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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 295] [Impact Index Per Article: 295.0] [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] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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Ma H, Sukonina V, Zhang W, Meng F, Subhash S, Palmgren H, Alexandersson I, Han H, Zhou S, Bartesaghi S, Kanduri C, Enerbäck S. The transcription factor Foxp1 regulates aerobic glycolysis in adipocytes and myocytes. J Biol Chem 2023:104795. [PMID: 37150320 DOI: 10.1016/j.jbc.2023.104795] [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: 03/01/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/09/2023] Open
Abstract
In recent years, lactate has been recognized as an important circulating energy substrate rather than only a dead-end metabolic waste product generated during glucose oxidation at low levels of oxygen. The term "aerobic glycolysis" has been coined to denote increased glucose uptake and lactate production despite normal oxygen levels and functional mitochondria. Hence, in "aerobic glycolysis" lactate production is a metabolic choice, whereas in "anaerobic glycolysis" it is a metabolic necessity based on inadequate levels of oxygen. Interestingly, lactate can be taken up by cells and oxidized to pyruvate and thus constitutes a source of pyruvate that is independent of insulin. Here, we show that the transcription factor Foxp1 regulates glucose uptake and lactate production in adipocytes and myocytes. Over-expression of Foxp1 leads to increased glucose uptake and lactate production. In addition, protein levels of several enzymes in the glycolytic pathway are upregulated, such as hexokinase 2, phosphofructokinase, aldolase, and lactate dehydrogenase. Using chromatin immunoprecipitation and real-time quantitative PCR (ChIP-qPCR) assays, we demonstrate that Foxp1 directly interacts with promoter consensus cis-elements that regulate expression of several of these target genes. Conversely, knock-down of Foxp1 suppresses these enzyme levels and lowers glucose uptake and lactate production. Moreover, mice with a targeted deletion of Foxp1 in muscle display systemic glucose intolerance with decreased muscle glucose uptake. In primary human adipocytes with induced expression of Foxp1, we find increased glycolysis and glycolytic capacity. Our results indicate Foxp1 may play an important role as a regulator of aerobic glycolysis in adipose tissue and muscle.
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Affiliation(s)
- Haixia Ma
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE405 30 Gothenburg, Sweden
| | - Valentina Sukonina
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE405 30 Gothenburg, Sweden
| | - Wei Zhang
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE405 30 Gothenburg, Sweden
| | - Fang Meng
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE405 30 Gothenburg, Sweden; Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China; Suzhou Institute of Systems Medicine, Suzhou 215123, Jiangsu, China
| | - Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE405 30 Gothenburg, Sweden; Karolinska Institutet, Department of Bioscience and Nutrition, Center for Innovative Medicine, Huddinge, Sweden
| | - Henrik Palmgren
- Bioscience Metabolism, Research and Early Development, Cardiovascular, Renal and metabolism (CVRM), BioPharmaceuticals R&D AstraZeneca, Gothenburg, Sweden
| | - Ida Alexandersson
- Bioscience Metabolism, Research and Early Development, Cardiovascular, Renal and metabolism (CVRM), BioPharmaceuticals R&D AstraZeneca, Gothenburg, Sweden
| | - Huiming Han
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE405 30 Gothenburg, Sweden; Department of Pathogen Biology, School of Basic Medical Sciences, Beihua University, Jilin, Jilin Province, 132013, China
| | - Shuping Zhou
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE405 30 Gothenburg, Sweden; School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Stefano Bartesaghi
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and metabolism (CVRM), BioPharmaceuticals R&D AstraZeneca, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE405 30 Gothenburg, Sweden
| | - Sven Enerbäck
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE405 30 Gothenburg, Sweden.
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Pandey GK, Kanduri C. Long Non-Coding RNAs: Tools for Understanding and Targeting Cancer Pathways. Cancers (Basel) 2022; 14:cancers14194760. [PMID: 36230680 PMCID: PMC9564174 DOI: 10.3390/cancers14194760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
The regulatory nature of long non-coding RNAs (lncRNAs) has been well established in various processes of cellular growth, development, and differentiation. Therefore, it is vital to examine their contribution to cancer development. There are ample examples of lncRNAs whose cellular levels are significantly associated with clinical outcomes. However, whether these non-coding molecules can work as either key drivers or barriers to cancer development remains unknown. The current review aims to discuss some well-characterised lncRNAs in the process of oncogenesis and extrapolate the extent of their decisive contribution to tumour development. We ask if these lncRNAs can independently initiate neoplastic lesions or they always need the modulation of well characterized oncogenes or tumour suppressors to exert their functional properties. Finally, we discuss the emerging genetic approaches and appropriate animal and humanised models that can significantly contribute to the functional dissection of lncRNAs in cancer development and progression.
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Affiliation(s)
- Gaurav Kumar Pandey
- Department of Zoology, Banaras Hindu University, Varanasi 221005, India
- Correspondence: (G.K.P.); (C.K.)
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Correspondence: (G.K.P.); (C.K.)
