1
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Agrawal S, Buyan A, Severin J, Koido M, Alam T, Abugessaisa I, Chang HY, Dostie J, Itoh M, Kere J, Kondo N, Li Y, Makeev VJ, Mendez M, Okazaki Y, Ramilowski JA, Sigorskikh AI, Strug LJ, Yagi K, Yasuzawa K, Yip CW, Hon CC, Hoffman MM, Terao C, Kulakovskiy IV, Kasukawa T, Shin JW, Carninci P, de Hoon MJL. Annotation of nuclear lncRNAs based on chromatin interactions. PLoS One 2024; 19:e0295971. [PMID: 38709794 PMCID: PMC11073715 DOI: 10.1371/journal.pone.0295971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/02/2023] [Indexed: 05/08/2024] Open
Abstract
The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.
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Affiliation(s)
- Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Andrey Buyan
- Autosome.org, Russia
- FANTOM Consortium, Dolgoprudny, Russia
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaru Koido
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Howard Y. Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, California, United States of America
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Naoto Kondo
- RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Yunjing Li
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | | | - Mickaël Mendez
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jordan A. Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | | | - Lisa J. Strug
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Ontario, Canada
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michael M. Hoffman
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jay W. Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
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2
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Ueno Y, Yoshida E, Nojiri S, Kato T, Ohtsu T, Takeshita T, Suzuki S, Yoshida H, Kato K, Itoh M, Notomi T, Usui K, Sozu T, Terao Y, Kawaji H, Kato H. Use of clinical variables for preoperative prediction of lymph node metastasis in endometrial cancer. Jpn J Clin Oncol 2024; 54:38-46. [PMID: 37815156 PMCID: PMC10773201 DOI: 10.1093/jjco/hyad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
OBJECTIVE Endometrial cancer is the most common gynaecological cancer, and most patients are identified during early disease stages. Noninvasive evaluation of lymph node metastasis likely will improve the quality of clinical treatment, for example, by omitting unnecessary lymphadenectomy. METHODS The study population comprised 611 patients with endometrial cancer who underwent lymphadenectomy at four types of institutions, comprising seven hospitals in total. We systematically assessed the association of 18 preoperative clinical variables with postoperative lymph node metastasis. We then constructed statistical models for preoperative lymph node metastasis prediction and assessed their performance with a previously proposed system, in which the score was determined by counting the number of high-risk variables among the four predefined ones. RESULTS Of the preoperative 18 variables evaluated, 10 were significantly associated with postoperative lymph node metastasis. A logistic regression model achieved an area under the curve of 0.85 in predicting lymph node metastasis; this value is significantly higher than that from the previous system (area under the curve, 0.74). When we set the false-negative rate to ~1%, the new predictive model increased the rate of true negatives to 21%, compared with 6.8% from the previous one. We also provide a spreadsheet-based tool for further evaluation of its ability to predict lymph node metastasis in endometrial cancer. CONCLUSIONS Our new lymph node metastasis prediction method, which was based solely on preoperative clinical variables, performed significantly better than the previous method. Although additional evaluation is necessary for its clinical use, our noninvasive system may help improve the clinical treatment of endometrial cancer, complementing minimally invasive sentinel lymph node biopsy.
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Affiliation(s)
- Yuta Ueno
- Department of Gynecology, Kanagawa Cancer Center, Yokohama, Japan
- Department of Obstetrics and Gynecology, Nippon Medical School, Tokyo, Japan
- Department of Obstetrics and Gynecology, NTT Medical Center Tokyo, Tokyo, Japan
| | - Emiko Yoshida
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
- Medical Technology Innovation Center, Juntendo University, Tokyo, Japan
| | - Shuko Nojiri
- Clinical Research and Trial Center, Juntendo University, Tokyo, Japan
| | - Tomoyasu Kato
- Department of Gynecology, National Cancer Center, Tokyo, Japan
| | - Takashi Ohtsu
- Division of Advanced Cancer Therapeutics, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Center for Cancer Genome Medicine, Kanagawa Cancer Center, Yokohama, Japan
| | - Toshiyuki Takeshita
- Department of Obstetrics and Gynecology, Nippon Medical School, Tokyo, Japan
| | - Shunji Suzuki
- Department of Obstetrics and Gynecology, Nippon Medical School, Tokyo, Japan
| | - Hiroshi Yoshida
- Department of Diagnostic Pathology, National Cancer Center, Tokyo, Japan
| | - Ken Kato
- Clinical Research Support Office, Biobank Translational Research Support Section, National Cancer Center Hospital, Tokyo, Japan
| | - Masayoshi Itoh
- Laboratory for Advanced Genomics Circuit, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tsuguto Notomi
- Department of Obstetrics and Gynecology, NTT Medical Center Tokyo, Tokyo, Japan
| | - Kengo Usui
- Medical Technology Innovation Center, Juntendo University, Tokyo, Japan
| | - Takashi Sozu
- Department of Information and Computer Technology, Faculty of Engineering, Tokyo University of Science, Tokyo, Japan
| | - Yasuhisa Terao
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Hideya Kawaji
- Research Center for Genome and Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hisamori Kato
- Department of Gynecology, Kanagawa Cancer Center, Yokohama, Japan
- Kanagawa Health Service Association, Yokohama, Japan
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3
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Kuroda T, Yasuda S, Matsuyama S, Miura T, Sawada R, Matsuyama A, Yamamoto Y, Morioka MS, Kawaji H, Kasukawa T, Itoh M, Akutsu H, Kawai J, Sato Y. ROR2 expression predicts human induced pluripotent stem cell differentiation into neural stem/progenitor cells and GABAergic neurons. Sci Rep 2024; 14:690. [PMID: 38184695 PMCID: PMC10771438 DOI: 10.1038/s41598-023-51082-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/30/2023] [Indexed: 01/08/2024] Open
Abstract
Despite the development of various in vitro differentiation protocols for the efficient derivation of specific cell types, human induced pluripotent stem cell (hiPSC) lines have varing ability to differentiate into specific lineages. Therefore, surrogate markers for accurately predicting the differentiation propensity of hiPSC lines may facilitate cell-based therapeutic product development and manufacture. We attempted to identify marker genes that could predict the differentiation propensity of hiPSCs into neural stem/progenitor cells (NS/PCs). Using Spearman's rank correlation coefficients, we investigated genes in the undifferentiated state, the expression levels of which were significantly correlated with the neuronal differentiation propensity of several hiPSC lines. Among genes significantly correlated with NS/PC differentiation (P < 0.01), we identified ROR2 as a novel predictive marker. ROR2 expression in hiPSCs was negatively correlated with NS/PC differentiation tendency, regardless of the differentiation method, whereas its knockdown enhanced differentiation. ROR2 regulates NS/PC differentiation, suggesting that ROR2 is functionally essential for NS/PC differentiation. Selecting cell lines with relatively low ROR2 expression facilitated identification of hiPSCs that can differentiate into NS/PCs. Cells with ROR2 knockdown showed increased efficiency of differentiation into forebrain GABAergic neurons compared to controls. These findings suggest that ROR2 is a surrogate marker for selecting hiPSC lines appropriate for NS/PC and GABAergic neuronal differentiations.
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Affiliation(s)
- Takuya Kuroda
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
- Life Science Technology Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
| | - Satoshi Yasuda
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
- Life Science Technology Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Department of Quality Assurance Science for Pharmaceuticals, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Satoko Matsuyama
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
- Center for Reverse TR, Osaka Habikino Medical Center, Osaka Prefectural Hospital Organization, Habikino, Osaka, Japan
| | - Takumi Miura
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
- Life Science Technology Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Center for Regenerative Medicine, National Center for Child Health and Development, Setagaya, Tokyo, Japan
| | - Rumi Sawada
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Akifumi Matsuyama
- Center for Reverse TR, Osaka Habikino Medical Center, Osaka Prefectural Hospital Organization, Habikino, Osaka, Japan
| | - Yumiko Yamamoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Research Center for Genome and Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development, Setagaya, Tokyo, Japan
| | - Jun Kawai
- Life Science Technology Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yoji Sato
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.
- Life Science Technology Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan.
- Department of Quality Assurance Science for Pharmaceuticals, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan.
- Division of Drugs, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan.
- Department of Cellular and Gene Therapy Products, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
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4
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Miura T, Kouno T, Takano M, Kuroda T, Yamamoto Y, Kusakawa S, Morioka MS, Sugawara T, Hirai T, Yasuda S, Sawada R, Matsuyama S, Kawaji H, Kasukawa T, Itoh M, Matsuyama A, Shin JW, Umezawa A, Kawai J, Sato Y. Single-Cell RNA-Seq Reveals LRRC75A-Expressing Cell Population Involved in VEGF Secretion of Multipotent Mesenchymal Stromal/Stem Cells Under Ischemia. Stem Cells Transl Med 2023; 12:379-390. [PMID: 37263619 PMCID: PMC10267575 DOI: 10.1093/stcltm/szad029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/15/2023] [Indexed: 06/03/2023] Open
Abstract
Human multipotent mesenchymal stromal/stem cells (MSCs) have been utilized in cell therapy for various diseases and their clinical applications are expected to increase in the future. However, the variation in MSC-based product quality due to the MSC heterogeneity has resulted in significant constraints in the clinical utility of MSCs. Therefore, we hypothesized that it might be important to identify and ensure/enrich suitable cell subpopulations for therapies using MSC-based products. In this study, we aimed to identify functional cell subpopulations to predict the efficacy of angiogenic therapy using bone marrow-derived MSCs (BM-MSCs). To assess its angiogenic potency, we observed various levels of vascular endothelial growth factor (VEGF) secretion among 11 donor-derived BM-MSC lines under in vitro ischemic culture conditions. Next, by clarifying the heterogeneity of BM-MSCs using single-cell RNA-sequencing analysis, we identified a functional cell subpopulation that contributed to the overall VEGF production in BM-MSC lines under ischemic conditions. We also found that leucine-rich repeat-containing 75A (LRRC75A) was more highly expressed in this cell subpopulation than in the others. Importantly, knockdown of LRRC75A using small interfering RNA resulted in significant inhibition of VEGF secretion in ischemic BM-MSCs, indicating that LRRC75A regulates VEGF secretion under ischemic conditions. Therefore, LRRC75A may be a useful biomarker to identify cell subpopulations that contribute to the angiogenic effects of BM-MSCs. Our work provides evidence that a strategy based on single-cell transcriptome profiles is effective for identifying functional cell subpopulations in heterogeneous MSC-based products.
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Affiliation(s)
- Takumi Miura
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kanagawa, Japan
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Megumi Takano
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kanagawa, Japan
| | - Takuya Kuroda
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kanagawa, Japan
| | - Yumiko Yamamoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shinji Kusakawa
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kanagawa, Japan
| | | | - Tohru Sugawara
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
- Biopharmaceutical and Regenerative Sciences, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Takamasa Hirai
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kanagawa, Japan
| | - Satoshi Yasuda
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kanagawa, Japan
| | - Rumi Sawada
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kanagawa, Japan
| | - Satoko Matsuyama
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kanagawa, Japan
- Center for Reverse TR, Osaka Habikino Medical Center, Osaka Prefectural Hospital Organization, Osaka, Japan
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akifumi Matsuyama
- Center for Reverse TR, Osaka Habikino Medical Center, Osaka Prefectural Hospital Organization, Osaka, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Genomic Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Jun Kawai
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Life Science Technology Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
| | - Yoji Sato
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, Kanagawa, Japan
- Life Science Technology Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Department of Cellular and Gene Therapy Products, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
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5
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Kanamori K, Suina K, Shukuya T, Takahashi F, Hayashi T, Hara K, Saito T, Mitsuishi Y, Shimamura SS, Winardi W, Tajima K, Ko R, Mimori T, Asao T, Itoh M, Kawaji H, Suehara Y, Takamochi K, Suzuki K, Takahashi K. CALML5 is a novel diagnostic marker for differentiating thymic squamous cell carcinoma from type B3 thymoma. Thorac Cancer 2023; 14:1089-1097. [PMID: 36924358 PMCID: PMC10125782 DOI: 10.1111/1759-7714.14853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Thymic squamous cell carcinoma and type B3 thymoma are primary neoplasms of the anterior mediastinum that are sometimes difficult to differentiate from one another histologically. However, only a few immunohistochemical markers are available for the differential diagnosis. The purpose of this study was to discover a novel marker for differentiating between thymic squamous cell carcinoma and type B3 thymoma. METHODS We used histological samples of thymic carcinomas (n = 26) and type B3 thymomas (n = 38) which were resected between 1986 and 2017. To search for candidates of differential markers, gene expression levels were evaluated in samples using promoter analysis by cap analysis of gene expression (CAGE) sequencing. RESULTS Promoter level expression of CALML5 genes was significantly higher in thymic carcinomas than in type B3 thymomas. We further validated the results of the CAGE analysis in all 26 thymic carcinomas and 38 type B3 thymomas by immunohistochemistry (IHC). CALML5 was strongly expressed in the cytoplasm in 19 of 26 cases with thymic carcinoma, whereas positivity at the protein level was shown in two of 38 type B3 thymomas. Thus, the sensitivity (73.1%) and specificity (94.7%) of CALML5 as markers for immunohistochemical diagnosis of thymic carcinoma were extremely high. CONCLUSION We identified CALML5 as a potential marker for differentiating thymic squamous cell carcinoma from type B3 thymoma. It is assumed that future clinical use of CALML5 may improve the diagnostic accuracy of differentiating between these two diseases.
