular Neuroimaging Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan.,Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, Japan
| | - K Fukushi
- Molecular Probe Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan
| | - T Irie
- Molecular Probe Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan
| | - M R Zhang
- Molecular Probe Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan
| | - M Higuchi
- Molecular Neuroimaging Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan
| | - S Kuwabara
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba, Japan
| | - T Suhara
- Molecular Neuroimaging Program, Molecular Imaging Center, National Institute of Radiological Sciences, Chiba-shi, Chiba, Japan
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Sakiyama Y, Shibata S, Sanayama H, Ono S, Maekawa M, Matsuo M, Irie T, Eto Y. Intrathecal 2-Hydroxypropyl-Beta-Cyclodextrin (HPBCD) therapy in adult-onset Niemann-Pick Disease Type C (NPC). J Neurol Sci 2015. [DOI: 10.1016/j.jns.2015.08.719] [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: 10/22/2022]
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25
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Maekawa S, Imamachi N, Irie T, Tani H, Matsumoto K, Mizutani R, Imamura K, Kakeda M, Yada T, Sugano S, Suzuki Y, Akimitsu N. Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance. BMC Genomics 2015; 16:154. [PMID: 25879614 PMCID: PMC4359779 DOI: 10.1186/s12864-015-1358-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [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: 05/19/2014] [Accepted: 02/19/2015] [Indexed: 12/28/2022] Open
Abstract
Background Histone epigenome data determined by chromatin immunoprecipitation sequencing (ChIP-seq) is used in identifying transcript regions and estimating expression levels. However, this estimation does not always correlate with eventual RNA expression levels measured by RNA sequencing (RNA-seq). Part of the inconsistency may arise from the variance in RNA stability, where the transcripts that are more or less abundant than predicted RNA expression from histone epigenome data are inferred to be more or less stable. However, there is little systematic analysis to validate this assumption. Here, we used stability data of whole transcriptome measured by 5′-bromouridine immunoprecipitation chase sequencing (BRIC-seq), which enabled us to determine the half-lives of whole transcripts including lincRNAs, and we integrated BRIC-seq with ChIP-seq to achieve better estimation of the eventual transcript levels and to understand the importance of post-transcriptional regulation that determine the eventual transcript levels. Results We identified discrepancies between the RNA abundance estimated by ChIP-seq and measured RNA expression from RNA-seq; for number of genes and estimated that the expression level of 865 genes was controlled at the level of RNA stability in HeLa cells. ENCODE data analysis supported the idea that RNA stability control aids to determine transcript levels in multiple cell types. We identified UPF1, EXOSC5 and STAU1, well-studied RNA degradation factors, as controlling factors for 8% of cases. Computational simulations reasonably explained the changes of eventual mRNA levels attributable to the changes in the rates of mRNA half-lives. In addition, we propose a feedback circuit that includes the regulated degradation of mRNAs encoding transcription factors to maintain the steady state level of RNA abundance. Intriguingly, these regulatory mechanisms were distinct between mRNAs and lincRNAs. Conclusions Integrative analysis of ChIP-seq, RNA-seq and our BRIC-seq showed that transcriptional regulation and RNA degradation are independently regulated. In addition, RNA stability is an important determinant of eventual transcript levels. RNA binding proteins, such as UPF1, STAU1 and EXOSC5 may play active roles in such controls. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1358-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sho Maekawa
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
| | - Naoto Imamachi
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Takuma Irie
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
| | - Hidenori Tani
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| | - Kyoko Matsumoto
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
| | - Rena Mizutani
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Katsutoshi Imamura
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Miho Kakeda
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Tetsushi Yada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan.
