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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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Abugessaisa I, Manabe RI, Kawashima T, Tagami M, Takahashi C, Okazaki Y, Bandinelli S, Kasukawa T, Ferrucci L. OVCH1 Antisense RNA 1 is differentially expressed between non-frail and frail old adults. GeroScience 2024; 46:2063-2081. [PMID: 37817005 PMCID: PMC10828349 DOI: 10.1007/s11357-023-00961-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/24/2023] [Indexed: 10/12/2023] Open
Abstract
While some old adults stay healthy and non-frail up to late in life, others experience multimorbidity and frailty often accompanied by a pro-inflammatory state. The underlying molecular mechanisms for those differences are still obscure. Here, we used gene expression analysis to understand the molecular underpinning between non-frail and frail individuals in old age. Twenty-four adults (50% non-frail and 50% frail) from InCHIANTI study were included. Total RNA extracted from whole blood was analyzed by Cap Analysis of Gene Expression (CAGE). CAGE identified transcription start site (TSS) and active enhancer regions. We identified a set of differentially expressed (DE) TSS and enhancer between non-frail and frail and male and female participants. Several DE TSSs were annotated as lncRNA (XIST and TTTY14) and antisense RNAs (ZFX-AS1 and OVCH1 Antisense RNA 1). The promoter region chr6:366,786,54-366,787,97;+ was DE and overlapping the longevity CDKN1A gene. GWAS-LD enrichment analysis identifies overlapping LD-blocks with the DE regions with reported traits in GWAS catalog (isovolumetric relaxation time and urinary tract infection frequency). Furthermore, we used weighted gene co-expression network analysis (WGCNA) to identify changes of gene expression associated with clinical traits and identify key gene modules. We performed functional enrichment analysis of the gene modules with significant trait/module correlation. One gene module is showing a very distinct pattern in hub genes. Glycogen Phosphorylase L (PYGL) was the top ranked hub gene between non-frail and frail. We predicted transcription factor binding sites (TFBS) and motif activity. TF involved in age-related pathways (e.g., FOXO3 and MYC) shows different expression patterns between non-frail and frail participants. Expanding the study of OVCH1 Antisense RNA 1 and PYGL may help understand the mechanisms leading to loss of homeostasis that ultimately causes frailty.
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Affiliation(s)
- Imad Abugessaisa
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
| | - Ri-Ichiroh Manabe
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Tsugumi Kawashima
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Michihira Tagami
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Chitose Takahashi
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yasushi Okazaki
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Stefania Bandinelli
- Azienda USL Toscana Centro, InCHIANTI, Villa Margherita, Primo piano Viale Michelangelo, 41, 50125, Firenze, Italy
| | - Takeya Kasukawa
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital 5th floor, 3001 S. Hanover Street, Baltimore, MD, 21225, USA
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3
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Abugessaisa I, Hasegawa A, Katayama S, Kere J, Kasukawa T. Computational approach to evaluate scRNA-seq data quality and gene body coverage with SkewC. STAR Protoc 2023; 4:102038. [PMID: 36853658 PMCID: PMC9873502 DOI: 10.1016/j.xpro.2022.102038] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/24/2022] [Accepted: 12/29/2022] [Indexed: 01/21/2023] Open
Abstract
SkewC is a single-cell RNA sequencing (scRNA-seq) data quality evaluation tool. The approach is based on determining gene body coverage, and its skewness, as a quality metric for each individual cell. SkewC distinguishes between two types of single cells: typical cells with prototypical gene body coverage profiles and skewed cells with skewed gene body coverage profiles. SkewC can be used on any scRNA-seq data as it is independent from the underlying technology used to generate the data. For complete details on the use and execution of this protocol, please refer to Abugessaisa et al. (2022).1.
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Affiliation(s)
- Imad Abugessaisa
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Shintaro Katayama
- Folkhälsan Research Center, Topeliuksenkatu 20, 00250 Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden; Stem Cells and Metabolism Research Program, University of Helsinki, P.O. Box 4 (Yliopistonkatu 3), Helsinki, Finland
| | - Juha Kere
- Folkhälsan Research Center, Topeliuksenkatu 20, 00250 Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden; Stem Cells and Metabolism Research Program, University of Helsinki, P.O. Box 4 (Yliopistonkatu 3), Helsinki, Finland.
| | - Takeya Kasukawa
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan; Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
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4
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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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Woogeng IN, Kaczkowski B, Abugessaisa I, Hu H, Tachibana A, Sahara Y, Hon CC, Hasegawa A, Sakai N, Nishida M, Sanyal H, Sho J, Kajita K, Kasukawa T, Takasato M, Carninci P, Maeda A, Mandai M, Arner E, Takahashi M, Kime C. Inducing human retinal pigment epithelium-like cells from somatic tissue. Stem Cell Reports 2022; 17:289-306. [PMID: 35030321 PMCID: PMC8828536 DOI: 10.1016/j.stemcr.2021.12.008] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/23/2022] Open
Abstract
Regenerative medicine relies on basic research outcomes that are only practical when cost effective. The human eyeball requires the retinal pigment epithelium (RPE) to interface the neural retina and the choroid at large. Millions of people suffer from age-related macular degeneration (AMD), a blinding multifactor genetic disease among RPE degradation pathologies. Recently, autologous pluripotent stem-cell-derived RPE cells were prohibitively expensive due to time; therefore, we developed a faster reprogramming system. We stably induced RPE-like cells (iRPE) from human fibroblasts (Fibs) by conditional overexpression of both broad plasticity and lineage-specific transcription factors (TFs). iRPE cells displayed critical RPE benchmarks and significant in vivo integration in transplanted retinas. Herein, we detail the iRPE system with comprehensive single-cell RNA sequencing (scRNA-seq) profiling to interpret and characterize its best cells. We anticipate that our system may enable robust retinal cell induction for basic research and affordable autologous human RPE tissue for regenerative cell therapy. Human Fibs reprogrammed to stable RPE-like cells Reprogramming factors selected for pioneering, plasticity, lineage, and target cell Nicotinamide (NIC) and Chetomin (CTM) improved the reprogramming outcomes scRNA-seq analysis identifies high-quality subpopulation resembling model cells
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Affiliation(s)
| | | | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Haiming Hu
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | | | - Yoshiki Sahara
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan; Laboratory of Molecular Cell Biology and Development, Department of Animal Development and Physiology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Department of Renal and Cardiovascular Research, New Drug Research Division, Otsuka Pharmaceutical Co. Ltd., Tokushima 771-0192, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Noriko Sakai
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | | | - Hashimita Sanyal
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Junki Sho
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Keisuke Kajita
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Minoru Takasato
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan; Laboratory of Molecular Cell Biology and Development, Department of Animal Development and Physiology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Human Technopole, Via Rita Levi Montalcini 1, Milan, Italy
| | - Akiko Maeda
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Michiko Mandai
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Masayo Takahashi
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Cody Kime
- RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.