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Affiliation(s)
- Koichiro Kanamori
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kentaro Suina
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Takehito Shukuya
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Fumiyuki Takahashi
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kieko Hara
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Yoichiro Mitsuishi
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Shoko Sonobe Shimamura
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Wira Winardi
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Ken Tajima
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Ryo Ko
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Tomoyasu Mimori
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Tetsuhiko Asao
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama, Japan.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama, Japan.,Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan.,Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yoshiyuki Suehara
- Department of Orthopedic Surgery, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kazuya Takamochi
- Department of General Thoracic Surgery, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kenji Suzuki
- Department of General Thoracic Surgery, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Graduate School of Medicine, Tokyo, Japan
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6
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Yip CW, Hon CC, Yasuzawa K, Sivaraman DM, Ramilowski JA, Shibayama Y, Agrawal S, Prabhu AV, Parr C, Severin J, Lan YJ, Dostie J, Petri A, Nishiyori-Sueki H, Tagami M, Itoh M, López-Redondo F, Kouno T, Chang JC, Luginbühl J, Kato M, Murata M, Yip WH, Shu X, Abugessaisa I, Hasegawa A, Suzuki H, Kauppinen S, Yagi K, Okazaki Y, Kasukawa T, de Hoon M, Carninci P, Shin JW. Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types. Cell Rep 2022; 41:111893. [PMID: 36577377 DOI: 10.1016/j.celrep.2022.111893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/30/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022] Open
Abstract
Within the scope of the FANTOM6 consortium, we perform a large-scale knockdown of 200 long non-coding RNAs (lncRNAs) in human induced pluripotent stem cells (iPSCs) and systematically characterize their roles in self-renewal and pluripotency. We find 36 lncRNAs (18%) exhibiting cell growth inhibition. From the knockdown of 123 lncRNAs with transcriptome profiling, 36 lncRNAs (29.3%) show molecular phenotypes. Integrating the molecular phenotypes with chromatin-interaction assays further reveals cis- and trans-interacting partners as potential primary targets. Additionally, cell-type enrichment analysis identifies lncRNAs associated with pluripotency, while the knockdown of LINC02595, CATG00000090305.1, and RP11-148B6.2 modulates colony formation of iPSCs. We compare our results with previously published fibroblasts phenotyping data and find that 2.9% of the lncRNAs exhibit a consistent cell growth phenotype, whereas we observe 58.3% agreement in molecular phenotypes. This highlights that molecular phenotyping is more comprehensive in revealing affected pathways.
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Affiliation(s)
- Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695 011, India
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Anika V Prabhu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Callum Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yan Jun Lan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, QC, Canada
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 2450, Denmark
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | | | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Masaki Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Wing Hin Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Xufeng Shu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 2450, Denmark
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Human Technopole, via Rita Levi Montalcini 1, Milan, Italy
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore.
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7
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de Hoon M, Bonetti A, Plessy C, Ando Y, Hon CC, Ishizu Y, Itoh M, Kato S, Lin D, Maekawa S, Murata M, Nishiyori H, Shin JW, Stolte J, Suzuki AM, Tagami M, Takahashi H, Thongjuea S, Forrest ARR, Hayashizaki Y, Kere J, Carninci P. Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs. Genome Res 2022; 32:gr.276647.122. [PMID: 35961773 PMCID: PMC9528987 DOI: 10.1101/gr.276647.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/09/2022] [Indexed: 12/03/2022]
Abstract
In eukaryotes, capped RNAs include long transcripts such as messenger RNAs and long noncoding RNAs, as well as shorter transcripts such as spliceosomal RNAs, small nucleolar RNAs, and enhancer RNAs. Long capped transcripts can be profiled using cap analysis gene expression (CAGE) sequencing and other methods. Here, we describe a sequencing library preparation protocol for short capped RNAs, apply it to a differentiation time course of the human cell line THP-1, and systematically compare the landscape of short capped RNAs to that of long capped RNAs. Transcription initiation peaks associated with genes in the sense direction have a strong preference to produce either long or short capped RNAs, with one out of six peaks detected in the short capped RNA libraries only. Gene-associated short capped RNAs have highly specific 3' ends, typically overlapping splice sites. Enhancers also preferentially generate either short or long capped RNAs, with 10% of enhancers observed in the short capped RNA libraries only. Enhancers producing either short or long capped RNAs show enrichment for GWAS-associated disease SNPs. We conclude that deep sequencing of short capped RNAs reveals new families of noncoding RNAs and elucidates the diversity of transcripts generated at known and novel promoters and enhancers.
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Affiliation(s)
- Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Alessandro Bonetti
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Charles Plessy
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshinari Ando
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yuri Ishizu
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Sachi Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Dongyan Lin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Mila, Montreal, Quebec H2S 3H1, Canada
| | - Sho Maekawa
- RIKEN Omics Science Center (OSC), Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Hiromi Nishiyori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138632, Singapore
| | - Jens Stolte
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ana Maria Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Hazuki Takahashi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Supat Thongjuea
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Western Australia 6009, Australia
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Kanagawa 230-0045, Japan
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, Helsinki 00290, Finland
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- Human Technopole, Milan 20157, Italy
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8
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Yoshida Y, Shaikhutdinov N, Kozlova O, Itoh M, Tagami M, Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Noma S, Cherkasov A, Gazizova G, Nasibullina A, Deviatiiarov R, Shagimardanova E, Ryabova A, Yamaguchi K, Bino T, Shigenobu S, Tokumoto S, Miyata Y, Cornette R, Yamada TG, Funahashi A, Tomita M, Gusev O, Kikawada T. High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance. NAR Genom Bioinform 2022; 4:lqac029. [PMID: 35387384 PMCID: PMC8982440 DOI: 10.1093/nargab/lqac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Non-biting midges (Chironomidae) are known to inhabit a wide range of environments, and certain species can tolerate extreme conditions, where the rest of insects cannot survive. In particular, the sleeping chironomid Polypedilum vanderplanki is known for the remarkable ability of its larvae to withstand almost complete desiccation by entering a state called anhydrobiosis. Chromosome numbers in chironomids are higher than in other dipterans and this extra genomic resource might facilitate rapid adaptation to novel environments. We used improved sequencing strategies to assemble a chromosome-level genome sequence for P. vanderplanki for deep comparative analysis of genomic location of genes associated with desiccation tolerance. Using whole genome-based cross-species and intra-species analysis, we provide evidence for the unique functional specialization of Chromosome 4 through extensive acquisition of novel genes. In contrast to other insect genomes, in the sleeping chironomid a uniquely high degree of subfunctionalization in paralogous anhydrobiosis genes occurs in this chromosome, as well as pseudogenization in a highly duplicated gene family. Our findings suggest that the Chromosome 4 in Polypedilum is a site of high genetic turnover, allowing it to act as a ‘sandbox’ for evolutionary experiments, thus facilitating the rapid adaptation of midges to harsh environments.
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Affiliation(s)
- Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Nurislam Shaikhutdinov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 21205, Russian Federation
| | - Olga Kozlova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Masayoshi Itoh
- Preventive Medicine & Diagnosis Innovation Program (PMI), RIKEN, Wako, Saitama 351-0198, Japan
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Michihira Tagami
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | | | - Miki Kojima-Ishiyama
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Shohei Noma
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Alexander Cherkasov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Guzel Gazizova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Aigul Nasibullina
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Ruslan Deviatiiarov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Elena Shagimardanova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Alina Ryabova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Takahiro Bino
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shoko Tokumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Yugo Miyata
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
| | - Richard Cornette
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
| | - Takahiro G Yamada
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa 252-0882, Japan
- Faculty of Environment and Information studies, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Oleg Gusev
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- Department of Regulatory Transcriptomics for Medical Genetic Diagnostics, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Takahiro Kikawada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
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9
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Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, Frith MC, Chatelain C, Carninci P, de Hoon MJL, Wasserman WW, Bréhélin L, Lecellier CH. Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat Commun 2022; 13:1200. [PMID: 35232988 PMCID: PMC8888638 DOI: 10.1038/s41467-022-28758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mathys Grapotte
- Institut de Biologie Computationnelle, Montpellier, France.,Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.,SANOFI R&D, Translational Sciences, Chilly Mazarin, France
| | - Manu Saraswat
- Institut de Biologie Computationnelle, Montpellier, France.,Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Chloé Bessière
- Institut de Biologie Computationnelle, Montpellier, France.,Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Christophe Menichelli
- Institut de Biologie Computationnelle, Montpellier, France.,LIRMM, Univ Montpellier, CNRS, Montpellier, France
| | | | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Shohei Noma
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Martin C Frith
- Artificial Intelligence Research Center, AIST, Tokyo, Japan.,Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan.,AIST-Waseda University CBBD-OIL, AIST, Tokyo, Japan
| | | | | | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Laurent Bréhélin
- Institut de Biologie Computationnelle, Montpellier, France. .,LIRMM, Univ Montpellier, CNRS, Montpellier, France.
| | - Charles-Henri Lecellier
- Institut de Biologie Computationnelle, Montpellier, France. .,Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France. .,LIRMM, Univ Montpellier, CNRS, Montpellier, France.
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10
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Ducoli L, Agrawal S, Hon CC, Ramilowski JA, Sibler E, Tagami M, Itoh M, Kondo N, Abugessaisa I, Hasegawa A, Kasukawa T, Suzuki H, Carninci P, Shin JW, de Hoon MJL, Detmar M. The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background. BMC Genom Data 2021; 22:33. [PMID: 34521352 PMCID: PMC8439024 DOI: 10.1186/s12863-021-00992-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/29/2021] [Indexed: 11/18/2022] Open
Abstract
Background The lymphatic and the blood vasculature are closely related systems that collaborate to ensure the organism’s physiological function. Despite their common developmental origin, they present distinct functional fates in adulthood that rely on robust lineage-specific regulatory programs. The recent technological boost in sequencing approaches unveiled long noncoding RNAs (lncRNAs) as prominent regulatory players of various gene expression levels in a cell-type-specific manner. Results To investigate the potential roles of lncRNAs in vascular biology, we performed antisense oligonucleotide (ASO) knockdowns of lncRNA candidates specifically expressed either in human lymphatic or blood vascular endothelial cells (LECs or BECs) followed by Cap Analysis of Gene Expression (CAGE-Seq). Here, we describe the quality control steps adopted in our analysis pipeline before determining the knockdown effects of three ASOs per lncRNA target on the LEC or BEC transcriptomes. In this regard, we especially observed that the choice of negative control ASOs can dramatically impact the conclusions drawn from the analysis depending on the cellular background. Conclusion In conclusion, the comparison of negative control ASO effects on the targeted cell type transcriptomes highlights the essential need to select a proper control set of multiple negative control ASO based on the investigated cell types. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00992-1.
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Affiliation(s)
- Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Eliane Sibler
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
| | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan.,Human Technopole, Via Cristina Belgioioso 171, 20157, Milan, Italy
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, 230-0045, Japan
| | - Michael Detmar
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.
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11
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Ito Y, Terao Y, Noma S, Tagami M, Yoshida E, Hayashizaki Y, Itoh M, Kawaji H. Nanopore sequencing reveals TACC2 locus complexity and diversity of isoforms transcribed from an intronic promoter. Sci Rep 2021; 11:9355. [PMID: 33931666 PMCID: PMC8087818 DOI: 10.1038/s41598-021-88018-9] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Gene expression is controlled at the transcriptional and post-transcriptional levels. The TACC2 gene was known to be associated with tumors but the control of its expression is unclear. We have reported that activity of the intronic promoter p10 of TACC2 in primary lesion of endometrial cancer is indicative of lymph node metastasis among a low-risk patient group. Here, we analyze the intronic promoter derived isoforms in JHUEM-1 endometrial cancer cells, and primary tissues of endometrial cancers and normal endometrium. Full-length cDNA amplicons are produced by long-range PCR and subjected to nanopore sequencing followed by computational error correction. We identify 16 stable, 4 variable, and 9 rare exons including 3 novel exons validated independently. All variable and rare exons reside N-terminally of the TACC domain and contribute to isoform variety. We found 240 isoforms as high-confidence, supported by more than 20 reads. The large number of isoforms produced from one minor promoter indicates the post-transcriptional complexity coupled with transcription at the TACC2 locus in cancer and normal cells.