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan. .,Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
| | - Nobuyoshi Akimitsu
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
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26
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Ichikawa Y, Watahiki J, Nampo T, Nose K, Yamamoto G, Irie T, Mishima K, Maki K. Differences in the developmental origins of the periosteum may influence bone healing. J Periodontal Res 2014; 50:468-78. [PMID: 25225160 DOI: 10.1111/jre.12229] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND OBJECTIVE The jaw bone, unlike most other bones, is derived from neural crest stem cells, so we hypothesized that it may have different characteristics to bones from other parts of the body, especially in the nature of its periosteum. The periosteum exhibits osteogenic potential and has received considerable attention as a grafting material for the repair of bone and joint defects. MATERIAL AND METHODS Gene expression profiles of jaw bone and periosteum were evaluated by DNA microarray and real-time polymerase chain reaction. Furthermore, we perforated an area 2 mm in diameter on mouse frontal and parietal bones. Bone regeneration of these calvarial defects was evaluated using microcomputed tomography and histological analysis. RESULTS The DNA microarray data revealed close homology between the gene expression profiles within the ilium and femur. The gene expression of Wnt-1, SOX10, nestin, and musashi-1 were significantly higher in the jaw bone than in other locations. Microcomputed tomography and histological analysis revealed that the jaw bone had superior bone regenerative abilities than other bones. CONCLUSION Jaw bone periosteum exhibits a unique gene expression profile that is associated with neural crest cells and has a positive influence on bone regeneration when used as a graft material to repair bone defects. A full investigation of the biological and mechanical properties of jaw bone as an alternative graft material for jaw reconstructive surgery is recommended.
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Affiliation(s)
- Y Ichikawa
- Department of Orthodontics, Showa University School of Dentistry, Ohta-ku, Tokyo, Japan
| | - J Watahiki
- Department of Orthodontics, Showa University School of Dentistry, Ohta-ku, Tokyo, Japan
| | - T Nampo
- Department of Orthodontics, Showa University School of Dentistry, Ohta-ku, Tokyo, Japan
| | - K Nose
- Department of Orthodontics, Showa University School of Dentistry, Ohta-ku, Tokyo, Japan
| | - G Yamamoto
- Department of Oral Pathology and Diagnosis, Showa University School of Dentistry, Shinagawa-ku, Tokyo, Japan
| | - T Irie
- Department of Oral Pathology and Diagnosis, Showa University School of Dentistry, Shinagawa-ku, Tokyo, Japan
| | - K Mishima
- Department of Oral Pathology and Diagnosis, Showa University School of Dentistry, Shinagawa-ku, Tokyo, Japan
| | - K Maki
- Department of Orthodontics, Showa University School of Dentistry, Ohta-ku, Tokyo, Japan
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Ochiai T, Shioya A, Honma H, Saitoh Y, Matsumura S, Ban D, Irie T, Kudo A, Nakamura N, Fujikawa T, Itai A, Tanaka S, Arii S, Yamaoka S, Tanabe M. Combination Treatment of IκB Kinase β Inhibitor IMD-0354 and Gemcitabine Suppresses Oncogenic Proliferation of Pancreatic Cancer Cells. J Surg Res 2014. [DOI: 10.1016/j.jss.2013.11.157] [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: 10/25/2022]
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Kaneko Y, Nakajima T, Irie T, Ota M, Iijima T, Tamura M, Iizuka T, Tamura S, Saito A, Kurabayashi M. Initial shortening of the tachycardia cycle length after the induction of fast-slow atrioventricular nodal reentrant tachycardia may support slow pathway as an antegrade limb of the reentry circuit. Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht310.p4969] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Imamachi N, Tani H, Mizutani R, Imamura K, Irie T, Suzuki Y, Akimitsu N. BRIC-seq: a genome-wide approach for determining RNA stability in mammalian cells. Methods 2013; 67:55-63. [PMID: 23872059 DOI: 10.1016/j.ymeth.2013.07.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [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: 04/27/2013] [Revised: 06/15/2013] [Accepted: 07/01/2013] [Indexed: 10/26/2022] Open
Abstract
We recently developed a novel transcriptome analysis method, termed 5'-bromo-uridine (BrU) immunoprecipitation chase-deep sequencing analysis (BRIC-seq). BRIC-seq enables the determination of genome-wide RNA stability by chasing chronological decreases of BrU-labeled RNAs under physiologically undisturbed conditions. The RNA half-life of each transcript is calculated from the decreasing number of BrU-labeled RNA sequence tags measured by deep sequencing of BrU-labeled RNAs. Here, we describe a detailed protocol and provide tips for BRIC-seq, followed by computational analysis.