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6
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Abugessaisa I, Hasegawa A, Noguchi S, Cardon M, Watanabe K, Takahashi M, Suzuki H, Katayama S, Kere J, Kasukawa T. SkewC: Identifying cells with skewed gene body coverage in single-cell RNA sequencing data. iScience 2022; 25:103777. [PMID: 35146392 PMCID: PMC8819117 DOI: 10.1016/j.isci.2022.103777] [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: 03/16/2021] [Revised: 09/07/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022] Open
Abstract
The analysis and interpretation of single-cell RNA sequencing (scRNA-seq) experiments are compromised by the presence of poor-quality cells. For meaningful analyses, such poor-quality cells should be excluded as they introduce noise in the data. We introduce SkewC, a quality-assessment tool, to identify skewed cells in scRNA-seq experiments. The tool’s methodology is based on the assessment of gene coverage for each cell, and its skewness as a quality measure; the gene body coverage is a unique characteristic for each protocol, and different protocols yield highly different coverage profiles. This tool is designed to avoid misclustering or false clusters by identifying, isolating, and removing cells with skewed gene body coverage profiles. SkewC is capable of processing any type of scRNA-seq dataset, regardless of the protocol. We envision SkewC as a distinctive QC method to be incorporated into scRNA-seq QC processing to preclude the possibility of scRNA-seq data misinterpretation. We developed a quality assessment method applicable to single-cell RNA-Seq data SkewC relies on the use of gene coverage profile of cells as a quality measure SkewC reveals two classes of cells: typical cells and skewed cells Typical with prototypical coverage profiles, and skewed with skewed profiles
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Affiliation(s)
- Imad Abugessaisa
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Akira Hasegawa
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Shuhei Noguchi
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Melissa Cardon
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Kazuhide Watanabe
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Masataka Takahashi
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Shintaro Katayama
- Folkhälsan Research Center, Topeliuksenkatu 20, 00250 Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki, P.O. Box 4 (Yliopistonkatu 3), Helsinki, Finland
| | - Juha Kere
- Folkhälsan Research Center, Topeliuksenkatu 20, 00250 Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki, P.O. Box 4 (Yliopistonkatu 3), Helsinki, Finland
- Corresponding author
| | - Takeya Kasukawa
- Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
- Corresponding author
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7
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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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8
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Gomez-Cabrero D, Walter S, Abugessaisa I, Miñambres-Herraiz R, Palomares LB, Butcher L, Erusalimsky JD, Garcia-Garcia FJ, Carnicero J, Hardman TC, Mischak H, Zürbig P, Hackl M, Grillari J, Fiorillo E, Cucca F, Cesari M, Carrie I, Colpo M, Bandinelli S, Feart C, Peres K, Dartigues JF, Helmer C, Viña J, Olaso G, García-Palmero I, Martínez JG, Jansen-Dürr P, Grune T, Weber D, Lippi G, Bonaguri C, Sinclair AJ, Tegner J, Rodriguez-Mañas L. A robust machine learning framework to identify signatures for frailty: a nested case-control study in four aging European cohorts. GeroScience 2021; 43:1317-1329. [PMID: 33599920 PMCID: PMC8190217 DOI: 10.1007/s11357-021-00334-0] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
Phenotype-specific omic expression patterns in people with frailty could provide invaluable insight into the underlying multi-systemic pathological processes and targets for intervention. Classical approaches to frailty have not considered the potential for different frailty phenotypes. We characterized associations between frailty (with/without disability) and sets of omic factors (genomic, proteomic, and metabolomic) plus markers measured in routine geriatric care. This study was a prevalent case control using stored biospecimens (urine, whole blood, cells, plasma, and serum) from 1522 individuals (identified as robust (R), pre-frail (P), or frail (F)] from the Toledo Study of Healthy Aging (R=178/P=184/F=109), 3 City Bordeaux (111/269/100), Aging Multidisciplinary Investigation (157/79/54) and InCHIANTI (106/98/77) cohorts. The analysis included over 35,000 omic and routine laboratory variables from robust and frail or pre-frail (with/without disability) individuals using a machine learning framework. We identified three protective biomarkers, vitamin D3 (OR: 0.81 [95% CI: 0.68-0.98]), lutein zeaxanthin (OR: 0.82 [95% CI: 0.70-0.97]), and miRNA125b-5p (OR: 0.73, [95% CI: 0.56-0.97]) and one risk biomarker, cardiac troponin T (OR: 1.25 [95% CI: 1.23-1.27]). Excluding individuals with a disability, one protective biomarker was identified, miR125b-5p (OR: 0.85, [95% CI: 0.81-0.88]). Three risks of frailty biomarkers were detected: pro-BNP (OR: 1.47 [95% CI: 1.27-1.7]), cardiac troponin T (OR: 1.29 [95% CI: 1.21-1.38]), and sRAGE (OR: 1.26 [95% CI: 1.01-1.57]). Three key frailty biomarkers demonstrated a statistical association with frailty (oxidative stress, vitamin D, and cardiovascular system) with relationship patterns differing depending on the presence or absence of a disability.