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Affiliation(s)
- Yosuke Ito
- Faculty of Medicine, Department of Obstetrics and Gynecology, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan.,Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Yasuhisa Terao
- Faculty of Medicine, Department of Obstetrics and Gynecology, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan.
| | - Shohei Noma
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Michihira Tagami
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Emiko Yoshida
- Faculty of Medicine, Department of Obstetrics and Gynecology, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan.,RIKEN Center for Integrative Medical Sciences, Nucleic Acid Diagnostic System Development Unit, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.,Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Yokohama, Saitama, 351-0198, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Yokohama, Saitama, 351-0198, Japan.,Laboratory for Advanced Genomics Circuit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Hideya Kawaji
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan. .,RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Yokohama, Saitama, 351-0198, Japan. .,Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
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12
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Iwai M, Tulafu M, Togo S, Kawaji H, Kadoya K, Namba Y, Jin J, Watanabe J, Okabe T, Hidayat M, Sumiyoshi I, Itoh M, Koyama Y, Ito Y, Orimo A, Takamochi K, Oh S, Suzuki K, Hayashizaki Y, Yoshida K, Takahashi K. Cancer-associated fibroblast migration in non-small cell lung cancers is modulated by increased integrin α11 expression. Mol Oncol 2021; 15:1507-1527. [PMID: 33682233 PMCID: PMC8096795 DOI: 10.1002/1878-0261.12937] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 02/11/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer‐associated fibroblasts (CAFs) regulate cancer progression through the modulation of extracellular matrix (ECM) and cancer cell adhesion. While undergoing a series of phenotypic changes, CAFs control cancer–stroma interactions through integrin receptor signaling. Here, we isolated CAFs from patients with non‐small‐cell lung cancer (NSCLC) and examined their gene expression profiles. We identified collagen type XI α1 (COL11A1), integrin α11 (ITGA11), and the ITGA11 major ligand collagen type I α1 (COL1A1) among the 390 genes that were significantly enriched in NSCLC‐associated CAFs. Increased ITGA11 expression in cancer stroma was correlated with a poor clinical outcome in patients with NSCLC. Increased expression of fibronectin and collagen type I induced ITGA11 expression in CAFs. The cellular migration of CAFs toward collagen type I and fibronectin was promoted via ERK1/2 signaling, independently of the fibronectin receptor integrin α5β1. Additionally, ERK1/2 signaling induced ITGA11 and COL11A1 expression in cancer stroma. We, therefore, propose that targeting ITGA11 and COL11A1 expressing CAFs to block cancer–stroma interactions may serve as a novel, promising anti‐tumor strategy.
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Affiliation(s)
- Moe Iwai
- Division of Respiratory Medicine, Juntendo University Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Miniwan Tulafu
- Leading Center for the Development and Research of Cancer Medicine, Juntendo University, Tokyo, Japan
| | - Shinsaku Togo
- Division of Respiratory Medicine, Juntendo University Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Hideya Kawaji
- Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Japan.,Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama, Japan
| | - Kotaro Kadoya
- Division of Respiratory Medicine, Juntendo University Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Yukiko Namba
- Division of Respiratory Medicine, Juntendo University Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Jin Jin
- Division of Respiratory Medicine, Juntendo University Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan.,Department of Respiratory and Critical Care Medicine, National Center of Gerontology, Beijing Hospital, China
| | - Junko Watanabe
- Division of Respiratory Medicine, Juntendo University Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Takahiro Okabe
- Leading Center for the Development and Research of Cancer Medicine, Juntendo University, Tokyo, Japan
| | - Moulid Hidayat
- Division of Respiratory Medicine, Juntendo University Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan.,Department of Pulmonology and Respiratory Medicine, Universitas Indonesia Faculty of Medicine, Jakarta, Indonesia
| | - Issei Sumiyoshi
- Division of Respiratory Medicine, Juntendo University Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama, Japan
| | - Yu Koyama
- Departments of Molecular Pathogenesis, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Department of Oral Pathobiological Science and Surgery, Tokyo Dental College, Japan
| | - Yasuhiko Ito
- Departments of Molecular Pathogenesis, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Akira Orimo
- Departments of Molecular Pathogenesis, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kazuya Takamochi
- Department of General Thoracic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Shiaki Oh
- Department of General Thoracic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Kenji Suzuki
- Department of General Thoracic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | | | - Koji Yoshida
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Kazuhisa Takahashi
- Division of Respiratory Medicine, Juntendo University Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
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13
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Chihara M, Asahina A, Itoh M. Corrigendum: A novel mutation in the KCNJ8 gene encoding the Kir6.1 subunit of an ATP-sensitive potassium channel in a Japanese patient with Cantú syndrome. J Eur Acad Dermatol Venereol 2021; 35:263. [PMID: 33617015 DOI: 10.1111/jdv.17015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M Chihara
- Department of Dermatology, The Jikei University School of Medicine, Tokyo, Japan
| | - A Asahina
- Department of Dermatology, The Jikei University School of Medicine, Tokyo, Japan
| | - M Itoh
- Department of Dermatology, The Jikei University School of Medicine, Tokyo, Japan.,Dermatology Clinic Itoiin, Shizuoka, Japan
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14
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Tanaka R, Ito-Hirano R, Fujimura S, Arita K, Hagiwara H, Mita T, Itoh M, Kawaji H, Ogawa T, Watada H, Masuda H, Asahara T, Mizuno H. Ex vivo conditioning of peripheral blood mononuclear cells of diabetic patients promotes vasculogenic wound healing. Stem Cells Transl Med 2021; 10:895-909. [PMID: 33599112 PMCID: PMC8133343 DOI: 10.1002/sctm.20-0309] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 07/10/2020] [Revised: 11/16/2020] [Accepted: 01/07/2021] [Indexed: 12/11/2022] Open
Abstract
The quality and quantity of endothelial progenitor cells (EPCs) are impaired in patients with diabetes mellitus patients, leading to reduced tissue repair during autologous EPC therapy. This study aimed to address the limitations of the previously described serum-free Quantity and Quality Control Culture System (QQc) using CD34+ cells by investigating the therapeutic potential of a novel mononuclear cell (MNC)-QQ. MNCs were isolated from 50 mL of peripheral blood of patients with diabetes mellitus and healthy volunteers (n = 13 each) and subjected to QQc for 7 days in serum-free expansion media with VEGF, Flt-3 ligand, TPO, IL-6, and SCF. The vascular regeneration capability of MNC-QQ cells pre- or post-QQc was evaluated with an EPC colony-forming assay, FACS, EPC culture, tube formation assay, and quantitative real time PCR. For in vivo assessment, 1 × 104 pre- and post-MNC-QQc cells from diabetic donors were injected into a murine wound-healing model using Balb/c nude mice. The percentage of wound closure and angio-vasculogenesis was then assessed. This study revealed vasculogenic, anti-inflammatory, and wound-healing effects of MNC-QQ therapy in both in vitro and in vivo models. This system addresses the low efficiency and efficacy of the current naïve MNC therapy for wound-healing in diabetic patients. As this technique requires a simple blood draw, isolation, and peripheral blood MNC suspension culture for only a week, it can be used as a simple and effective outpatient-based vascular and regenerative therapy for patients with diabetes mellitus.
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Affiliation(s)
- Rica Tanaka
- Division of Regenerative Therapy, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Department of Plastic and Reconstructive Surgery, Juntendo University School of Medicine, Tokyo, Japan.,Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Rie Ito-Hirano
- Division of Regenerative Therapy, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Center for Genomic and Regenerative Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Satoshi Fujimura
- Division of Regenerative Therapy, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kayo Arita
- Division of Regenerative Therapy, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hiroko Hagiwara
- Department of Plastic and Reconstructive Surgery, Juntendo University School of Medicine, Tokyo, Japan.,Center for Genomic and Regenerative Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomoya Mita
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan.,Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Takasuke Ogawa
- Department of Dermatology, Juntendo University School of Medicine, Tokyo, Japan
| | - Hirotaka Watada
- Department of Metabolism & Endocrinology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Haruchika Masuda
- Department of Basic Clinical Science, Division of Regenerative Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Takayuki Asahara
- Department of Basic Clinical Science, Division of Regenerative Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Hiroshi Mizuno
- Department of Plastic and Reconstructive Surgery, Juntendo University School of Medicine, Tokyo, Japan.,Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
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15
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Morishita S, Yasuda H, Yamawaki S, Kawaji H, Itoh M, Edahiro Y, Imai M, Kogo Y, Tsuneda S, Ohsaka A, Hayashizaki Y, Ito M, Araki M, Komatsu N. CREB3L1 overexpression as a potential diagnostic marker of Philadelphia chromosome-negative myeloproliferative neoplasms. Cancer Sci 2021; 112:884-892. [PMID: 33280191 PMCID: PMC7893984 DOI: 10.1111/cas.14763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 10/16/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/31/2022] Open
Abstract
Discrimination of Philadelphia-negative myeloproliferative neoplasms (Ph-MPNs) from reactive hypercytosis and myelofibrosis requires a constellation of testing including driver mutation analysis and bone marrow biopsies. We searched for a biomarker that can more easily distinguish Ph-MPNs from reactive hypercytosis and myelofibrosis by using RNA-seq analysis utilizing platelet-rich plasma (PRP)-derived RNAs from patients with essential thrombocythemia (ET) and reactive thrombocytosis, and CREB3L1 was found to have an extremely high impact in discriminating the two disorders. To validate and further explore the result, expression levels of CREB3L1 in PRP were quantified by reverse-transcription quantitative PCR and compared among patients with ET, other Ph-MPNs, chronic myeloid leukemia (CML), and reactive hypercytosis and myelofibrosis. A CREB3L1 expression cutoff value determined based on PRP of 18 healthy volunteers accurately discriminated 150 driver mutation-positive Ph-MPNs from other entities (71 reactive hypercytosis and myelofibrosis, 6 CML, and 18 healthy volunteers) and showed both sensitivity and specificity of 1.0000. Importantly, CREB3L1 expression levels were significantly higher in ET compared with reactive thrombocytosis (P < .0001), and polycythemia vera compared with reactive erythrocytosis (P < .0001). Pathology-affirmed triple-negative ET (TN-ET) patients were divided into a high- and low-CREB3L1-expression group, and some patients in the low-expression group achieved a spontaneous remission during the clinical course. In conclusion, CREB3L1 analysis has the potential to single-handedly discriminate driver mutation-positive Ph-MPNs from reactive hypercytosis and myelofibrosis, and also may identify a subgroup within TN-ET showing distinct clinical features including spontaneous remission.
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Affiliation(s)
- Soji Morishita
- Department of Transfusion Medicine and Stem Cell RegulationJuntendo University Graduate School of MedicineTokyoJapan
| | - Hajime Yasuda
- Department of HematologyJuntendo University Graduate School of MedicineTokyoJapan
| | - Saya Yamawaki
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation ProgramYokohamaJapan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation ProgramYokohamaJapan
| | - Yoko Edahiro
- Department of HematologyJuntendo University Graduate School of MedicineTokyoJapan
| | - Misa Imai
- Department of HematologyJuntendo University Graduate School of MedicineTokyoJapan
| | - Yasushi Kogo
- RIKEN Preventive Medicine and Diagnosis Innovation ProgramYokohamaJapan
| | - Satoshi Tsuneda
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Akimichi Ohsaka
- Department of Transfusion Medicine and Stem Cell RegulationJuntendo University Graduate School of MedicineTokyoJapan
| | | | - Masafumi Ito
- Department of PathologyJapanese Red Cross Nagoya First HospitalNagoyaJapan
| | - Marito Araki
- Department of Transfusion Medicine and Stem Cell RegulationJuntendo University Graduate School of MedicineTokyoJapan
| | - Norio Komatsu
- Department of HematologyJuntendo University Graduate School of MedicineTokyoJapan
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16
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Abstract
It is difficult to correlate the direction of mandibular canal branches (MCBs) with altered sensation in dental treatments. In contrast, calcitonin gene-related peptide (CGRP) is related to vasodilation, bone formation, and the interaction with the peripheral nervous system. Therefore, we investigated the detailed morphological characteristics of MCBs using cone-beam computed tomography (CBCT) and observation of the CGRP distribution around the MCB. The MCB measurements were evaluated using principal component analysis (PCA) to identify morphological correlations. A total of 168 sides of mandibles from 84 cadavers were analyzed in this study. Most of the MCBs were primarily in the direction of the clock model from X to XI in sagittal sections and XII to I in coronal sections of the mandible. The structure of the MCB was divided into the fine canal branch (60.4%, 223/369), partial branch (24.4%, 90/369), and no canal branch (15.2%, 56/369). PCA indicated that the measurement element with the MCB and its structures were correlated in contrast to tooth factors. Positive CGRP reactions were clearly observed in the no-canal branch group compared to other groups. These data provide useful suggestions for MCB dynamics and information for clinical dental treatment.