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Affiliation(s)
- Naoto Imamachi
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hidenori Tani
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba 305-8569, Japan
| | - Rena Mizutani
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Katsutoshi Imamura
- The Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takuma Irie
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Nobuyoshi Akimitsu
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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Hayashi S, Tanaka J, Okada S, Isobe T, Yamamoto G, Yasuhara R, Irie T, Akiyama C, Kohno Y, Tachikawa T, Mishima K. Lin28a is a putative factor in regulating cancer stem cell-like properties in side population cells of oral squamous cell carcinoma. Exp Cell Res 2013; 319:1220-8. [PMID: 23500413 DOI: 10.1016/j.yexcr.2013.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 02/24/2013] [Accepted: 03/02/2013] [Indexed: 01/06/2023]
Abstract
Cancer stem cells (CSCs) are among the target cells of cancer therapy because they are uniquely involved in both cancer progression and sensitivity to chemotherapeutic agents. We identified side population (SP) cells, which are known to be an enriched population of CSC, in five oral squamous cell carcinoma (OSCC) cells (SCC9, SCC25, TOSCC7, TOSCC17, and TOSCC23). The percentages of SP cells ranged from 0% to 3.3%, with TOSCC23 cells showing the highest percentages of SP cells (3.3% of the total cell population). The SP cells isolated from TOSCC23 cells also showed greater cell proliferation and invasion compared to non-SP (MP) cells. Therefore, our initial findings suggested that SP cells were enriched for CSC-like cells. Furthermore, DNA microarray analysis revealed that the expression of cell proliferation-related and anti-apoptotic genes was greater in SP cells compared to MP cells. We focused on Lin28a, which showed the highest expression (approximately 22-fold) among the upregulated genes. The overexpression of Lin28a in TOSCC23 cells increased their proliferation, colony formation, and invasion. These findings suggest that Lin28a is an appropriate CSC target molecule for OSCC treatment.
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Affiliation(s)
- S Hayashi
- Division of Pathology, Department of Oral Diagnostic Sciences, School of Dentistry, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
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Tani H, Imamachi N, Salam KA, Mizutani R, Ijiri K, Irie T, Yada T, Suzuki Y, Akimitsu N. Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability. RNA Biol 2012; 9:1370-9. [PMID: 23064114 DOI: 10.4161/rna.22360] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [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: 02/06/2023] Open
Abstract
UPF1 eliminates aberrant mRNAs harboring premature termination codons, and regulates the steady-state levels of normal physiological mRNAs. Although genome-wide studies of UPF1 targets performed, previous studies did not distinguish indirect UPF1 targets because they could not determine UPF1-dependent altered RNA stabilities. Here, we measured the decay rates of the whole transcriptome in UPF1-depleted HeLa cells using BRIC-seq, an inhibitor-free method for directly measuring RNA stability. We determined the half-lives and expression levels of 9,229 transcripts. An amount of 785 transcripts were stabilized in UPF1-depleted cells. Among these, the expression levels of 76 transcripts were increased, but those of the other 709 transcripts were not altered. RNA immunoprecipitation showed UPF1 bound to the stabilized transcripts, suggesting that UPF1 directly degrades the 709 transcripts. Many UPF1 targets in this study were newly identified. This study clearly demonstrates that direct determination of RNA stability is a powerful approach for identifying targets of RNA degradation factors.