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Affiliation(s)
- David Gomez-Cabrero
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Stefan Walter
- Dept. of Medicine and Public Health, Rey Juan Carlos University, Alcorcon, Spain
| | | | | | | | - Lee Butcher
- Department of Biomedical Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - Jorge D Erusalimsky
- Department of Biomedical Sciences, Cardiff Metropolitan University, Cardiff, UK
| | | | - José Carnicero
- Dept. of Geriatric Medicine, Complejo Hospitalario Universitario de Toledo (CHUT), Toledo, Spain
| | | | - Harald Mischak
- Mosaiques Diagnostics GmbH, Rotenburger Str. 20, 30659, Hannover, Germany
| | - Petra Zürbig
- Mosaiques Diagnostics GmbH, Rotenburger Str. 20, 30659, Hannover, Germany
| | - Matthias Hackl
- Evercyte GmbH; BOKU-University of Natural Resources and Life Sciences Vienna, Department of Biotechnology, Ludwig Boltzmann Institute of Experimental and Clinical Traumatology, Vienna, Austria
| | - Johannes Grillari
- Evercyte GmbH; BOKU-University of Natural Resources and Life Sciences Vienna, Department of Biotechnology, Ludwig Boltzmann Institute of Experimental and Clinical Traumatology, Vienna, Austria
| | - Edoardo Fiorillo
- Instituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy
| | - Francesco Cucca
- Instituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy
| | - Matteo Cesari
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | | | | | | | - Catherine Feart
- Univ. Bordeaux, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
| | - Karine Peres
- Univ. Bordeaux, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
| | - Jean-François Dartigues
- Univ. Bordeaux, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
| | - Catherine Helmer
- Univ. Bordeaux, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
| | - José Viña
- Freshage, University of Valencia, Valencia, Spain
| | - Gloria Olaso
- Freshage, University of Valencia, Valencia, Spain
| | | | | | - Pidder Jansen-Dürr
- Research Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Tilman Grune
- German Institute for Human Nutrition, Potsdam, Germany
| | - Daniela Weber
- German Institute for Human Nutrition, Potsdam, Germany
| | - Giuseppe Lippi
- Clinical Biochemistry and Molecular Biology, Universita di Verona, Verona, Italy
| | - Chiara Bonaguri
- Laboratoy Medicine Technical Sciences, Parma University, Parma, Italy
| | | | - Jesper Tegner
- Dept. of Medicine, Karolinska Institute, Stockholm, Sweden
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Leocadio Rodriguez-Mañas
- CIBER of Frailty and Healthy Aging, Madrid, Spain.
- Dept. of Geriatric Medicine, Getafe University Hospital, Getafe, Spain.
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9
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Abugessaisa I, Ramilowski JA, Lizio M, Severin J, Hasegawa A, Harshbarger J, Kondo A, Noguchi S, Yip CW, Ooi J, Tagami M, Hori F, Agrawal S, Hon C, Cardon M, Ikeda S, Ono H, Bono H, Kato M, Hashimoto K, Bonetti A, Kato M, Kobayashi N, Shin J, de Hoon M, Hayashizaki Y, Carninci P, Kawaji H, Kasukawa T. FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. Nucleic Acids Res 2021; 49:D892-D898. [PMID: 33211864 PMCID: PMC7779024 DOI: 10.1093/nar/gkaa1054] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 11/15/2022] Open
Abstract
The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.
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Affiliation(s)
- Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Jesicca Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Jayson Harshbarger
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Atsushi Kondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Fumi Hori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Melissa Cardon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shuya Ikeda
- Database Center for Life Science, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Hiromasa Ono
- Database Center for Life Science, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Hidemasa Bono
- Database Center for Life Science, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University
| | - Masaki Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Alessandro Bonetti
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Karolinska Institutet, Stockholm, Sweden
| | - Masaki Kato
- RIKEN Head Office for Information Systems and Cybersecurity, Wako, Saitama, Japan
| | - Norio Kobayashi
- RIKEN Head Office for Information Systems and Cybersecurity, Wako, Saitama, Japan
| | - Jay Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | | | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hideya Kawaji
- Correspondence may also be addressed to Hideya Kawaji.