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Affiliation(s)
- M Takiguchi
- Department of Anatomy, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - I Sato
- Department of Anatomy, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - Z L Li
- Department of Anatomy, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - H Miyaso
- Department of Anatomy, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - S Kawata
- Department of Anatomy, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
| | - M Itoh
- Department of Anatomy, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan
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17
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Takahashi H, Nishiyori-Sueki H, Ramilowski JA, Itoh M, Carninci P. Low Quantity Single Strand CAGE (LQ-ssCAGE) Maps Regulatory Enhancers and Promoters. Methods Mol Biol 2021; 2351:67-90. [PMID: 34382184 DOI: 10.1007/978-1-0716-1597-3_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Cap Analysis of Gene Expression (CAGE) is a powerful method to identify Transcription Start Sites (TSSs) of capped RNAs while simultaneously measuring transcripts expression level. CAGE allows mapping at single nucleotide resolution at all active promoters and enhancers. Large CAGE datasets have been produced over the years from individual laboratories and consortia, including the Encyclopedia of DNA Elements (ENCODE) and Functional Annotation of the Mammalian Genome (FANTOM) consortia. These datasets constitute open resource for TSS annotations and gene expression analysis. Here, we provide an experimental protocol for the most recent CAGE method called Low Quantity (LQ) single strand (ss) CAGE "LQ-ssCAGE", which enables cost-effective profiling of low quantity RNA samples. LQ-ssCAGE is especially useful for samples derived from cells cultured in small volumes, cellular compartments such as nuclear RNAs or for samples from developmental stages. We demonstrate the reproducibility and effectiveness of the method by constructing 240 LQ-ssCAGE libraries from 50 ng of THP-1 cell extracted RNAs and discover lowly expressed novel enhancer and promoter-derived lncRNAs.
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Affiliation(s)
- Hazuki Takahashi
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan.
| | | | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan.
- Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa, Japan.
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan.
- Human Technopole, Milano, Italy.
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18
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Hanami T, Tanabe T, Hanashi T, Yamaguchi M, Nakata H, Mitani Y, Kimura Y, Soma T, Usui K, Isobe M, Ogawa T, Itoh M, Hayashizaki Y, Kondo S. Scanning single-molecule counting system for Eprobe with highly simple and effective approach. PLoS One 2020; 15:e0243319. [PMID: 33320908 PMCID: PMC7737986 DOI: 10.1371/journal.pone.0243319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023] Open
Abstract
Here, we report a rapid and ultra-sensitive detection technique for fluorescent molecules called scanning single molecular counting (SSMC). The method uses a fluorescence-based digital measurement system to count single molecules in a solution. In this technique, noise is reduced by conforming the signal shape to the intensity distribution of the excitation light via a circular scan of the confocal region. This simple technique allows the fluorescent molecules to freely diffuse into the solution through the confocal region and be counted one by one and does not require statistical analysis. Using this technique, 28 to 62 aM fluorescent dye was detected through measurement for 600 s. Furthermore, we achieved a good signal-to-noise ratio (S/N = 2326) under the condition of 100 pM target nucleic acid by only mixing a hybridization-sensitive fluorescent probe, called Eprobe, into the target oligonucleotide solution. Combination of SSMC and Eprobe provides a simple, rapid, amplification-free, and high-sensitive target nucleic acid detection system. This method is promising for future applications to detect particularly difficult to design primers for amplification as miRNAs and other short oligo nucleotide biomarkers by only hybridization with high sensitivity.
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Affiliation(s)
- Takeshi Hanami
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan
| | - Tetsuya Tanabe
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | - Takuya Hanashi
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | - Mitsushiro Yamaguchi
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | - Hidetaka Nakata
- RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
| | | | | | - Takahiro Soma
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan
| | - Kengo Usui
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan
| | | | | | - Masayoshi Itoh
- Genetic Diagnosis Technology Unit, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,RIKEN Innovation Center, Wako, Saitama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | | | - Seiji Kondo
- RIKEN Innovation Center, Wako, Saitama, Japan.,Advanced Analysis Technology Dept., Medical Technology R&D Division, Olympus Corporation, Hachioji, Tokyo, Japan
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19
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Tokumoto S, Miyata Y, Usui K, Deviatiiarov R, Ohkawa T, Kondratieva S, Shagimardanova E, Gusev O, Cornette R, Itoh M, Hayashizaki Y, Kikawada T. Development of a Tet-On Inducible Expression System for the Anhydrobiotic Cell Line, Pv11. Insects 2020; 11:E781. [PMID: 33187095 PMCID: PMC7696976 DOI: 10.3390/insects11110781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022]
Abstract
The Pv11 cell line established from an African chironomid, Polypedilum vanderplanki, is the only cell line tolerant to complete desiccation. In Pv11 cells, a constitutive expression system for Pv11 cells was previously exploited and several reporter genes were successfully expressed. Here we report the identification of an effective minimal promoter for Pv11 cells and its application to the Tet-On inducible expression system. First, using a luciferase reporter assay, we showed that a 202 bp deletion fragment derived from the constitutively active 121-promoter functions in Pv11 cells as an appropriate minimal promoter with the Tet-On inducible expression system. The AcGFP1 (Aequorea coerulescens green fluorescent protein) was also successfully expressed in Pv11 cells using the inducible system. In addition to these reporter genes, the avian myeloblastosis virus reverse transcriptase α subunit (AMV RTα), which is one of the most widely commercially available RNA-dependent DNA polymerases, was successfully expressed through the inducible expression system and its catalytic activity was verified. These results demonstrate the establishment of an inducible expression system in cells that can be preserved in the dry state and highlight a possible application to the production of large and complex proteins.
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Affiliation(s)
- Shoko Tokumoto
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan; (S.T.); (R.C.)
| | - Yugo Miyata
- Institute of Agrobiological Sciences, National Institute of Agriculture and Food Research Organization (NARO), Tsukuba 305-0851, Japan;
| | - Kengo Usui
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan; (K.U.); (T.O.)
| | - Ruslan Deviatiiarov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan 420012, Russia; (R.D.); (S.K.); (E.S.); (O.G.)
| | - Takahiro Ohkawa
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan; (K.U.); (T.O.)
| | - Sabina Kondratieva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan 420012, Russia; (R.D.); (S.K.); (E.S.); (O.G.)
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan 420012, Russia; (R.D.); (S.K.); (E.S.); (O.G.)
| | - Oleg Gusev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan 420012, Russia; (R.D.); (S.K.); (E.S.); (O.G.)
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan; (M.I.); (Y.H.)
| | - Richard Cornette
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan; (S.T.); (R.C.)
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan; (M.I.); (Y.H.)
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan; (M.I.); (Y.H.)
| | - Takahiro Kikawada
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan; (S.T.); (R.C.)
- Institute of Agrobiological Sciences, National Institute of Agriculture and Food Research Organization (NARO), Tsukuba 305-0851, Japan;
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20
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJ, Rackham OJ, Rizzu P, Martinez DFS, Sandelin A, Sanjana P, Semple CA, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest AR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJ, Shin JW, Carninci P. Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020. [DOI: 10.1101/gr.270330.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Chihara M, Asahina A, Itoh M. A novel mutation in the KCNJ8 gene encoding the Kir6.1 subunit of an ATP-sensitive potassium channel in a Japanese patient with Cantú syndrome. J Eur Acad Dermatol Venereol 2020; 34:e476-e478. [PMID: 32215968 DOI: 10.1111/jdv.16384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 03/16/2020] [Indexed: 11/27/2022]
Affiliation(s)
- M Chihara
- Department of Dermatology, The Jikei University School of Medicine, Tokyo, Japan
| | - A Asahina
- Department of Dermatology, The Jikei University School of Medicine, Tokyo, Japan
| | - M Itoh
- Department of Dermatology, The Jikei University School of Medicine, Tokyo, Japan.,Dermatology Clinic Itoiin, Shizuoka, Japan
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22
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Alam T, Agrawal S, Severin J, Young RS, Andersson R, Arner E, Hasegawa A, Lizio M, Ramilowski JA, Abugessaisa I, Ishizu Y, Noma S, Tarui H, Taylor MS, Lassmann T, Itoh M, Kasukawa T, Kawaji H, Marchionni L, Sheng G, R R Forrest A, Khachigian LM, Hayashizaki Y, Carninci P, de Hoon MJL. Comparative transcriptomics of primary cells in vertebrates. Genome Res 2020; 30:951-961. [PMID: 32718981 PMCID: PMC7397866 DOI: 10.1101/gr.255679.119] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 08/08/2019] [Accepted: 06/09/2020] [Indexed: 12/18/2022]
Abstract
Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type many genes were differentially expressed between species. Expression of genes with products involved in transcription, RNA processing, and transcriptional regulation was more likely to be conserved, while expression of genes encoding proteins involved in intercellular communication was more likely to have diverged during evolution. Conservation of expression correlated positively with the evolutionary age of genes, suggesting that divergence in expression levels of genes critical for cell function was restricted during evolution. Motif activity analysis showed that both promoters and enhancers are activated by the same transcription factors in different species. An analysis of expression levels of mature miRNAs and of primary miRNAs identified by CAGE revealed that evolutionary old miRNAs are more likely to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.
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Affiliation(s)
- Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Robert S Young
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom.,MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | | | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yuri Ishizu
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama 230-0045, Japan
| | - Shohei Noma
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Hiroshi Tarui
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama 230-0045, Japan
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Timo Lassmann
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Guojun Sheng
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto 860-0811, Japan
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Harry Perkins Institute of Medical Research, and the Centre for Medical Research, University of Western Australia, QEII Medical Centre, Perth, WA 6009, Australia
| | - Levon M Khachigian
- Vascular Biology and Translational Research, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052 Australia
| | | | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
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23
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJF, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020; 30:1060-1072. [PMID: 32718982 PMCID: PMC7397864 DOI: 10.1101/gr.254219.119] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/24/2020] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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Affiliation(s)
- Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yari Ciani
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Mickaël Mendez
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | | | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Leonie Roos
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max Delbrük Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Ivan V Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alessandro Bonetti
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Beatrice Borsari
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Christopher JF Cameron
- School of Computer Science, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden 01062, Germany.,Center for Complex Network Intelligence (CCNI) at the Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Bioengineering, Tsinghua University, Beijing 100084, China
| | - Ryan Cardenas
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Melissa Cardon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Howard Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, California 94305, USA
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich 8093, Switzerland
| | - Alexander Favorov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Alexandre Fort
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Diego Garrido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Noa Gil
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Juliette Gimenez
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome 00179, Italy
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lusy Handoko
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki Hasegawa
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Norihito Hayatsu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Peter Heutink
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Eddie L Imada
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Bogumil Kaczkowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Aditi Kanhere
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Emily Kawabata
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Tsugumi Kawashima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - S Thomas Kelly
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Miki Kojima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Anton Kratz
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Mariola Kurowska-Stolarska
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, Scotland G12 8QQ, United Kingdom
| | - Andrew Tae Jun Kwon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jeffrey Leek
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Fernando López-Redondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shiori Maeda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Vsevolod J Makeev
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Aki Minoda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hiromi Nishiyori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuhiro R Nitta
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yukihiko Noro
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ramil Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Valerio Orlando
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Denis Paquette
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Callum J C Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Patrizia Rizzu
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | | | - Albin Sandelin
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Pillay Sanjana
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Colin A M Semple
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Martin S Taylor
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Malte Thodberg
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Supat Thongjuea
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Vidisha Tripathi
- National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roberto Verardo
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ilya E Vorontsov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Chinatsu Yamamoto
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Robert S Young
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Western Australia 6009, Australia
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia 08002, Spain
| | | | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen N-5008, Norway
| | - Claudio Schneider
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy.,Department of Medicine and Consorzio Interuniversitario Biotecnologie p.zle Kolbe 1 University of Udine, Udine 33100, Italy
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
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24
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Imada EL, Sanchez DF, Collado-Torres L, Wilks C, Matam T, Dinalankara W, Stupnikov A, Lobo-Pereira F, Yip CW, Yasuzawa K, Kondo N, Itoh M, Suzuki H, Kasukawa T, Hon CC, de Hoon MJL, Shin JW, Carninci P, Jaffe AE, Leek JT, Favorov A, Franco GR, Langmead B, Marchionni L. Recounting the FANTOM CAGE-Associated Transcriptome. Genome Res 2020; 30:1073-1081. [PMID: 32079618 PMCID: PMC7397872 DOI: 10.1101/gr.254656.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 02/11/2020] [Indexed: 02/02/2023]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression across cells and tissues is key to understanding their role in determining phenotypes, including human diseases. We present here FC-R2, a comprehensive expression atlas across a broadly defined human transcriptome, inclusive of over 109,000 coding and noncoding genes, as described in the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) study. This atlas greatly extends the gene annotation used in the original recount2 resource. We demonstrate the utility of the FC-R2 atlas by reproducing key findings from published large studies and by generating new results across normal and diseased human samples. In particular, we (a) identify tissue-specific transcription profiles for distinct classes of coding and noncoding genes, (b) perform differential expression analysis across thirteen cancer types, identifying novel noncoding genes potentially involved in tumor pathogenesis and progression, and (c) confirm the prognostic value for several enhancer lncRNAs expression in cancer. Our resource is instrumental for the systematic molecular characterization of lncRNA by the FANTOM6 Consortium. In conclusion, comprised of over 70,000 samples, the FC-R2 atlas will empower other researchers to investigate functions and biological roles of both known coding genes and novel lncRNAs.