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Affiliation(s)
- Hidenori Tani
- Radioisotope Center, University of Tokyo, Tokyo, Japan
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Zhang MR, Tsuchiyama A, Haradahira T, Yoshida Y, Irie T, Suzuki K. An automated synthesis of [18F]Fluoroethyl bromide by distillation and its application to the synthesis of [18F]Fluoroethyl-P4A, a pet tracer for measurement of acetylcholinesterase activity. J Labelled Comp Radiopharm 2012. [DOI: 10.1002/jlcr.25804401310] [Citation(s) in RCA: 3] [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: 11/09/2022]
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Shimada H, Hirano S, Shinotoh H, Aotsuka A, Sato K, Tanaka N, Ota T, Asahina M, Fukushi K, Kuwabara S, Irie T, Ito H, Suhara T. 2.021 DEMENTIA WITH LEWY BODIES CAN BE WELL-DIFFERENTIATED FROM ALZHEIMER'S DISEASE BY MEASUREMENT OF BRAIN ACETYLCHOLIN ESTERASE ACTIVITY BY PET. Parkinsonism Relat Disord 2012. [DOI: 10.1016/s1353-8020(11)70454-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Miyagawa T, Ishikawa S, Ichioka D, Emura M, Kojima T, Tsutsumi M, Irie T, Kondou M, Mitake T. UP-02.133 Real-time Virtual Sonography for Prostate-Targeted Biopsy Based on MRI Data: Evaluation of Accuracy with Resected Specimens. Urology 2011. [DOI: 10.1016/j.urology.2011.07.951] [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: 11/25/2022]
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Abstract
We developed a computer program that can predict the intrinsic promoter activities of primary human DNA sequences. We observed promoter activity using a quantitative luciferase assay and generated a prediction model using multiple linear regression. Our program achieved a prediction accuracy correlation coefficient of 0.87 between the predicted and observed promoter activities. We evaluated the prediction accuracy of the program using massive sequencing analysis of transcriptional start sites in vivo. We found that it is still difficult to predict transcript levels in a strictly quantitative manner in vivo; however, it was possible to select active promoters in a given cell from the other silent promoters. Using this program, we analyzed the transcriptional landscape of the entire human genome. We demonstrate that many human genomic regions have potential promoter activity, and the expression of some previously uncharacterized putatively non-protein-coding transcripts can be explained by our prediction model. Furthermore, we found that nucleosomes occasionally formed open chromatin structures with RNA polymerase II recruitment where the program predicted significant promoter activities, although no transcripts were observed.
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Affiliation(s)
- Takuma Irie
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwashi, Chiba 277-8562, Japan
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Uekama K, Adachi H, Irie T, Yano T, Saita M, Noda K. Improved transdermal delivery of prostaglandin E1 through hairless mouse skin: combined use of carboxymethyl-ethyl-β-cyclodextrin and penetration enhancers. J Pharm Pharmacol 2011; 44:119-21. [PMID: 1352811 DOI: 10.1111/j.2042-7158.1992.tb03574.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [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: 11/29/2022]
Abstract
Abstract
The optimal prescription of transdermal preparations of prostaglandin E1 (PGE1) for treatment of peripheral vascular diseases has been investigated. The chemical stability of PGE1 in fatty alcohol/propylene glycol (FAPG) ointment was markedly improved by carboxymethyl-ethyl-β-cyclodextrin (CME-β-CyD). Application of a PGE1 ointment containing the penetration enhancer, 1-dodecylazacycloheptane-2-one (Azone) or 1-[2-(decylthio)ethyl]azacyclopentane-2-one (HPE-101), onto the skin of hairless mice showed the increase of blood flow in the skin due to the vasodilating action of PGE1. In particular, the ointment containing a PGE1-CME-β-CyD complex supplemented with HPE-101 showed the most prominent increase of the blood flow. Compared with other ointments, this ointment was found to show significantly greater transfer of HPE-101 into in-vitro preparations of the skin of hairless mice. Transfer of PGE1 into the skin was thought to be facilitated by this increased transfer of HPE-101. These results suggest that a combination of CME-β-CyD and HPE-101 is useful for designing PGE1 ointments for topical application with good chemical stability and percutaneous permeability.