| | - Takeya Kasukawa
- To whom correspondence should be addressed. Tel: +81 45 503 9222; Fax: +81 45 503 9219;
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10
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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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11
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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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12
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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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13
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Abugessaisa I, Noguchi S, Böttcher M, Hasegawa A, Kouno T, Kato S, Tada Y, Ura H, Abe K, Shin JW, Plessy C, Carninci P, Kasukawa T. SCPortalen: human and mouse single-cell centric database. Nucleic Acids Res 2019; 46:D781-D787. [PMID: 29045713 PMCID: PMC5753281 DOI: 10.1093/nar/gkx949] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [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: 08/15/2017] [Accepted: 10/05/2017] [Indexed: 01/07/2023] Open
Abstract
Published single-cell datasets are rich resources for investigators who want to address questions not originally asked by the creators of the datasets. The single-cell datasets might be obtained by different protocols and diverse analysis strategies. The main challenge in utilizing such single-cell data is how we can make the various large-scale datasets to be comparable and reusable in a different context. To challenge this issue, we developed the single-cell centric database ‘SCPortalen’ (http://single-cell.clst.riken.jp/). The current version of the database covers human and mouse single-cell transcriptomics datasets that are publicly available from the INSDC sites. The original metadata was manually curated and single-cell samples were annotated with standard ontology terms. Following that, common quality assessment procedures were conducted to check the quality of the raw sequence. Furthermore, primary data processing of the raw data followed by advanced analyses and interpretation have been performed from scratch using our pipeline. In addition to the transcriptomics data, SCPortalen provides access to single-cell image files whenever available. The target users of SCPortalen are all researchers interested in specific cell types or population heterogeneity. Through the web interface of SCPortalen users are easily able to search, explore and download the single-cell datasets of their interests.
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Affiliation(s)
- Imad Abugessaisa
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
| | - Shuhei Noguchi
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
| | - Michael Böttcher
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
| | - Tsukasa Kouno
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
| | - Sachi Kato
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
| | - Yuhki Tada
- RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hiroki Ura
- RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Kuniya Abe
- RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Jay W Shin
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
| | - Charles Plessy
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan
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14
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Abugessaisa I, Noguchi S, Hasegawa A, Kondo A, Kawaji H, Carninci P, Kasukawa T. refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites. J Mol Biol 2019; 431:2407-2422. [DOI: 10.1016/j.jmb.2019.04.045] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 01/22/2023]
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15
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Kouno T, Moody J, Kwon ATJ, Shibayama Y, Kato S, Huang Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin JW. C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nat Commun 2019; 10:360. [PMID: 30664627 PMCID: PMC6341120 DOI: 10.1038/s41467-018-08126-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 12/19/2018] [Indexed: 01/06/2023] Open
Abstract
Single-cell transcriptomic profiling is a powerful tool to explore cellular heterogeneity. However, most of these methods focus on the 3′-end of polyadenylated transcripts and provide only a partial view of the transcriptome. We introduce C1 CAGE, a method for the detection of transcript 5′-ends with an original sample multiplexing strategy in the C1TM microfluidic system. We first quantifiy the performance of C1 CAGE and find it as accurate and sensitive as other methods in the C1 system. We then use it to profile promoter and enhancer activities in the cellular response to TGF-β of lung cancer cells and discover subpopulations of cells differing in their response. We also describe enhancer RNA dynamics revealing transcriptional bursts in subsets of cells with transcripts arising from either strand in a mutually exclusive manner, validated using single molecule fluorescence in situ hybridization. Single-cell transcriptomic profiling allows the exploration of cellular heterogeneity but commonly focuses on the 3′-end of the transcript. Here the authors introduce C1 CAGE, which detects the 5′ transcript end in a multiplexed microfluidic system.
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Affiliation(s)
- Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Jonathan Moody
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Andrew Tae-Jun Kwon
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Sachi Kato
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yi Huang
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,ACT Genomics Co. Ltd., 3F., No. 345, Xinhu 2nd Rd, Neihu Dist., Taipei City, 114, Taiwan
| | - Michael Böttcher
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Efthymios Motakis
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Yong Loo Lin School of Medicine MD6, #08-01, 14 Medical Drive, National University of Singapore, Singapore, 117599, Singapore
| | - Mickaël Mendez
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Princess Margaret Cancer Research Tower 11-401, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoshi Takizawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takahiro Arakawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masaaki Furuno
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Naveen Ramalingam
- Single-Cell Research and Development, Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, 94080, CA, USA
| | - Jay West
- Single-Cell Research and Development, Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, 94080, CA, USA
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Timo Lassmann
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Telethon Kids Institute, The University of Western Australia, Perth Children's Hospital, 15 Hospital Ave, Nedlands, 6009, WA, Australia
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Charles Plessy
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. .,Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
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16
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Quistrebert J, Hässler S, Bachelet D, Mbogning C, Musters A, Tak PP, Wijbrandts CA, Herenius M, Bergstra SA, Akdemir G, Johannesson M, Combe B, Fautrel B, Chollet-Martin S, Gleizes A, Donnellan N, Deisenhammer F, Davidson J, Hincelin-Mery A, Dönnes P, Fogdell-Hahn A, De Vries N, Huizinga T, Abugessaisa I, Saevarsdottir S, Hacein-Bey-Abina S, Pallardy M, Broët P, Mariette X. Incidence and risk factors for adalimumab and infliximab anti-drug antibodies in rheumatoid arthritis: A European retrospective multicohort analysis. Semin Arthritis Rheum 2018; 48:967-975. [PMID: 30420245 DOI: 10.1016/j.semarthrit.2018.10.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 09/19/2018] [Accepted: 10/08/2018] [Indexed: 12/23/2022]
Abstract
OBJECTIVES To evaluate the incidence of anti-drug antibody (ADA) occurrences and ADA-related risk factors under adalimumab and infliximab treatment in rheumatoid arthritis (RA) patients. METHODS The study combined retrospective cohorts from the ABIRISK project totaling 366 RA patients treated with adalimumab (n = 240) or infliximab (n = 126), 92.4% of them anti-TNF naive (n = 328/355) and 96.6% of them co-treated with methotrexate (n = 341/353) with up to 18 months follow-up. ADA positivity was measured by enzyme-linked immunosorbent assay. The cumulative incidence of ADA was estimated, and potential bio-clinical factors were investigated using a Cox regression model on interval-censored data. RESULTS ADAs were detected within 18 months in 19.2% (n = 46) of the adalimumab-treated patients and 29.4% (n = 37) of the infliximab-treated patients. The cumulative incidence of ADA increased over time. In the adalimumab and infliximab groups, respectively, the incidence was 15.4% (5.2-20.2) and 0% (0-5.9) at 3 months, 17.6% (11.4-26.4) and 0% (0-25.9) at 6 months, 17.7% (12.6-37.5) and 34.1% (11.4-46.3) at 12 months, 50.0% (25.9-87.5) and 37.5% (25.9-77.4) at 15 months and 50.0% (25.9-87.5) and 66.7% (37.7-100) at 18 months. Factors associated with a higher risk of ADA development were: longer disease duration (1-3 vs. < 1 year; adalimumab: HR 3.0, 95% CI 1.0-8.7; infliximab: HR 2.7, 95% CI 1.1-6.8), moderate disease activity (DAS28 3.2-5.1 vs. < 3.2; adalimumab: HR 6.6, 95% CI 1.3-33.7) and lifetime smoking (infliximab: HR 2.7, 95% CI 1.2-6.3). CONCLUSIONS The current study focusing on patients co-treated with methotrexate for more than 95% of them found a late occurrence of ADAs not previously observed, whereby the risk continued to increase over 18 months. Disease duration, DAS28 and lifetime smoking are clinical predictors of ADA development.