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Affiliation(s)
- Eddie Luidy Imada
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21827, USA.,Departamento de Bioqúımica e Imunologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Diego Fernando Sanchez
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21827, USA
| | | | - Christopher Wilks
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Tejasvi Matam
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21827, USA
| | - Wikum Dinalankara
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21827, USA
| | - Aleksey Stupnikov
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21827, USA
| | - Francisco Lobo-Pereira
- Departamento de Biologia General, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Chi-Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN, Preventive Medicine and Diagnostic Innovation Program, Yokohama, 351-0198, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | | | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, Maryland 21205, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Jeffrey T Leek
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Alexander Favorov
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21827, USA.,Laboratory of Systems Biology and Computational Genetics, VIGG RAS, 117971 Moscow, Russia
| | - Gloria R Franco
- Departamento de Bioqúımica e Imunologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21827, USA
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25
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Morioka MS, Kawaji H, Nishiyori-Sueki H, Murata M, Kojima-Ishiyama M, Carninci P, Itoh M. Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites. Methods Mol Biol 2020; 2120:277-301. [PMID: 32124327 DOI: 10.1007/978-1-0716-0327-7_20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 12/15/2022]
Abstract
Cap analysis of gene expression (CAGE) is an approach to identify and monitor the activity (transcription initiation frequency) of transcription start sites (TSSs) at single base-pair resolution across the genome. It has been effectively used to identify active promoter and enhancer regions in cancer cells, with potential utility to identify key factors to immunotherapy. Here, we overview a series of CAGE protocols and describe detailed experimental steps of the latest protocol based on the Illumina sequencing platform; both experimental steps (see Subheadings 3.1-3.11) and computational processing steps (see Subheadings 3.12-3.20) are described.
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Affiliation(s)
- Masaki Suimye Morioka
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Hideya Kawaji
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Yokohama, Kanagawa, Japan.,Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hiromi Nishiyori-Sueki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Mitsuyoshi Murata
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Miki Kojima-Ishiyama
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Yokohama, Kanagawa, Japan.
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26
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Proshutinsky A, Krishfield R, Toole JM, Timmermans M, Williams W, Zimmermann S, Yamamoto‐Kawai M, Armitage TWK, Dukhovskoy D, Golubeva E, Manucharyan GE, Platov G, Watanabe E, Kikuchi T, Nishino S, Itoh M, Kang S, Cho K, Tateyama K, Zhao J. Analysis of the Beaufort Gyre Freshwater Content in 2003-2018. J Geophys Res Oceans 2019; 124:9658-9689. [PMID: 32055432 PMCID: PMC7003849 DOI: 10.1029/2019jc015281] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 11/25/2019] [Accepted: 12/02/2019] [Indexed: 05/31/2023]
Abstract
Hydrographic data collected from research cruises, bottom-anchored moorings, drifting Ice-Tethered Profilers, and satellite altimetry in the Beaufort Gyre region of the Arctic Ocean document an increase of more than 6,400 km3 of liquid freshwater content from 2003 to 2018: a 40% growth relative to the climatology of the 1970s. This fresh water accumulation is shown to result from persistent anticyclonic atmospheric wind forcing (1997-2018) accompanied by sea ice melt, a wind-forced redirection of Mackenzie River discharge from predominantly eastward to westward flow, and a contribution of low salinity waters of Pacific Ocean origin via Bering Strait. Despite significant uncertainties in the different observations, this study has demonstrated the synergistic value of having multiple diverse datasets to obtain a more comprehensive understanding of Beaufort Gyre freshwater content variability. For example, Beaufort Gyre Observational System (BGOS) surveys clearly show the interannual increase in freshwater content, but without satellite or Ice-Tethered Profiler measurements, it is not possible to resolve the seasonal cycle of freshwater content, which in fact is larger than the year-to-year variability, or the more subtle interannual variations.
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Affiliation(s)
| | | | - J. M. Toole
- Woods Hole Oceanographic InstitutionWoods HoleMAUSA
| | | | - W. Williams
- Fisheries and Oceans CanadaInstitute of Ocean SciencesSidneyBritish ColumbiaCanada
| | - S. Zimmermann
- Fisheries and Oceans CanadaInstitute of Ocean SciencesSidneyBritish ColumbiaCanada
| | - M. Yamamoto‐Kawai
- Graduate School of Marine Science and TechnologyTokyo University of Marine Science and TechnologyTokyoJapan
| | - T. W. K. Armitage
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - D. Dukhovskoy
- Center for Ocean‐Atmospheric Prediction StudiesFlorida State UniversityTallahasseeFLUSA
| | - E. Golubeva
- Institute of Computational Mathematics and Mathematical GeophysicsSiberian Branch of Russian Academy of ScienceNovosibirskRussia
- Laboratory of Mathematical Modeling of Atmosphere and Hydrosphere ProcessesNovosibirsk State UniversityNovosibirskRussia
| | - G. E. Manucharyan
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - G. Platov
- Institute of Computational Mathematics and Mathematical GeophysicsSiberian Branch of Russian Academy of ScienceNovosibirskRussia
- Laboratory of Mathematical Modeling of Atmosphere and Hydrosphere ProcessesNovosibirsk State UniversityNovosibirskRussia
| | - E. Watanabe
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
| | - T. Kikuchi
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
| | - S. Nishino
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
| | - M. Itoh
- Japan Agency for Marine‐Earth Science and TechnologyYokosukaJapan
| | - S.‐H. Kang
- Korea Polar Research InstituteIncheonRepublic of Korea
| | - K.‐H. Cho
- Korea Polar Research InstituteIncheonRepublic of Korea
| | - K. Tateyama
- Kitami Institute of TechnologyKitami, HokkaidoJapan
| | - J. Zhao
- Physical Oceanography LaboratoryOcean University of China, QingdaoChina
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27
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Matsunaga H, Machida Y, Nakagawa M, Yamaguchi M, Ogawara Y, Shima Y, Yamagata K, Katsumoto T, Hattori A, Itoh M, Seki T, Nishiya Y, Nakamura K, Suzuki K, Imaoka T, Suzuki M, Sampetrean O, Saya H, Ichimura K, Kitabayashi I. Characterization of a novel BBB-permeable mutant IDH1 inhibitor, DS-1001b. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz243.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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28
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Ha TJ, Zhang PGY, Robert R, Yeung J, Swanson DJ, Mathelier A, Wasserman WW, Im S, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest ARR, Goldowitz D. Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. BMC Genomics 2019; 20:718. [PMID: 31533632 PMCID: PMC6751898 DOI: 10.1186/s12864-019-6063-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 10/02/2018] [Accepted: 08/26/2019] [Indexed: 12/11/2022] Open
Abstract
Background The work of the FANTOM5 Consortium has brought forth a new level of understanding of the regulation of gene transcription and the cellular processes involved in creating diversity of cell types. In this study, we extended the analysis of the FANTOM5 Cap Analysis of Gene Expression (CAGE) transcriptome data to focus on understanding the genetic regulators involved in mouse cerebellar development. Results We used the HeliScopeCAGE library sequencing on cerebellar samples over 8 embryonic and 4 early postnatal times. This study showcases temporal expression pattern changes during cerebellar development. Through a bioinformatics analysis that focused on transcription factors, their promoters and binding sites, we identified genes that appear as strong candidates for involvement in cerebellar development. We selected several candidate transcriptional regulators for validation experiments including qRT-PCR and shRNA transcript knockdown. We observed marked and reproducible developmental defects in Atf4, Rfx3, and Scrt2 knockdown embryos, which support the role of these genes in cerebellar development. Conclusions The successful identification of these novel gene regulators in cerebellar development demonstrates that the FANTOM5 cerebellum time series is a high-quality transcriptome database for functional investigation of gene regulatory networks in cerebellar development. Electronic supplementary material The online version of this article (10.1186/s12864-019-6063-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas J Ha
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Peter G Y Zhang
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Remi Robert
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Douglas J Swanson
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Anthony Mathelier
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0372, Oslo, Norway
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sujin Im
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Masayoshi Itoh
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Hideya Kawaji
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Timo Lassmann
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan.,Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, Western Australia, 6008, Australia
| | - Carsten O Daub
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Erik Arner
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | | | - Piero Carninci
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Alistair R R Forrest
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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29
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Itoh M, Kawagoe S, Tamai K, Nakagawa H, Asahina A, Okano H. 584 Footprint-free gene mutation correction in induced pluripotent stem cell (iPSC) derived from recessive dystrophic epidermolysis bullosa (RDEB) using CRISPR/Cas9 and piggyBac transposon system. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.07.588] [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: 10/26/2022]
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30
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Aoki T, Koseki H, Miyata H, Itoh M, Kawaji H, Takizawa K, Kawashima A, Ujiie H, Higa T, Minamimura K, Kimura T, Kasuya H, Nozaki K, Morita A, Sano H, Narumiya S. RNA sequencing analysis revealed the induction of CCL3 expression in human intracranial aneurysms. Sci Rep 2019; 9:10387. [PMID: 31316152 PMCID: PMC6637171 DOI: 10.1038/s41598-019-46886-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 12/04/2018] [Accepted: 07/08/2019] [Indexed: 11/10/2022] Open
Abstract
Intracranial aneurysm (IA) is a socially important disease as a major cause of subarachnoid hemorrhage. Recent experimental studies mainly using animal models have revealed a crucial role of macrophage-mediated chronic inflammatory responses in its pathogenesis. However, as findings from comprehensive analysis of unruptured human IAs are limited, factors regulating progression and rupture of IAs in humans remain unclear. Using surgically dissected human unruptured IA lesions and control arterial walls, gene expression profiles were obtained by RNA sequence analysis. RNA sequencing analysis was done with read count about 60~100 million which yielded 6~10 billion bases per sample. 79 over-expressed and 329 under-expressed genes in IA lesions were identified. Through Gene Ontology analysis, ‘chemokine activity’, ‘defense response’ and ‘extracellular region’ were picked up as over-represented terms which included CCL3 and CCL4 in common. Among these genes, quantitative RT-PCR analysis using another set of samples reproduced the above result. Finally, increase of CCL3 protein compared with that in control arterial walls was clarified in IA lesions. Findings of the present study again highlight importance of macrophage recruitment via CCL3 in the pathogenesis of IA progression.