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Affiliation(s)
- K Uekama
- Faculty of Pharmaceutical Sciences, Kumamoto University, Japan
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Toru S, Matumura K, Kawaguchi R, Kobayashi T, Irie T. Widespread cortical lesions on diffusion-weighted imaging in acute portal systemic shunt encephalopathy caused by primary biliary cirrhosis. AJNR Am J Neuroradiol 2011; 32:E55-6. [PMID: 21233224 DOI: 10.3174/ajnr.a2466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Okamura T, Kikuchi T, Irie T. PET imaging of MRP1 function in the living brain: method development and future perspectives. Curr Top Med Chem 2011; 10:1810-9. [PMID: 20645911 DOI: 10.2174/156802610792927988] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2010] [Accepted: 01/20/2010] [Indexed: 11/22/2022]
Abstract
Multidrug resistance-associated protein 1 (MRP1) functions as a primary active transporter utilizing energy from ATP hydrolysis. In the central nervous system (CNS), MRP1 plays an important role in limiting the permeation of xenobiotic and endogenous substrates across the blood-brain and blood-cerebrospinal fluid barriers, and across brain parenchymal cells. While MRP1 contributes to minimizing the neurotoxic effects of drugs, it may also restrict the distribution of drugs for the treatment of CNS diseases. Moreover, neurodegenerative disease may be associated with abnormal expression of efflux transporters in the brain. Noninvasive measurement of MRP1 function will therefore be useful for directly evaluating the effect of modulators on enhancing the penetration of drugs into the brain and for examining the pathophysiological role of MRP1 in the brain. Positron emission tomography (PET) is a powerful molecular imaging technique. While several PET probes have been proposed for imaging function of the efflux transporter P-glycoprotein, few reports discuss the probes for imaging MRP1 function in the brain. Ideally, brain radioactivity should consist of a single radioactive compound that is selectively transported by the efflux transporter of interest, without other efflux routes. However, most PET probes for MRP1 or P-glycoprotein are eliminated by both a transporter and simple diffusion, resulting in inaccurate measurement of pump function. This review addresses a new strategy to avoid this problem, and suggests the design of a PET probe based on this strategy, particularly for MRP1 imaging. Several published reports on imaging MRP1 function with PET are also discussed.
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Affiliation(s)
- T Okamura
- Probe Research Section, Department of Molecular Probe, Molecular Imaging Center, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
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Yada T, Yoshida K, Morita M, Taniguchi T, Irie T, Suzuki Y. Linear regression models predicting strength of transcriptional activity of promoters. Genome Inform 2011; 25:53-60. [PMID: 22230939] [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: 05/31/2023]
Abstract
We developed linear regression models which predict strength of transcriptional activity of promoters from their sequences. Intrinsic transcriptional strength data of 451 human promoter sequences in three cell lines (HEK293, MCF7 and 3T3), which were measured by systematic luciferase reporter gene assays, were used to build the models. The models sum up contributions of CG dinucleotide content and transcription factor binding sites (TFBSs) to transcriptional strength. We evaluated prediction accuracies of the models by cross validation tests and found that they have adequate ability for predicting transcriptional strength of promoters in spite of their simple formalization. We also evaluated statistical significance of the contributions and proposed a picture of regulatory code hidden in promoter sequences. That is, CG dinucleotide content and TFBSs mainly determine strength of transcriptional activity under ubiquitous and specific environments, respectively.
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Affiliation(s)
- Tetsushi Yada
- Graduate School of Informatics, Kyoto University, Sakyo-ku, Kyoto, Japan.