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Affiliation(s)
- Jocelyn Quistrebert
- CESP, INSERM UMR 1018, Faculty of Medicine, Paris-Sud University, Paris-Saclay University, UVSQ, Villejuif, France
| | - Signe Hässler
- CESP, INSERM UMR 1018, Faculty of Medicine, Paris-Sud University, Paris-Saclay University, UVSQ, Villejuif, France
| | - Delphine Bachelet
- CESP, INSERM UMR 1018, Faculty of Medicine, Paris-Sud University, Paris-Saclay University, UVSQ, Villejuif, France
| | - Cyprien Mbogning
- CESP, INSERM UMR 1018, Faculty of Medicine, Paris-Sud University, Paris-Saclay University, UVSQ, Villejuif, France
| | - Anne Musters
- Amsterdam Rheumatology and Immunology Center, Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands
| | - Paul Peter Tak
- Amsterdam Rheumatology and Immunology Center, Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands; GlaxoSmithKline, Stevenage, UK; University of Cambridge, Cambridge, UK; Ghent University, Ghent, Belgium
| | - Carla Ann Wijbrandts
- Amsterdam Rheumatology and Immunology Center, Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands; Medical Center Slotervaart, Amsterdam, the Netherlands
| | - Marieke Herenius
- Amsterdam Rheumatology and Immunology Center, Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands
| | - Sytske Anne Bergstra
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Gülşah Akdemir
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martina Johannesson
- Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Bernard Combe
- Department of Rheumatology, Lapeyronie Hospital, Montpellier University, Montpellier, France
| | - Bruno Fautrel
- Department of Rheumatology, AP-HP, Pitié Salpétrière Hospital, Paris, France; UPMC, GRC 08, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Sylvie Chollet-Martin
- INSERM UMR 996, Faculty of Pharmacy, Paris-Sud University, Paris-Saclay University, Châtenay-Malabry, France
| | - Aude Gleizes
- INSERM UMR 996, Faculty of Pharmacy, Paris-Sud University, Paris-Saclay University, Châtenay-Malabry, France; Clinical Immunology Laboratory, AP-HP, Paris-Sud University Hospitals, Le Kremlin Bicêtre Hospital, Le Kremlin Bicêtre, France
| | | | | | | | | | | | - Anna Fogdell-Hahn
- Department of Clinical Neuroscience, Clinical Neuroimmunology, Karolinska Institutet, Stockholm, Sweden
| | - Niek De Vries
- Amsterdam Rheumatology and Immunology Center, Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands
| | - Tom Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Imad Abugessaisa
- Unit of Computational Medicine, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Saedis Saevarsdottir
- Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Salima Hacein-Bey-Abina
- Clinical Immunology Laboratory, AP-HP, Paris-Sud University Hospitals, Le Kremlin Bicêtre Hospital, Le Kremlin Bicêtre, France; UTCBS, CNRS UMR 8258, INSERM U1022, Faculty of Pharmacy, Paris-Descartes-Sorbonne-Cité University, Paris, France
| | - Marc Pallardy
- INSERM UMR 996, Faculty of Pharmacy, Paris-Sud University, Paris-Saclay University, Châtenay-Malabry, France
| | - Philippe Broët
- CESP, INSERM UMR 1018, Faculty of Medicine, Paris-Sud University, Paris-Saclay University, UVSQ, Villejuif, France; AP-HP, Paris-Sud University Hospitals, Paul Brousse Hospital, Villejuif, France; CHU Sainte Justine, Quebec, Canada
| | - Xavier Mariette
- INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, Paris-Sud University, Paris-Saclay University, Le Kremlin-Bicêtre, France; Department of Rheumatology, AP-HP, Paris-Sud University Hospitals, Le Kremlin Bicêtre Hospital, Le Kremlin-Bicêtre, France.