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Affiliation(s)
- Tomohiro Aoki
- Innovation Center for Immunoregulation Technologies and Drugs (AK project), Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan. .,Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Osaka, 565-8565, Japan. .,Core Research for Evolutional Science and Technology (CREST) from Japan Agency for Medical Research and Development (AMED), Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan.
| | - Hirokazu Koseki
- Innovation Center for Immunoregulation Technologies and Drugs (AK project), Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan.,Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Osaka, 565-8565, Japan.,Core Research for Evolutional Science and Technology (CREST) from Japan Agency for Medical Research and Development (AMED), Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan.,Department of Neurosurgery, Tokyo Women's Medical University Medical Center East, Tokyo, 116-8567, Japan
| | - Haruka Miyata
- Innovation Center for Immunoregulation Technologies and Drugs (AK project), Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan.,Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Osaka, 565-8565, Japan.,Core Research for Evolutional Science and Technology (CREST) from Japan Agency for Medical Research and Development (AMED), Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan.,Department of Neurosurgery, Shiga University of Medical Science, Shiga, 520-2192, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Innovation Program, Saitama, 351-0198, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Innovation Program, Saitama, 351-0198, Japan
| | - Katsumi Takizawa
- Department of Neurosurgery, Japanese Red Cross Asahikawa Hospital, Hokkaido, 070-8530, Japan
| | - Akitsugu Kawashima
- Department of Neurosurgery, Tokyo Women's Medical University Yachiyo Medical Center, Chiba, 276-8524, Japan
| | - Hiroshi Ujiie
- Department of Neurosurgery, Tokyo Rosai Hospital, Tokyo, 143-0013, Japan
| | - Takashi Higa
- Department of Neurosurgery, Tokyo Rosai Hospital, Tokyo, 143-0013, Japan
| | - Kenzo Minamimura
- Department of Neurosurgery, Shinkawahashi Hospital, Kanagawa, 210-0013, Japan
| | - Toshikazu Kimura
- Department of Neurosurgery, NTT Medical Center Tokyo, Tokyo, 141-8625, Japan.,Department of Neurosurgery, Japanese Red Cross Medical Center, Tokyo, 150-8935, Japan
| | - Hidetoshi Kasuya
- Department of Neurosurgery, Tokyo Women's Medical University Medical Center East, Tokyo, 116-8567, Japan
| | - Kazuhiko Nozaki
- Department of Neurosurgery, Shiga University of Medical Science, Shiga, 520-2192, Japan
| | - Akio Morita
- Department of Neurosurgery, NTT Medical Center Tokyo, Tokyo, 141-8625, Japan.,Department of Neurological Surgery, Nippon Medical School, Tokyo, 113-8603, Japan
| | - Hirotoshi Sano
- Department of Neurosurgery, Shinkawahashi Hospital, Kanagawa, 210-0013, Japan
| | - Shuh Narumiya
- Innovation Center for Immunoregulation Technologies and Drugs (AK project), Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
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31
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Sakaue S, Hirata J, Maeda Y, Kawakami E, Nii T, Kishikawa T, Ishigaki K, Terao C, Suzuki K, Akiyama M, Suita N, Masuda T, Ogawa K, Yamamoto K, Saeki Y, Matsushita M, Yoshimura M, Matsuoka H, Ikari K, Taniguchi A, Yamanaka H, Kawaji H, Lassmann T, Itoh M, Yoshitomi H, Ito H, Ohmura K, R Forrest AR, Hayashizaki Y, Carninci P, Kumanogoh A, Kamatani Y, de Hoon M, Yamamoto K, Okada Y. Integration of genetics and miRNA-target gene network identified disease biology implicated in tissue specificity. Nucleic Acids Res 2019; 46:11898-11909. [PMID: 30407537 PMCID: PMC6294505 DOI: 10.1093/nar/gky1066] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) modulate the post-transcriptional regulation of target genes and are related to biology of complex human traits, but genetic landscape of miRNAs remains largely unknown. Given the strikingly tissue-specific miRNA expression profiles, we here expand a previous method to quantitatively evaluate enrichment of genome-wide association study (GWAS) signals on miRNA-target gene networks (MIGWAS) to further estimate tissue-specific enrichment. Our approach integrates tissue-specific expression profiles of miRNAs (∼1800 miRNAs in 179 cells) with GWAS to test whether polygenic signals enrich in miRNA-target gene networks and whether they fall within specific tissues. We applied MIGWAS to 49 GWASs (nTotal = 3 520 246), and successfully identified biologically relevant tissues. Further, MIGWAS could point miRNAs as candidate biomarkers of the trait. As an illustrative example, we performed differentially expressed miRNA analysis between rheumatoid arthritis (RA) patients and healthy controls (n = 63). We identified novel biomarker miRNAs (e.g. hsa-miR-762) by integrating differentially expressed miRNAs with MIGWAS results for RA, as well as novel associated loci with significant genetic risk (rs56656810 at MIR762 at 16q11; n = 91 482, P = 3.6 × 10-8). Our result highlighted that miRNA-target gene network contributes to human disease genetics in a cell type-specific manner, which could yield an efficient screening of miRNAs as promising biomarkers.
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Affiliation(s)
- Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8655, Japan
| | - Jun Hirata
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Pharmaceutical Discovery Research Laboratories, TEIJIN PHARMA LIMITED, Hino 191-8512, Japan
| | - Yuichi Maeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.,Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology, Tokyo 100-0004, Japan
| | - Eiryo Kawakami
- Healthcare and Medical Data Driven AI based Predictive Reasoning Development Unit, Medical Sciences Innovation Hub Program (MIH), RIKEN, Yokohama 230-0045, Japan.,Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.,Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology, Tokyo 100-0004, Japan
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Department of Otorhinolaryngology - Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Chikashi Terao
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Clinical Research Center, Shizuoka General Hospital, Shizuoka 420-0881, Japan.,The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.,Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Ken Suzuki
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Naomasa Suita
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Discovery Technology Research Laboratories, Tsukuba Research Institute, Ono Pharmaceutical Co., Ltd., Tsukuba 300-4247, Japan
| | - Tatsuo Masuda
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Department of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kotaro Ogawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Department of Pediatrics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Yukihiko Saeki
- Department of Clinical Research, National Hospital Organization (NHO) Osaka Minami Medical Center, Japan
| | - Masato Matsushita
- Department of Rheumatology and Allergology, Saiseikai Senri Hospital, Suita 565-0862, Japan.,Department of Rheumatology and Allergology, National Hospital Organization (NHO) Osaka Minami Medical Center, Japan
| | - Maiko Yoshimura
- Department of Rheumatology and Allergology, National Hospital Organization (NHO) Osaka Minami Medical Center, Japan
| | - Hidetoshi Matsuoka
- Department of Rheumatology and Allergology, National Hospital Organization (NHO) Osaka Minami Medical Center, Japan
| | - Katsunori Ikari
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo 162-0054, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 162-0054, Japan
| | - Atsuo Taniguchi
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo 162-0054, Japan
| | - Hisashi Yamanaka
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo 162-0054, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan.,Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Timo Lassmann
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,Telethon Kids Institute, the University of Western Australia, Western Australia 6008, Australia
| | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Hiroyuki Yoshitomi
- Laboratory of Tissue Regeneration, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.,Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Hiromu Ito
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Alistair R R Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Western Australia 6009, Australia
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045 Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Michiel de Hoon
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,Laboratory for Applied Computational Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045 Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
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Marryanna L, Noguchi S, Kosugi Y, Niiyama K, Itoh M, Sato T, Takanashi S, Siti-Aisah S, Abd-Rahman K. SPATIAL DISTRIBUTION OF SOIL MOISTURE AND ITS INFLUENCE ON STAND STRUCTURE IN A LOWLAND DIPTEROCARP FOREST IN PENINSULAR MALAYSIA. JTFS 2019; 31:135-150. [DOI: 10.26525/jtfs2019.31.2.135150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Ohashi F, Miyagawa S, Yasuda S, Miura T, Kuroda T, Itoh M, Kawaji H, Ito E, Yoshida S, Saito A, Sameshima T, Kawai J, Sawa Y, Sato Y. CXCL4/PF4 is a predictive biomarker of cardiac differentiation potential of human induced pluripotent stem cells. Sci Rep 2019; 9:4638. [PMID: 30874579 PMCID: PMC6420577 DOI: 10.1038/s41598-019-40915-w] [Citation(s) in RCA: 8] [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] [Received: 08/31/2018] [Accepted: 02/21/2019] [Indexed: 12/23/2022] Open
Abstract
Selection of human induced pluripotent stem cell (hiPSC) lines with high cardiac differentiation potential is important for regenerative therapy and drug screening. We aimed to identify biomarkers for predicting cardiac differentiation potential of hiPSC lines by comparing the gene expression profiles of six undifferentiated hiPSC lines with different cardiac differentiation capabilities. We used three platforms of gene expression analysis, namely, cap analysis of gene expression (CAGE), mRNA array, and microRNA array to efficiently screen biomarkers related to cardiac differentiation of hiPSCs. Statistical analysis revealed candidate biomarker genes with significant correlation between the gene expression levels in the undifferentiated hiPSCs and their cardiac differentiation potential. Of the candidate genes, PF4 was validated as a biomarker expressed in undifferentiated hiPSCs with high potential for cardiac differentiation in 13 additional hiPSC lines. Our observations suggest that PF4 may be a useful biomarker for selecting hiPSC lines appropriate for the generation of cardiomyocytes.
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Affiliation(s)
- Fumiya Ohashi
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan.,Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan.,Department of Cellular & Gene Therapy Products, Osaka University Graduate School of Pharmaceutical Sciences, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Terumo Corporation, 1500 Inokuchi, Nakai-machi, Ashigarakami-gun, Kanagawa, 259-0151, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Satoshi Yasuda
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takumi Miura
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takuya Kuroda
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Masayoshi Itoh
- Preventive Medicine and Diagnosis Innovation Program, RIKEN Center, 1-7-22, Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hideya Kawaji
- Preventive Medicine and Diagnosis Innovation Program, RIKEN Center, 1-7-22, Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Emiko Ito
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Shohei Yoshida
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Atsuhiro Saito
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Tadashi Sameshima
- Terumo Corporation, 1500 Inokuchi, Nakai-machi, Ashigarakami-gun, Kanagawa, 259-0151, Japan
| | - Jun Kawai
- Preventive Medicine and Diagnosis Innovation Program, RIKEN Center, 1-7-22, Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshiki Sawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Yoji Sato
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan. .,Department of Cellular & Gene Therapy Products, Osaka University Graduate School of Pharmaceutical Sciences, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Department of Quality Assurance Science for Pharmaceuticals, Nagoya City University Graduate School of Pharmaceutical Sciences, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan. .,Department of Translational Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka, 812-8582, Japan. .,LiSE Laboratory, Kanagawa Institute of Industrial Science and Technology, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-0821, Japan.
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Zucchelli S, Fedele S, Vatta P, Calligaris R, Heutink P, Rizzu P, Itoh M, Persichetti F, Santoro C, Kawaji H, Lassmann T, Hayashizaki Y, Carninci P, Forrest ARR, Gustincich S. Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases. Mol Neurobiol 2019; 56:5392-5415. [PMID: 30610612 PMCID: PMC6614138 DOI: 10.1007/s12035-018-1465-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 10/03/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022]
Abstract
Natural antisense transcripts are common features of mammalian genes providing additional regulatory layers of gene expression. A comprehensive description of antisense transcription in loci associated to familial neurodegenerative diseases may identify key players in gene regulation and provide tools for manipulating gene expression. We take advantage of the FANTOM5 sequencing datasets that represent the largest collection to date of genome-wide promoter usage in almost 2000 human samples. Transcription start sites (TSSs) are mapped at high resolution by the use of a modified protocol of cap analysis of gene expression (CAGE) for high-throughput single molecule next-generation sequencing with Helicos (hCAGE). Here we present the analysis of antisense transcription at 17 loci associated to hereditary Alzheimer’s disease, Frontotemporal Dementia, Parkinson’s disease, Amyotrophic Lateral Sclerosis, and Huntington’s disease. We focused our analysis on libraries derived from brain tissues and primary cells. We also screened libraries from total blood and blood cell populations in the quest for peripheral biomarkers of neurodegenerative diseases. We identified 63 robust promoters in antisense orientation to genes associated to familial neurodegeneration. When applying a less stringent cutoff, this number increases to over 400. A subset of these promoters represents alternative TSSs for 24 FANTOM5 annotated long noncoding RNA (lncRNA) genes, in antisense orientation to 13 of the loci analyzed here, while the remaining contribute to the expression of additional transcript variants. Intersection with GWAS studies, sample ontology, and dynamic expression reveals association to specific genetic traits as well as cell and tissue types, not limited to neurodegenerative diseases. Antisense transcription was validated for a subset of genes, including those encoding for Microtubule-Associated Protein Tau, α-synuclein, Parkinsonism-associated deglycase DJ-1, and Leucin-Rich Repeat Kinase 2. This work provides evidence for the existence of additional regulatory mechanisms of the expression of neurodegenerative disease-causing genes by previously not-annotated and/or not-validated antisense long noncoding RNAs.
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Affiliation(s)
- Silvia Zucchelli
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | | | - Paolo Vatta
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Raffaella Calligaris
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Medical, Surgical and Health Sciences, Clinical Neurology Unit, Cattinara University Hospital, Trieste, Italy
| | - Peter Heutink
- Section Medical Genomics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
- Genome Biology of Neurodegenerative Diseases, Deutsches Zentrum fur Neurodegenerative Erkrankungen (DZNE), Standort, Tübingen, Germany
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
| | - Patrizia Rizzu
- Section Medical Genomics, Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
- Applied Genomics for Neurodegenerative Diseases, Deutsches Zentrum fur Neurodegenerative Erkrankungen (DZNE), Standort, Tübingen, Germany
| | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wakō, Japan
| | - Francesca Persichetti
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Claudio Santoro
- Department of Health Sciences and Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wakō, Japan
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Timo Lassmann
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, WA 6008 Australia
- Laboratory for Applied Computational Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wakō, Japan
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Alistair R. R. Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Omics Science Center, Yokohama, Japan
- Laboratory for Genome Information Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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Uchiyama A, Harada K, Sakamoto K, Dammalapati U, Inoue T, Itoh M, Ito S, Kawamura H, Tanaka KS, Yoshioka R, Sakemi Y. Effective multiple sideband generation using an electro-optic modulator for a multiple isotope magneto-optical trap. Rev Sci Instrum 2018; 89:123111. [PMID: 30599547 DOI: 10.1063/1.5054748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/18/2018] [Indexed: 06/09/2023]
Abstract
Herein, we report an effective method for the generation of radio-frequency (RF) sidebands in an electro-optic modulator for the simultaneous magneto-optical trapping of two isotopes. This is achieved by switching the RF signals alternately, which suppresses the generation of unwanted frequency signals and improves the laser power per sideband. The generated sidebands are successfully applied to a dual-rubidium-isotope magneto-optical trap (MOT), which results in an increased number of trapped atoms. This simple, flexible, and robust technique can be implemented in experiments that require a large number of atoms in multiple-isotope MOTs and for various applications.