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Arii S, Tanaka S, Mitsunori Y, Nakamura N, Kudo A, Noguchi N, Irie T. Surgical Strategies for Hepatocellular Carcinoma with Special Reference to Anatomical Hepatic Resection and Intraoperative Contrast-Enhanced Ultrasonography. Oncology 2010; 78 Suppl 1:125-30. [DOI: 10.1159/000315240] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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41
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Suzuki M, Yasui K, Ishikawa H, Nomura M, Watanabe T, Mikami H, Yamazaki T, Irie T, Yamano T, Ono S. FP57-FR-06 Increased neurotrophin-3 of skin in amyotrophic lateral sclerosis: an immunohistochemical study. J Neurol Sci 2009. [DOI: 10.1016/s0022-510x(09)70574-x] [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: 11/25/2022]
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Shimada H, Hirano S, Shinotoh H, Aotsuka A, Sato K, Tanaka N, Ota T, Asahina M, Fukushi K, Kuwabara S, Hattori T, Suhara T, Irie T. Mapping of brain acetylcholinesterase alterations in Lewy body disease by PET. Neurology 2009; 73:273-8. [PMID: 19474411 DOI: 10.1212/wnl.0b013e3181ab2b58] [Citation(s) in RCA: 227] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE To characterize brain cholinergic deficits in Parkinson disease (PD), PD with dementia (PDD), and dementia with Lewy bodies (DLB). METHODS Participants included 18 patients with PD, 21 patients with PDD/DLB, and 26 healthy controls. The PD group consisted of nine patients with early PD, each with a disease duration of less than 3 years, five of whom were de novo PD patients, and nine patients with advanced PD, each with a disease duration greater than or equal to 3 years. The PDD/DLB group consisted of 10 patients with PDD and 11 patients with DLB. All subjects underwent PET scans with N-[11C]-methyl-4-piperidyl acetate to measure brain acetylcholinesterase (AChE) activity. Brain AChE activity levels were estimated voxel-by-voxel in a three-compartment analysis using the arterial input function, and compared among our subject groups through both voxel-based analysis using the statistical parametric mapping software SPM5 and volume-of-interest analysis. RESULTS Among patients with PD, AChE activity was significantly decreased in the cerebral cortex and especially in the medial occipital cortex (% reduction compared with the normal mean = -12%) (false discovery rate-corrected p value <0.01). Patients with PDD/DLB, however, had even lower AChE activity in the cerebral cortex (% reduction = -27%) (p < 0.01). There was no significant difference between early PD and advanced PD groups or between DLB and PDD groups in the amount by which regional AChE activity in the brain was reduced. CONCLUSIONS Brain cholinergic dysfunction occurs in the cerebral cortex, especially in the medial occipital cortex. It begins in early Parkinson disease, and is more widespread and profound in both Parkinson disease with dementia and dementia with Lewy bodies.
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Affiliation(s)
- H Shimada
- Molecular Neuroimaging Group, Molecular Imaging Center, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba-shi, Chiba 260-8555, Japan.
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Tsuchihara K, Suzuki Y, Wakaguri H, Irie T, Tanimoto K, Hashimoto SI, Matsushima K, Mizushima-Sugano J, Yamashita R, Nakai K, Bentley D, Esumi H, Sugano S. Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res 2009; 37:2249-63. [PMID: 19237398 PMCID: PMC2673422 DOI: 10.1093/nar/gkp066] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [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] [Indexed: 11/14/2022] Open
Abstract
Combining our full-length cDNA method and the massively parallel sequencing technology, we developed a simple method to collect precise positional information of transcriptional start sites (TSSs) together with digital information of the gene-expression levels in a high throughput manner. We applied this method to observe gene-expression changes in a colon cancer cell line cultured in normoxic and hypoxic conditions. We generated more than 100 million 36-base TSS-tag sequences and revealed comprehensive features of hypoxia responsive alterations in the transcriptional landscape of the human genome. The features include presence of inducible 'hot regions' in 54 genomic regions, 220 novel hypoxia inducible promoters that may drive non-protein-coding transcripts, 191 hypoxia responsive alternative promoters and detailed views of 120 novel as well as known hypoxia responsive genes. We further analyzed hypoxic response of different cells using additional 60 million TSS-tags and found that the degree of the gene-expression changes were different among cell lines, possibly reflecting cellular robustness against hypoxia. The novel dynamic figure of the human gene transcriptome will deepen our understanding of the transcriptional program of the human genome as well as bringing new insights into the biology of cancer cells in hypoxia.