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17
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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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18
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Bertin N, Mendez M, Hasegawa A, Lizio M, Abugessaisa I, Severin J, Sakai-Ohno M, Lassmann T, Kasukawa T, Kawaji H, Hayashizaki Y, Forrest ARR, Carninci P, Plessy C. Linking FANTOM5 CAGE peaks to annotations with CAGEscan. Sci Data 2017; 4:170147. [PMID: 28972578 PMCID: PMC5625555 DOI: 10.1038/sdata.2017.147] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/09/2017] [Indexed: 01/22/2023] Open
Abstract
The FANTOM5 expression atlas is a quantitative measurement of the activity of nearly 200,000 promoter regions across nearly 2,000 different human primary cells, tissue types and cell lines. Generation of this atlas was made possible by the use of CAGE, an experimental approach to localise transcription start sites at single-nucleotide resolution by sequencing the 5′ ends of capped RNAs after their conversion to cDNAs. While 50% of CAGE-defined promoter regions could be confidently associated to adjacent transcriptional units, nearly 100,000 promoter regions remained gene-orphan. To address this, we used the CAGEscan method, in which random-primed 5′-cDNAs are paired-end sequenced. Pairs starting in the same region are assembled in transcript models called CAGEscan clusters. Here, we present the production and quality control of CAGEscan libraries from 56 FANTOM5 RNA sources, which enhances the FANTOM5 expression atlas by providing experimental evidence associating core promoter regions with their cognate transcripts.
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Affiliation(s)
- Nicolas Bertin
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Mickaël Mendez
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Marina Lizio
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Jessica Severin
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Mizuho Sakai-Ohno
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Timo Lassmann
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan
| | - Alistair R R Forrest
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Charles Plessy
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
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19
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Gomez-Cabrero D, Walter S, Abugessaisa I, Rodríguez-Mañas L, Tegner J. OMIC SIGNATURES IN FRAILTY AND FRAILTY DIAGNOSIS. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.3239] [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: 11/14/2022] Open
Affiliation(s)
- D. Gomez-Cabrero
- Karolinska Institutet, Stockholm, Sweden,
- King’s College London, London, United Kingdom,
- On behalf of FRAILOMIC Initiative, Madrid, Spain
| | - S. Walter
- Geriatric Department, Hospital Universitario de Getafe, Madrid, Spain,
- On behalf of FRAILOMIC Initiative, Madrid, Spain
| | - I. Abugessaisa
- Karolinska Institutet, Stockholm, Sweden,
- On behalf of FRAILOMIC Initiative, Madrid, Spain
| | - L. Rodríguez-Mañas
- Geriatric Department, Hospital Universitario de Getafe, Madrid, Spain,
- On behalf of FRAILOMIC Initiative, Madrid, Spain
| | - J. Tegner
- Karolinska Institutet, Stockholm, Sweden,
- On behalf of FRAILOMIC Initiative, Madrid, Spain
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20
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Abstract
The dynamic structure and functions of genomes are being revealed simultaneously with the progress of technologies and researches in genomics. Evidence indicating genome regional characteristics (genome annotations in a broad sense) provide the basis for further analyses. Target listing and screening can be effectively performed in silico using such data. Here, we describe steps to obtain publicly available genome annotations or to construct new annotations based on your own analyses, as well as an overview of the types of available genome annotations and corresponding resources.
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Affiliation(s)
- Imad Abugessaisa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takeya Kasukawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. .,RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan. .,Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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21
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Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest ARR, Kasukawa T, Kawaji H. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Res 2016; 45:D737-D743. [PMID: 27794045 PMCID: PMC5210666 DOI: 10.1093/nar/gkw995] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [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: 09/30/2016] [Accepted: 10/17/2016] [Indexed: 12/26/2022] Open
Abstract
Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives.
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Affiliation(s)
- Marina Lizio
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shuei Noguchi
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Kondo
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jessica Severin
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chris Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, 84R01, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - David Arenillas
- Centre for Molecular Medicine and Therapeutics at BC Children's Hospital Research, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada
| | - Anthony Mathelier
- 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, 0372 Oslo, Norway
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Leninsky prospect, 33, build. 2, 119071 Moscow, Russia.,Vavilov Institute of General Genetics, Russian Academy of Science, Gubkina str. 3, Moscow 119991, Russia
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7-9, 14183 Huddinge, Sweden
| | - Finn Drabløs
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), P.O. Box 8905, NO-7491 Trondheim, Norway
| | - Jordan A Ramilowski
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Owen Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke's National University of Singapore Medical School, 8 College Road, Singapore 169857, Singapore
| | - Julian Gough
- Department of Computer Science, University of Bristol, Merchant Venturers Building, Woodland Road, Bristol BS8 1UB UK
| | - Robin Andersson
- The Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Albin Sandelin
- Section for Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Hans Ienasescu
- Section for Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Hiromasa Ono
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS), 1111 Yata, Mishima 411-8540, Japan
| | - Hidemasa Bono
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS), 1111 Yata, Mishima 411-8540, Japan
| | - Yoshihide Hayashizaki
- Preventive medicine and applied genomics unit, RIKEN Advanced Center for Computing and Communication, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Systems biology and Genomics, Harry Perkins Institute of MedicalResearch, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6008, Australia
| | - Piero Carninci
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takeya Kasukawa
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan .,RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Preventive medicine and applied genomics unit, RIKEN Advanced Center for Computing and Communication, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Lippi G, Jansen-Duerr P, Viña J, Durrance-Bagale A, Abugessaisa I, Gomez-Cabrero D, Tegnér J, Grillari J, Erusalimsky J, Sinclair A, Rodriguez-Manãs L. Laboratory biomarkers and frailty: presentation of the FRAILOMIC initiative. Clin Chem Lab Med 2016; 53:e253-5. [PMID: 25993734 DOI: 10.1515/cclm-2015-0147] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 02/18/2015] [Indexed: 11/15/2022]
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Abugessaisa I, Shimoji H, Sahin S, Kondo A, Harshbarger J, Lizio M, Hayashizaki Y, Carninci P, Forrest A, Kasukawa T, Kawaji H. FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. Database (Oxford) 2016; 2016:baw105. [PMID: 27402679 PMCID: PMC4940433 DOI: 10.1093/database/baw105] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Indexed: 11/24/2022]