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Affiliation(s)
- A Uchiyama
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - K Harada
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - K Sakamoto
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - U Dammalapati
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - T Inoue
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - M Itoh
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - S Ito
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - H Kawamura
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - K S Tanaka
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - R Yoshioka
- Cyclotron and Radioisotope Center (CYRIC), Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Y Sakemi
- Center for Nuclear Study (CNS), The University of Tokyo, Wako, Saitama 351-0198, Japan
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37
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Alhendi AMN, Patrikakis M, Daub CO, Kawaji H, Itoh M, de Hoon M, Carninci P, Hayashizaki Y, Arner E, Khachigian LM. Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β. Sci Rep 2018; 8:13164. [PMID: 30177712 PMCID: PMC6120868 DOI: 10.1038/s41598-018-30702-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/03/2018] [Indexed: 01/22/2023] Open
Abstract
Smooth muscle cells (SMC) in blood vessels are normally growth quiescent and transcriptionally inactive. Our objective was to understand promoter usage and dynamics in SMC acutely exposed to a prototypic growth factor or pro-inflammatory cytokine. Using cap analysis gene expression (FANTOM5 project) we report differences in promoter dynamics for immediate-early genes (IEG) and other genes when SMC are exposed to fibroblast growth factor-2 or interleukin-1β. Of the 1871 promoters responding to FGF2 or IL-1β considerably more responded to FGF2 (68.4%) than IL-1β (18.5%) and 13.2% responded to both. Expression clustering reveals sets of genes induced, repressed or unchanged. Among IEG responding rapidly to FGF2 or IL-1β were FOS, FOSB and EGR-1, which mediates human SMC migration. Motif activity response analysis (MARA) indicates most transcription factor binding motifs in response to FGF2 were associated with a sharp induction at 1 h, whereas in response to IL-1β, most motifs were associated with a biphasic change peaking generally later. MARA revealed motifs for FOS_FOS{B,L1}_JUN{B,D} and EGR-1..3 in the cluster peaking 1 h after FGF2 exposure whereas these motifs were in clusters peaking 1 h or later in response to IL-1β. Our findings interrogating CAGE data demonstrate important differences in promoter usage and dynamics in SMC exposed to FGF2 or IL-1β.
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Affiliation(s)
- Ahmad M N Alhendi
- Vascular Biology and Translational Research, School of Medical Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Margaret Patrikakis
- Vascular Biology and Translational Research, School of Medical Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Carsten O Daub
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies) (CLST DGT), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biosciences and Nutrition and Science for Life Laboratory, Karolinska Institutet, SE-141 86, Stockholm, Sweden
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies) (CLST DGT), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies) (CLST DGT), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Michiel de Hoon
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies) (CLST DGT), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, 230-0045, Japan
- Laboratory for Applied Computational Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies) (CLST DGT), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, 230-0045, Japan
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Erik Arner
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies) (CLST DGT), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama, 230-0045, Japan
- Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Levon M Khachigian
- Vascular Biology and Translational Research, School of Medical Sciences, University of New South Wales, Sydney, 2052, Australia.
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Vacca A, Itoh M, Kawaji H, Arner E, Lassmann T, Daub CO, Carninci P, Forrest ARR, Hayashizaki Y, Aitken S, Semple CA. Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli. Open Biol 2018; 8:180011. [PMID: 30089658 PMCID: PMC6119861 DOI: 10.1098/rsob.180011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 01/22/2018] [Accepted: 07/04/2018] [Indexed: 01/15/2023] Open
Abstract
The promoters of immediate early genes (IEGs) are rapidly activated in response to an external stimulus. These genes, also known as primary response genes, have been identified in a range of cell types, under diverse extracellular signals and using varying experimental protocols. Whereas genomic dissection on a case-by-case basis has not resulted in a comprehensive catalogue of IEGs, a rigorous meta-analysis of eight genome-wide FANTOM5 CAGE (cap analysis of gene expression) time course datasets reveals successive waves of promoter activation in IEGs, recapitulating known relationships between cell types and stimuli: we obtain a set of 57 (42 protein-coding) candidate IEGs possessing promoters that consistently drive a rapid but transient increase in expression over time. These genes show significant enrichment for known IEGs reported previously, pathways associated with the immediate early response, and include a number of non-coding RNAs with roles in proliferation and differentiation. Surprisingly, we also find strong conservation of the ordering of activation for these genes, such that 77 pairwise promoter activation orderings are conserved. Using the leverage of comprehensive CAGE time series data across cell types, we also document the extensive alternative promoter usage by such genes, which is likely to have been a barrier to their discovery until now. The common activation ordering of the core set of early-responding genes we identify may indicate conserved underlying regulatory mechanisms. By contrast, the considerably larger number of transiently activated genes that are specific to each cell type and stimulus illustrates the breadth of the primary response.
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Affiliation(s)
- Annalaura Vacca
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2F Main Research Building, 2-1 Hirosawa, Wako, Japan
| | - Hideya Kawaji
- RIKEN Advanced Center for Computing and Communication, RIKEN Yokohama Campus, Yokohama 230-0045, Japan
| | - Erik Arner
- RIKEN Center for Life Sciences Technologies, RIKEN Yokohama Campus, Yokohama 230-0045, Japan
| | - Timo Lassmann
- Telethon Kids Institute, The University of Western Australia, Roberts Road, Subiaco, Western Australia, Australia
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Piero Carninci
- RIKEN Center for Life Sciences Technologies, RIKEN Yokohama Campus, Yokohama 230-0045, Japan
| | - Alistair R R Forrest
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, Western Australia 6009, Australia
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2F Main Research Building, 2-1 Hirosawa, Wako, Japan
| | - Stuart Aitken
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Colin A Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
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Imamura K, Shimane A, Matsuyama S, Itoh M, Yokoi K, Taniguchi Y, Yasaka Y, Kawai H. P5782Very long-term outcome of arrhythmogenic right ventricular cardiomyopathy patients with or without an implantable cardioverter defibrillator. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy566.p5782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- K Imamura
- Himeji Cardiovascular Center, Himeji, Japan
| | - A Shimane
- Himeji Cardiovascular Center, Himeji, Japan
| | | | - M Itoh
- Himeji Cardiovascular Center, Himeji, Japan
| | - K Yokoi
- Himeji Cardiovascular Center, Himeji, Japan
| | | | - Y Yasaka
- Himeji Cardiovascular Center, Himeji, Japan
| | - H Kawai
- Himeji Cardiovascular Center, Himeji, Japan
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40
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Nakamura K, Kigure K, Kitahara Y, Rokukawa S, Itoh M, Ito I, Kagami I, Nakao K, Itoga S. An electrical scalpel conization versus shimodaira-taniguchi conization procedure for cervical intraepithelial neoplasia. Gynecol Oncol 2018. [DOI: 10.1016/j.ygyno.2018.04.195] [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: 11/17/2022]
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41
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Kawakami T, Itoh M, Jimbow K. 1269 Approach for the derivation of melanocytes from induced pluripotent stem (iPS) cells. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.1285] [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: 10/17/2022]
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42
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Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, Itoh M, Kondo N, Lassmann T, Kawai J, Mole D, Bajic VB, Heutink P, Rehli M, Kawaji H, Sandelin A, Suzuki H, Satsangi J, Wells CA, Hacohen N, Freeman TC, Hayashizaki Y, Carninci P, Forrest ARR, Hume DA. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS Comput Biol 2018; 14:e1005934. [PMID: 29494619 PMCID: PMC5849332 DOI: 10.1371/journal.pcbi.1005934] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 03/13/2018] [Accepted: 12/18/2017] [Indexed: 12/13/2022] Open
Abstract
Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn's disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits.
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Affiliation(s)
- J. Kenneth Baillie
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, United Kingdom
| | - Andrew Bretherick
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Christopher S. Haley
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sara Clohisey
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Alan Gray
- Edinburgh Parallel Computing Centre, The University of Edinburgh, Edinburgh, United Kingdom
| | - Lucile P. A. Neyton
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Jeffrey Barrett
- Statistical Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Eli A. Stahl
- Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Albert Tenesa
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - J. Ben Brown
- Department of Statistics, University of California, Berkeley, United States of America
| | - Geoffrey J. Faulkner
- Mater Research Institute, University of Queensland, University of Queensland, Brisbane, Australia
| | - Marina Lizio
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Ulf Schaefer
- Department for Infectious Disease Informatics, Public Health England, Colindale, United Kingdom
| | - Carsten Daub
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Masayoshi Itoh
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Naoto Kondo
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Timo Lassmann
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Jun Kawai
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - IIBDGC Consortium
- Harry Perkins Institute of Medical Research, and the Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, Perth, Western Australia, Australia
| | - Damian Mole
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center, Thuwal, Kingdom of Saudi Arabia
| | - Peter Heutink
- German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Michael Rehli
- Dept. Hematology, University Hospital Regensburg, Regensburg, Germany
| | - Hideya Kawaji
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Harukazu Suzuki
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Jack Satsangi
- Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Christine A. Wells
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Brisbane Australia
| | - Nir Hacohen
- Broad Institute of Harvard and MIT, Cambridge, United States of America
| | - Thomas C. Freeman
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Piero Carninci
- RIKEN Omics Science Center, Yokohama, Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Alistair R. R. Forrest
- Harry Perkins Institute of Medical Research, and the Centre for Medical Research, University of Western Australia, QEII Medical Centre, Nedlands, Perth, Western Australia, Australia
| | - David A. Hume
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Mater Research Institute, University of Queensland, University of Queensland, Brisbane, Australia
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43
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Zhang P, Dimont E, Ha T, Swanson DJ, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest ARR, Hide W, Goldowitz D. Correction to: Relatively frequent switching of transcription start sites during cerebellar development. BMC Genomics 2018; 19:39. [PMID: 29325522 PMCID: PMC5763542 DOI: 10.1186/s12864-017-4291-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Peter Zhang
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Emmanuel Dimont
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.,Harvard Stem Cell Institute, 1350 Massachusetts Ave, Cambridge, MA, 02138, USA
| | - Thomas Ha
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Douglas J Swanson
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Timo Lassmann
- Division of Genomic Technologies, RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan.,Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, WA, 6008, Australia
| | - Carsten O Daub
- Division of Genomic Technologies, RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Erik Arner
- Division of Genomic Technologies, RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | | | - Piero Carninci
- Division of Genomic Technologies, RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Yoshihide Hayashizaki
- Division of Genomic Technologies, RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Alistair R R Forrest
- Division of Genomic Technologies, RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Winston Hide
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.,Harvard Stem Cell Institute, 1350 Massachusetts Ave, Cambridge, MA, 02138, USA.,Department of Neuroscience, Sheffield Institute of Translational Neuroscience, University of Sheffield, Room B37 385a Glossop Road, Sheffield, South Yorkshire, S10 2HQ, UK
| | - Dan Goldowitz
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
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44
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Yoshihara M, Hara S, Tsujikawa M, Kawasaki S, Hayashizaki Y, Itoh M, Kawaji H, Nishida K. Restricted Presence of POU6F2 in Human Corneal Endothelial Cells Uncovered by Extension of the Promoter-level Expression Atlas. EBioMedicine 2017; 25:175-186. [PMID: 29113774 PMCID: PMC5704063 DOI: 10.1016/j.ebiom.2017.10.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 09/11/2017] [Revised: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 12/13/2022] Open
Abstract
Corneal endothelial cells (CECs) are essential for maintaining the clarity of the cornea. Because CECs have limited proliferative ability, interest is growing in their potentially therapeutic regeneration from pluripotent stem cells. However, the molecular mechanisms of human CEC differentiation remain largely unknown. To determine the key regulators of CEC characteristics, here we generated a comprehensive promoter-level expression profile of human CECs, using cap analysis of gene expression (CAGE) with a single molecule sequencer. Integration with the FANTOM5 promoter-level expression atlas, which includes transcriptome profiles of various human tissues and cells, enabled us to identify 45 promoters at 28 gene loci that are specifically expressed in CECs. We further discovered that the expression of transcription factor POU class 6 homeobox 2 (POU6F2) is restricted to CECs, and upregulated during human CEC differentiation, suggesting that POU6F2 is pivotal to terminal differentiation of CECs. These CEC-specific promoters would be useful for the assessment of fully differentiated CECs derived from pluripotent stem cells. These findings promote the development of corneal regenerative medicine. We comprehensively profiled promoter-level expression of human corneal endothelial cells. Integrative transcriptome analysis identified 28 corneal endothelial cell-specific marker genes. POU6F2 expression is restricted to corneal endothelial cells, and upregulated during differentiation.