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Affiliation(s)
- Katsuya Tsuchihara
- Cancer Physiology Project, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
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Ishikawa S, Miyagawa T, Kimura T, Suetomi T, Tsutsumi M, Irie T, Kondoh M, Arai O, Mitake T. POD-5.05: Prostate-Targeted Biopsy Navigated by Real-time Virtual Sonography Acquired from MRI Volume Data. Urology 2008. [DOI: 10.1016/j.urology.2008.08.106] [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: 11/26/2022]
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Hashino S, Morioka M, Irie T, Shiroshita N, Kawamura T, Suzuki S, Iwasaki H, Umehara S, Kakinoki Y, Kurosawa M, Kahata K, Izumiyama K, Kobayashi H, Onozawa M, Takahata M, Fujisawa F, Kondo T, Asaka M. Cost benefit and clinical efficacy of low-dose granulocyte colony-stimulating factor after standard chemotherapy in patients with non-Hodgkin's lymphoma. Int J Lab Hematol 2008; 30:292-9. [PMID: 18665826 DOI: 10.1111/j.1751-553x.2007.00955.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High costs of molecule-targeted drugs, such as rituximab, ibritumomab, and tositumomab have given rise to an economical issue for treating patients with non-Hodgkin's lymphoma (NHL). Granulocyte colony-stimulating factors (G-CSFs), which are also expensive, are widely used for treating neutropenia after chemotherapy. In Japan, lenograstim at 2 microg/kg (about 100 microg/body) or filgrastim at 50 microg/m(2) (about 75 microg/body) is commonly administered for patients with NHL after chemotherapy. Therefore, cost-effectiveness is an important issue in treatment for NHL. Patients with advanced-stage NHL who needed chemotherapy with cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) or a CHOP-like regimen with or without rituximab were enrolled in this randomized cross-over trial to investigate the efficacy and safety of low-dose G-CSF. Half of the patients were administered 75 microg filgrastim in the first course after neutropenia and 50 microg lenograstim in the second course, and the other half were crossed over. Forty-seven patients were enrolled in this cross-over trial, and 24 patients completed the trial. Frequencies and durations of grade 4 leukocytopenia and neutropenia were similar in the two groups. Severe infection was rare and was observed at similar frequency. Frequencies of antibiotics use were also similar. The total cost of G-CSF (cost/drug x duration of administration) was significantly lower in patients who received 50 microg lenograstim. Hence, a low dose of lenograstim might be safe, effective and pharmaco-economically beneficial in patients with advanced-stage NHL.
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Affiliation(s)
- S Hashino
- Department of Gastroenterology and Hematology, Hokkaido University School of Medicine, Sapporo, Japan.
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Takeda JI, Suzuki Y, Sakate R, Sato Y, Seki M, Irie T, Takeuchi N, Ueda T, Nakao M, Sugano S, Gojobori T, Imanishi T. Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs. Nucleic Acids Res 2008; 36:6386-95. [PMID: 18838389 PMCID: PMC2582632 DOI: 10.1093/nar/gkn677] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [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] [Indexed: 12/20/2022] Open
Abstract
Using full-length cDNA sequences, we compared alternative splicing (AS) in humans and mice. The alignment of the human and mouse genomes showed that 86% of 199 426 total exons in human AS variants were conserved in the mouse genome. Of the 20 392 total human AS variants, however, 59% consisted of all conserved exons. Comparing AS patterns between human and mouse transcripts revealed that only 431 transcripts from 189 loci were perfectly conserved AS variants. To exclude the possibility that the full-length human cDNAs used in the present study, especially those with retained introns, were cloning artefacts or prematurely spliced transcripts, we experimentally validated 34 such cases. Our results indicate that even retained-intron type transcripts are typically expressed in a highly controlled manner and interact with translating ribosomes. We found non-conserved AS exons to be predominantly outside the coding sequences (CDSs). This suggests that non-conserved exons in the CDSs of transcripts cause functional constraint. These findings should enhance our understanding of the relationship between AS and species specificity of human genes.
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Affiliation(s)
- Jun-Ichi Takeda
- Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research Building, Aomi 2-42, Koto-ku, Tokyo, Japan
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Kambayashi T, Irie T, Nakatsukasa H, Takaki Y. [Lung abscess which ruptured during the medical treatment of lung abscess; report of a case]. Kyobu Geka 2008; 61:254-257. [PMID: 18323196] [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: 05/26/2023]
Abstract
63-year-old man was admitted to our hospital with fever and cough for about 2 months. Laboratory data showed marked inflammatory changes, and chest computed tomography (CT) scans revealed right-sided hydrothorax, atelectasis of the right middle lobe, and a cystic mass in the right middle lobe. We diagnosed the patients as having lung abscess and empyema. Following the intravenous antibiotic chemotherapy, symptoms and laboratory data showed the improvement, however, on the 11th hospital day, he developed high fever again. A chest CT showed pneumopyothorax suggesting the rupture of lung abscess. Since the chest tube drainage was ineffective, open chest surgery was performed. Curettage of both thoracic and abscess cavity with closure of air leakage successfully cured the pyothorax.