Abstract
The Functional Annotation of the Mammalian Genome project (FANTOM5) mapped transcription start sites (TSSs) and measured their activities in a diverse range of biological samples. The FANTOM5 project generated a large data set; including detailed information about the profiled samples, the uncovered TSSs at high base-pair resolution on the genome, their transcriptional initiation activities, and further information of transcriptional regulation. Data sets to explore transcriptome in individual cellular states encoded in the mammalian genomes have been enriched by a series of additional analysis, based on the raw experimental data, along with the progress of the research activities. To make the heterogeneous data set accessible and useful for investigators, we developed a web-based database called Semantic catalog of Samples, Transcription initiation And Regulators (SSTAR). SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project. Our use of SMW demonstrates the utility of the framework for dissemination of large-scale analysis results. SSTAR is a case study in handling biological data generated from a large-scale research project in terms of maintenance and growth alongside research activities. Database URL:http://fantom.gsc.riken.jp/5/sstar/
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Affiliation(s)
- Imad Abugessaisa
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan
| | - Hisashi Shimoji
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Serkan Sahin
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Atsushi Kondo
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Jayson Harshbarger
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Marina Lizio
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 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, Wako, Saitama 351-0198, Japan
| | - Piero Carninci
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Alistair Forrest
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Takeya Kasukawa
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), 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, Wako, Saitama 351-0198, Japan Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Kanagawa 230-0045, Japan
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Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AMN, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJL, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C, Hume DA, Forrest ARR, Sandelin A, Carninci P, Hayashizaki Y. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science 2015; 347:1010-4. [PMID: 25678556 PMCID: PMC4681433 DOI: 10.1126/science.1259418] [Citation(s) in RCA: 405] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - David A. Hume
- Corresponding author. (D.A.H.); (A.R.R.F.); (A.S.); (P.C.); (Y.H.)
| | | | - Albin Sandelin
- Corresponding author. (D.A.H.); (A.R.R.F.); (A.S.); (P.C.); (Y.H.)
| | - Piero Carninci
- Corresponding author. (D.A.H.); (A.R.R.F.); (A.S.); (P.C.); (Y.H.)
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Gomez-Cabrero D, Menche J, Cano I, Abugessaisa I, Huertas-Migueláñez M, Tenyi A, Marin de Mas I, Kiani NA, Marabita F, Falciani F, Burrowes K, Maier D, Wagner P, Selivanov V, Cascante M, Roca J, Barabási AL, Tegnér J. Systems Medicine: from molecular features and models to the clinic in COPD. J Transl Med 2014; 12 Suppl 2:S4. [PMID: 25471042 PMCID: PMC4255907 DOI: 10.1186/1479-5876-12-s2-s4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background and hypothesis Chronic Obstructive Pulmonary Disease (COPD) patients are characterized by heterogeneous clinical manifestations and patterns of disease progression. Two major factors that can be used to identify COPD subtypes are muscle dysfunction/wasting and co-morbidity patterns. We hypothesized that COPD heterogeneity is in part the result of complex interactions between several genes and pathways. We explored the possibility of using a Systems Medicine approach to identify such pathways, as well as to generate predictive computational models that may be used in clinic practice. Objective and method Our overarching goal is to generate clinically applicable predictive models that characterize COPD heterogeneity through a Systems Medicine approach. To this end we have developed a general framework, consisting of three steps/objectives: (1) feature identification, (2) model generation and statistical validation, and (3) application and validation of the predictive models in the clinical scenario. We used muscle dysfunction and co-morbidity as test cases for this framework. Results In the study of muscle wasting we identified relevant features (genes) by a network analysis and generated predictive models that integrate mechanistic and probabilistic models. This allowed us to characterize muscle wasting as a general de-regulation of pathway interactions. In the co-morbidity analysis we identified relevant features (genes/pathways) by the integration of gene-disease and disease-disease associations. We further present a detailed characterization of co-morbidities in COPD patients that was implemented into a predictive model. In both use cases we were able to achieve predictive modeling but we also identified several key challenges, the most pressing being the validation and implementation into actual clinical practice. Conclusions The results confirm the potential of the Systems Medicine approach to study complex diseases and generate clinically relevant predictive models. Our study also highlights important obstacles and bottlenecks for such approaches (e.g. data availability and normalization of frameworks among others) and suggests specific proposals to overcome them.
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Abugessaisa I, Saevarsdottir S, Tsipras G, Lindblad S, Sandin C, Nikamo P, Ståhle M, Malmström V, Klareskog L, Tegnér J. Accelerating translational research by clinically driven development of an informatics platform--a case study. PLoS One 2014; 9:e104382. [PMID: 25203647 PMCID: PMC4159182 DOI: 10.1371/journal.pone.0104382] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 07/14/2014] [Indexed: 12/21/2022] Open
Abstract
Translational medicine is becoming increasingly dependent upon data generated from health care, clinical research, and molecular investigations. This increasing rate of production and diversity in data has brought about several challenges, including the need to integrate fragmented databases, enable secondary use of patient clinical data from health care in clinical research, and to create information systems that clinicians and biomedical researchers can readily use. Our case study effectively integrates requirements from the clinical and biomedical researcher perspectives in a translational medicine setting. Our three principal achievements are (a) a design of a user-friendly web-based system for management and integration of clinical and molecular databases, while adhering to proper de-identification and security measures; (b) providing a real-world test of the system functionalities using clinical cohorts; and (c) system integration with a clinical decision support system to demonstrate system interoperability. We engaged two active clinical cohorts, 747 psoriasis patients and 2001 rheumatoid arthritis patients, to demonstrate efficient query possibilities across the data sources, enable cohort stratification, extract variation in antibody patterns, study biomarker predictors of treatment response in RA patients, and to explore metabolic profiles of psoriasis patients. Finally, we demonstrated system interoperability by enabling integration with an established clinical decision support system in health care. To assure the usefulness and usability of the system, we followed two approaches. First, we created a graphical user interface supporting all user interactions. Secondly we carried out a system performance evaluation study where we measured the average response time in seconds for active users, http errors, and kilobits per second received and sent. The maximum response time was found to be 0.12 seconds; no server or client errors of any kind were detected. In conclusion, the system can readily be used by clinicians and biomedical researchers in a translational medicine setting.