Corneal endothelial cells (CECs) are essential for maintaining corneal transparency. Owing to the high prevalence of corneal endothelial disorders, CECs are important targets in regenerative medicine. However, it has been difficult to evaluate the final CEC products owing to the lack of appropriate CEC-specific markers. In this study, we identified 28 CEC-specific marker genes by integrative transcriptome analysis. One gene of particular interest, POU6F2, is expressed almost exclusively in CECs, and upregulated during differentiation. These markers would be useful for the assessment of CECs derived from pluripotent stem cells, and this study will facilitate the translation of corneal regenerative medicine.
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Affiliation(s)
- Masahito Yoshihara
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Susumu Hara
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; Department of Stem Cells and Applied Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Motokazu Tsujikawa
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; Department of Visual Regenerative Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Satoshi Kawasaki
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; Department of Ocular Immunology and Regenerative Medicine, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan; Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Kanagawa 230-0045, Japan.
| | - Kohji Nishida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan.
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45
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Francescatto M, Lizio M, Philippens I, Pardo LM, Bontrop R, Sakai M, Watanabe S, Itoh M, Hasegawa A, Lassmann T, Severin J, Harshbarger J, Abugessaisa I, Kasukawa T, Carninci P, Hayashizaki Y, Forrest ARR, Kawaji H, Rizzu P, Heutink P. Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system. Sci Data 2017; 4:170163. [PMID: 29087374 PMCID: PMC5663209 DOI: 10.1038/sdata.2017.163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 12/06/2016] [Accepted: 08/29/2017] [Indexed: 01/10/2023] Open
Abstract
Rhesus macaque was the second non-human primate whose genome has been fully
sequenced and is one of the most used model organisms to study human biology and
disease, thanks to the close evolutionary relationship between the two species.
But compared to human, where several previously unknown RNAs have been
uncovered, the macaque transcriptome is less studied. Publicly available RNA
expression resources for macaque are limited, even for brain, which is highly
relevant to study human cognitive abilities. In an effort to complement those
resources, FANTOM5 profiled 15 distinct anatomical regions of the aged macaque
central nervous system using Cap Analysis of Gene Expression, a high-resolution,
annotation-independent technology that allows monitoring of transcription
initiation events with high accuracy. We identified 25,869 CAGE peaks,
representing bona fide promoters. For each peak we provide detailed annotation,
expanding the landscape of ‘known’ macaque genes, and we show
concrete examples on how to use the resulting data. We believe this data
represents a useful resource to understand the central nervous system in
macaque.
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Affiliation(s)
- Margherita Francescatto
- Italian Institute of Technology, Department of Neuroscience and Brain Technologies, Via Morego 30, Genova 16163, Italy
| | - Marina Lizio
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Ingrid Philippens
- Biomedical Primate Research Centre, Postbox 3306, Rijswijk 2280 GH, The Netherlands
| | | | - Ronald Bontrop
- Biomedical Primate Research Centre, Postbox 3306, Rijswijk 2280 GH, The Netherlands
| | - Mizuho Sakai
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Shoko Watanabe
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Timo Lassmann
- RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Western Australia 6008, Australia
| | - Jessica Severin
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,Harry Perkins Institute of Medical Research, 6 Verdun St, Nedlands, Western Australia 6009, Australia
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Advanced Center for Computing and Communication, Preventive Medicine and Applied Genomics Unit, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases, Otfried-Müller Straße 23, Tübingen 72076, Germany
| | - Peter Heutink
- German Center for Neurodegenerative Diseases, Otfried-Müller Straße 23, Tübingen 72076, Germany
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Yoshida E, Terao Y, Hayashi N, Mogushi K, Arakawa A, Tanaka Y, Ito Y, Ohmiya H, Hayashizaki Y, Takeda S, Itoh M, Kawaji H. Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis. Sci Rep 2017; 7:14160. [PMID: 29074988 PMCID: PMC5658375 DOI: 10.1038/s41598-017-14418-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 03/14/2017] [Accepted: 10/11/2017] [Indexed: 12/21/2022] Open
Abstract
For endometrial cancer patients, lymphadenectomy is recommended to exclude rarely metastasized cancer cells. This procedure is performed even in patients with low risk of recurrence despite the risk of complications such as lymphedema. A method to accurately identify cases with no lymph node metastases (LN-) before lymphadenectomy is therefore highly required. We approached this clinical problem by examining primary lesions of endometrial cancers with CAGE (Cap Analysis Gene Expression), which quantifies promoter-level expression across the genome. Fourteen profiles delineated distinct transcriptional networks between LN + and LN- cases, within those classified as having the low or intermediate risk of recurrence. Subsequent quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses of 115 primary tumors showed SEMA3D mRNA and TACC2 isoforms expressed through a novel promoter as promising biomarkers with high accuracy (area under the receiver operating characteristic curve, 0.929) when used in combination. Our high-resolution transcriptome provided evidence of distinct molecular profiles underlying LN + /LN- status in endometrial cancers, raising the possibility of preoperative diagnosis to reduce unnecessary operations in patients with minimum recurrence risk.
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Affiliation(s)
- Emiko Yoshida
- Department of Obstetrics & Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Yasuhisa Terao
- Department of Obstetrics & Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan.
| | - Noriko Hayashi
- Department of Obstetrics & Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Kaoru Mogushi
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Atsushi Arakawa
- Department of Human Pathology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Yuji Tanaka
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan
| | - Yosuke Ito
- Department of Obstetrics & Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
- Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan
| | - Hiroko Ohmiya
- Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan
| | | | - Satoru Takeda
- Department of Obstetrics & Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
- Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
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Kiso M, Yabe S, Akimoto N, Sato T, Hayashi N, Itoh M, Nakagawa H, Okochi H. 289 Immortalization of primary human dermal papilla cells by Bmi-1 and TERT. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.287] [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: 11/30/2022]
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48
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Nakagawa K, Ueda M, Itoh M, Hayakawa-Ogura M, Ana T, Islam S, Nakagawa T. Improvement of memory impairment by dietary quercetin supplementation through suppressing ATF4 expression in a murine model of early-stage Alzheimer’s disease with obesity and diabetes. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.2156] [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: 11/29/2022]
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Lizio M, Deviatiiarov R, Nagai H, Galan L, Arner E, Itoh M, Lassmann T, Kasukawa T, Hasegawa A, Ros MA, Hayashizaki Y, Carninci P, Forrest ARR, Kawaji H, Gusev O, Sheng G. Systematic analysis of transcription start sites in avian development. PLoS Biol 2017; 15:e2002887. [PMID: 28873399 PMCID: PMC5600399 DOI: 10.1371/journal.pbio.2002887] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 05/08/2017] [Revised: 09/15/2017] [Accepted: 08/18/2017] [Indexed: 01/07/2023] Open
Abstract
Cap Analysis of Gene Expression (CAGE) in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs) and genome-wide capture of promoter activities in differentiated and steady state cell populations. Much less is known about whether TSS profiling can characterize diverse and non-steady state cell populations, such as the approximately 400 transitory and heterogeneous cell types that arise during ontogeny of vertebrate animals. To gain such insight, we used the chick model and performed CAGE-based TSS analysis on embryonic samples covering the full 3-week developmental period. In total, 31,863 robust TSS peaks (>1 tag per million [TPM]) were mapped to the latest chicken genome assembly, of which 34% to 46% were active in any given developmental stage. ZENBU, a web-based, open-source platform, was used for interactive data exploration. TSSs of genes critical for lineage differentiation could be precisely mapped and their activities tracked throughout development, suggesting that non-steady state and heterogeneous cell populations are amenable to CAGE-based transcriptional analysis. Our study also uncovered a large set of extremely stable housekeeping TSSs and many novel stage-specific ones. We furthermore demonstrated that TSS mapping could expedite motif-based promoter analysis for regulatory modules associated with stage-specific and housekeeping genes. Finally, using Brachyury as an example, we provide evidence that precise TSS mapping in combination with Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-on technology enables us, for the first time, to efficiently target endogenous avian genes for transcriptional activation. Taken together, our results represent the first report of genome-wide TSS mapping in birds and the first systematic developmental TSS analysis in any amniote species (birds and mammals). By facilitating promoter-based molecular analysis and genetic manipulation, our work also underscores the value of avian models in unravelling the complex regulatory mechanism of cell lineage specification during amniote development.
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Affiliation(s)
- Marina Lizio
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
| | - Ruslan Deviatiiarov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Hiroki Nagai
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
- RIKEN Center for Developmental Biology, Kobe, Japan
| | - Laura Galan
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria-SODERCAN), Santander, Spain
| | - Erik Arner
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
| | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Japan
| | - Timo Lassmann
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
| | - Takeya Kasukawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
| | - Akira Hasegawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
| | - Marian A. Ros
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria-SODERCAN), Santander, Spain
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center (OSC), Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Japan
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
| | - Alistair R. R. Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Japan
- * E-mail: (GS); (HK); (OG)
| | - Oleg Gusev
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Japan
- RIKEN Innovation Center, Wako, Japan
- * E-mail: (GS); (HK); (OG)
| | - Guojun Sheng
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
- RIKEN Center for Developmental Biology, Kobe, Japan
- * E-mail: (GS); (HK); (OG)
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50
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Horie M, Kaczkowski B, Ohshima M, Matsuzaki H, Noguchi S, Mikami Y, Lizio M, Itoh M, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Takai D, Yamaguchi Y, Micke P, Saito A, Nagase T. Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC. Mol Cancer Res 2017; 15:1354-1365. [PMID: 28698358 DOI: 10.1158/1541-7786.mcr-17-0191] [Citation(s) in RCA: 21] [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] [Received: 04/11/2017] [Revised: 06/12/2017] [Accepted: 06/28/2017] [Indexed: 11/16/2022]
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. The majority of cancer driver mutations have been identified; however, relevant epigenetic regulation involved in tumorigenesis has only been fragmentarily analyzed. Epigenetically regulated genes have a great theranostic potential, especially in tumors with no apparent driver mutations. Here, epigenetically regulated genes were identified in lung cancer by an integrative analysis of promoter-level expression profiles from Cap Analysis of Gene Expression (CAGE) of 16 non-small cell lung cancer (NSCLC) cell lines and 16 normal lung primary cell specimens with DNA methylation data of 69 NSCLC cell lines and 6 normal lung epithelial cells. A core set of 49 coding genes and 10 long noncoding RNAs (lncRNA), which are upregulated in NSCLC cell lines due to promoter hypomethylation, was uncovered. Twenty-two epigenetically regulated genes were validated (upregulated genes with hypomethylated promoters) in the adenocarcinoma and squamous cell cancer subtypes of lung cancer using The Cancer Genome Atlas data. Furthermore, it was demonstrated that multiple copies of the REP522 DNA repeat family are prominently upregulated due to hypomethylation in NSCLC cell lines, which leads to cancer-specific expression of lncRNAs, such as RP1-90G24.10, AL022344.4, and PCAT7. Finally, Myeloma Overexpressed (MYEOV) was identified as the most promising candidate. Functional studies demonstrated that MYEOV promotes cell proliferation, survival, and invasion. Moreover, high MYEOV expression levels were associated with poor prognosis.Implications: This report identifies a robust list of 22 candidate driver genes that are epigenetically regulated in lung cancer; such genes may complement the known mutational drivers.Visual Overview: http://mcr.aacrjournals.org/content/molcanres/15/10/1354/F1.large.jpg Mol Cancer Res; 15(10); 1354-65. ©2017 AACR.
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Affiliation(s)
- Masafumi Horie
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Division for Health Service Promotion, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Bogumil Kaczkowski
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan.
| | - Mitsuhiro Ohshima
- Department of Biochemistry, Ohu University School of Pharmaceutical Sciences, Koriyama, Fukushima, Japan
| | - Hirotaka Matsuzaki
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Satoshi Noguchi
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yu Mikami
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Department of Clinical Laboratory, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Marina Lizio
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | - Masayoshi Itoh
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Timo Lassmann
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
- Telethon Kids Institute, the University of Western Australia, Perth, Western Australia, Australia
| | - Piero Carninci
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
| | | | - Alistair R R Forrest
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Daiya Takai
- Department of Clinical Laboratory, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yoko Yamaguchi
- Department of Biochemistry, Nihon University School of Dentistry, Chiyoda-ku, Tokyo, Japan
- Division of Functional Morphology Dental Research Center Nihon University School of Dentistry, Chiyoda-ku, Tokyo, Japan
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Akira Saito
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Division for Health Service Promotion, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takahide Nagase
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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