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Seki C, Tokunaga M, Hattori S, Shidahara M, Nakao R, Maeda J, Toyama H, Irie T, Higuchi M, Suhara T, Kanno I, Kimura Y. Quantification of 11C-PIB kinetics in mouse brain using metabolite-corrected arterial input function. Neuroimage 2008. [DOI: 10.1016/j.neuroimage.2008.04.206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Majima T, Irie T, Sawaguchi N, Funakoshi T, Iwasaki N, Harada K, Minami A, Nishimura SI. Chitosan-based hyaluronan hybrid polymer fibre scaffold for ligament and tendon tissue engineering. Proc Inst Mech Eng H 2007; 221:537-46. [PMID: 17822155 DOI: 10.1243/09544119jeim203] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [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: 11/18/2022]
Abstract
To establish medical use of tissue engineering technology for ligament and tendon injuries, a scaffold was developed which has sufficient ability for cell growth, cell differentiation, and mechanical properties. The scaffold made from chitosan and 0.1 per cent hyaluronic acid has adequate biodegradability and biocompatibility. An animal experiment showed that the scaffold has less toxicity and less inflammation induction. Furthermore, in-vivo animal experiments showed that the mechanical properties of the engineered ligament or tendon had the possibility to stabilize the joint. It was shown that newly developed hybrid-polymer fibre scaffold has feasibility for joint tissue engineering.
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Affiliation(s)
- T Majima
- Department of Orthopaedic Surgery, Hokkaido University School of Medicine, Sapporo, 060-8638, Japan.
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Tsuritani K, Irie T, Yamashita R, Sakakibara Y, Wakaguri H, Kanai A, Mizushima-Sugano J, Sugano S, Nakai K, Suzuki Y. Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes. Genome Res 2007; 17:1005-14. [PMID: 17567985 PMCID: PMC1899111 DOI: 10.1101/gr.6030107] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Although recent studies have revealed that the majority of human genes are subject to regulation of alternative promoters, the biological relevance of this phenomenon remains unclear. We have also demonstrated that roughly half of the human RefSeq genes examined contain putative alternative promoters (PAPs). Here we report large-scale comparative studies of PAPs between human and mouse counterpart genes. Detailed sequence comparison of the 17,245 putative promoter regions (PPRs) in 5463 PAP-containing human genes revealed that PPRs in only a minor fraction of genes (807 genes) showed clear evolutionary conservation as one or more pairs. Also, we found that there were substantial qualitative differences between conserved and non-conserved PPRs, with the latter class being AT-rich PPRs of relative minor usage, enriched in repetitive elements and sometimes producing transcripts that encode small or no proteins. Systematic luciferase assays of these PPRs revealed that both classes of PPRs did have promoter activity, but that their strength ranges were significantly different. Furthermore, we demonstrate that these characteristic features of the non-conserved PPRs are shared with the PPRs of previously discovered putative non-protein coding transcripts. Taken together, our data suggest that there are two distinct classes of promoters in humans, with the latter class of promoters emerging frequently during evolution.
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Affiliation(s)
- Katsuki Tsuritani
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minatoku, Tokyo 108-8639, Japan
| | - Takuma Irie
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Riu Yamashita
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minatoku, Tokyo 108-8639, Japan
| | - Yuta Sakakibara
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Hiroyuki Wakaguri
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Akinori Kanai
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Junko Mizushima-Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
- Laboratory of Viral Infection II Kitasato Institute for Life Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minatoku, Tokyo 108-8639, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
- Corresponding author.E-mail ; fax +81-4-7136-3607
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