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Affiliation(s)
- Imad Abugessaisa
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Saedis Saevarsdottir
- Rheumatology Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giorgos Tsipras
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Staffan Lindblad
- Medical Management Center, Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Stockholm, Sweden
| | - Charlotta Sandin
- Rheumatology Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pernilla Nikamo
- Dermatology and Venereology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Mona Ståhle
- Dermatology and Venereology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vivianne Malmström
- Rheumatology Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Tegnér
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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Hernández-de-Diego R, Boix-Chova N, Gómez-Cabrero D, Tegner J, Abugessaisa I, Conesa A. STATegra EMS: an Experiment Management System for complex next-generation omics experiments. BMC Syst Biol 2014; 8 Suppl 2:S9. [PMID: 25033091 PMCID: PMC4101697 DOI: 10.1186/1752-0509-8-s2-s9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
High-throughput sequencing assays are now routinely used to study different aspects of genome organization. As decreasing costs and widespread availability of sequencing enable more laboratories to use sequencing assays in their research projects, the number of samples and replicates in these experiments can quickly grow to several dozens of samples and thus require standardized annotation, storage and management of preprocessing steps. As a part of the STATegra project, we have developed an Experiment Management System (EMS) for high throughput omics data that supports different types of sequencing-based assays such as RNA-seq, ChIP-seq, Methyl-seq, etc, as well as proteomics and metabolomics data. The STATegra EMS provides metadata annotation of experimental design, samples and processing pipelines, as well as storage of different types of data files, from raw data to ready-to-use measurements. The system has been developed to provide research laboratories with a freely-available, integrated system that offers a simple and effective way for experiment annotation and tracking of analysis procedures.
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Gomez-Cabrero D, Abugessaisa I, Maier D, Teschendorff A, Merkenschlager M, Gisel A, Ballestar E, Bongcam-Rudloff E, Conesa A, Tegnér J. Data integration in the era of omics: current and future challenges. BMC Syst Biol 2014; 8 Suppl 2:I1. [PMID: 25032990 PMCID: PMC4101704 DOI: 10.1186/1752-0509-8-s2-i1] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To integrate heterogeneous and large omics data constitutes not only a conceptual challenge but a practical hurdle in the daily analysis of omics data. With the rise of novel omics technologies and through large-scale consortia projects, biological systems are being further investigated at an unprecedented scale generating heterogeneous and often large data sets. These data-sets encourage researchers to develop novel data integration methodologies. In this introduction we review the definition and characterize current efforts on data integration in the life sciences. We have used a web-survey to assess current research projects on data-integration to tap into the views, needs and challenges as currently perceived by parts of the research community.
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Abugessaisa I. Geospatial metadata extraction from product description document applying methods from ontology engineering. ACTA ACUST UNITED AC 2010. [DOI: 10.1504/ijmso.2010.035554] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lizio M, Abugessaisa I, Noguchi S, Kondo A, Hasegawa A, Hon CC, de Hoon M, Severin J, Oki S, Hayashizaki Y, Carninci P, Kasukawa T, Kawaji H. Biochemical characterization of high-affinity 3H-opioid binding. Further evidence for Mu1 sites. Mol Pharmacol 1984; 47:D752-D758. [PMID: 30407557 PMCID: PMC6323950 DOI: 10.1093/nar/gky1099] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.3] [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: 09/15/2018] [Accepted: 10/20/2018] [Indexed: 11/17/2022] Open
Abstract
The FANTOM web resource (http://fantom.gsc.riken.jp/) was developed to provide easy access to the data produced by the FANTOM project. It contains the most complete and comprehensive sets of actively transcribed enhancers and promoters in the human and mouse genomes. We determined the transcription activities of these regulatory elements by CAGE (Cap Analysis of Gene Expression) for both steady and dynamic cellular states in all major and some rare cell types, consecutive stages of differentiation and responses to stimuli. We have expanded the resource by employing different assays, such as RNA-seq, short RNA-seq and a paired-end protocol for CAGE (CAGEscan), to provide new angles to study the transcriptome. That yielded additional atlases of long noncoding RNAs, miRNAs and their promoters. We have also expanded the CAGE analysis to cover rat, dog, chicken, and macaque species for a limited number of cell types. The CAGE data obtained from human and mouse were reprocessed to make them available on the latest genome assemblies. Here, we report the recent updates of both data and interfaces in the FANTOM web resource.
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Affiliation(s)
- Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Kondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- 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
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Shinya Oki
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198 Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- To whom correspondence should be addressed. Tel: +81 45 503 9218; Fax: +81 45 503 9219; . Correspondence may also be addressed to Takeya Kasukawa.
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198 Japan
- To whom correspondence should be addressed. Tel: +81 45 503 9218; Fax: +81 45 503 9219; . Correspondence may also be addressed to Takeya Kasukawa.
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