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4
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Mahale S, Setia M, Prajapati B, Subhash S, Yadav MP, Thankaswamy Kosalai S, Deshpande A, Kuchlyan J, Di Marco M, Westerlund F, Wilhelmsson LM, Kanduri C, Kanduri M. HnRNPK maintains single strand RNA through controlling double-strand RNA in mammalian cells. Nat Commun 2022; 13:4865. [PMID: 36038571 PMCID: PMC9424213 DOI: 10.1038/s41467-022-32537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/04/2022] [Indexed: 11/09/2022] Open
Abstract
Although antisense transcription is a widespread event in the mammalian genome, double-stranded RNA (dsRNA) formation between sense and antisense transcripts is very rare and mechanisms that control dsRNA remain unknown. By characterizing the FGF-2 regulated transcriptome in normal and cancer cells, we identified sense and antisense transcripts IER3 and IER3-AS1 that play a critical role in FGF-2 controlled oncogenic pathways. We show that IER3 and IER3-AS1 regulate each other's transcription through HnRNPK-mediated post-transcriptional regulation. HnRNPK controls the mRNA stability and colocalization of IER3 and IER3-AS1. HnRNPK interaction with IER3 and IER3-AS1 determines their oncogenic functions by maintaining them in a single-stranded form. hnRNPK depletion neutralizes their oncogenic functions through promoting dsRNA formation and cytoplasmic accumulation. Intriguingly, hnRNPK loss-of-function and gain-of-function experiments reveal its role in maintaining global single- and double-stranded RNA. Thus, our data unveil the critical role of HnRNPK in maintaining single-stranded RNAs and their physiological functions by blocking RNA-RNA interactions.
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Affiliation(s)
- Sagar Mahale
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Meenakshi Setia
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Bharat Prajapati
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Mukesh Pratap Yadav
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Ananya Deshpande
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Jagannath Kuchlyan
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Mirco Di Marco
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden.
| | - Meena Kanduri
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530, Gothenburg, Sweden.
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Juvvuna PK, Mondal T, Di Marco M, Kosalai ST, Kanduri M, Kanduri C. NBAT1/CASC15-003/USP36 control MYCN expression and its downstream pathway genes in neuroblastoma. Neurooncol Adv 2021; 3:vdab056. [PMID: 34056606 PMCID: PMC8156975 DOI: 10.1093/noajnl/vdab056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Background MYCN has been an attractive therapeutic target in neuroblastoma considering the widespread amplification of the MYCN locus in neuroblastoma, and its established role in neuroblastoma development and progression. Thus, understanding neuroblastoma-specific control of MYCN expression at the transcriptional and post-transcriptional level would lead to identification of novel MYCN-dependent oncogenic pathways and potential therapeutic strategies. Methods By performing loss- and gain-of-function experiments of the neuroblastoma hotspot locus 6p22.3 derived lncRNAs CASC15-003 and NBAT1, together with coimmunoprecipitation and immunoblotting of MYCN, we have shown that both lncRNAs post-translationally control the expression of MYCN through regulating a deubiquitinase enzyme USP36. USP36 oncogenic properties were investigated using cancer cell lines and in vivo models. RNA-seq analysis of loss-of-function experiments of CASC15-003/NBAT1/MYCN/USP36 and JQ1-treated neuroblastoma cells uncovered MYCN-dependent oncogenic pathways. Results We show that NBAT1/CASC15-003 control the stability of MYCN protein through their common interacting protein partner USP36. USP36 harbors oncogenic properties and its higher expression in neuroblastoma patients correlates with poor prognosis, and its downregulation significantly reduces tumor growth in neuroblastoma cell lines and xenograft models. Unbiased integration of RNA-seq data from CASC15-003, NBAT1, USP36, and MYCN knockdowns and neuroblastoma cells treated with MYCN inhibitor JQ1, identified genes that are jointly regulated by the NBAT1/CASC15-003/USP36/MYCN pathway. Functional experiments on one of the target genes, COL18A1, revealed its role in the NBAT1/CASC15-003-dependent cell adhesion feature in neuroblastoma cells. Conclusion Our data show post-translational regulation of MYCN by NBAT1/CASC15-003/USP36, which represents a new regulatory layer in the complex multilayered gene regulatory network that controls MYCN expression.
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Affiliation(s)
- Prasanna Kumar Juvvuna
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Tanmoy Mondal
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Mirco Di Marco
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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Zhou AX, Mondal T, Tabish AM, Abadpour S, Ericson E, Smith DM, Knöll R, Scholz H, Kanduri C, Tyrberg B, Althage M. The long noncoding RNA TUNAR modulates Wnt signaling and regulates human β-cell proliferation. Am J Physiol Endocrinol Metab 2021; 320:E846-E857. [PMID: 33682459 DOI: 10.1152/ajpendo.00335.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many long noncoding RNAs (lncRNAs) are enriched in pancreatic islets and several lncRNAs are linked to type 2 diabetes (T2D). Although they have emerged as potential players in β-cell biology and T2D, little is known about their functions and mechanisms in human β-cells. We identified an islet-enriched lncRNA, TUNAR (TCL1 upstream neural differentiation-associated RNA), which was upregulated in β-cells of patients with T2D and promoted human β-cell proliferation via fine-tuning of the Wnt pathway. TUNAR was upregulated following Wnt agonism by a glycogen synthase kinase-3 (GSK3) inhibitor in human β-cells. Reciprocally, TUNAR repressed a Wnt antagonist Dickkopf-related protein 3 (DKK3) and stimulated Wnt pathway signaling. DKK3 was aberrantly expressed in β-cells of patients with T2D and displayed a synchronized regulatory pattern with TUNAR at the single cell level. Mechanistically, DKK3 expression was suppressed by the repressive histone modifier enhancer of zeste homolog 2 (EZH2). TUNAR interacted with EZH2 in β-cells and facilitated EZH2-mediated suppression of DKK3. These findings reveal a novel cell-specific epigenetic mechanism via islet-enriched lncRNA that fine-tunes the Wnt pathway and subsequently human β-cell proliferation.NEW & NOTEWORTHY The discovery that long noncoding RNA TUNAR regulates β-cell proliferation may be important in designing new treatments for diabetes.
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Affiliation(s)
- Alex-Xianghua Zhou
- Research and Early Development Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Tanmoy Mondal
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ali Mustafa Tabish
- Integrated Cardio Metabolic Centre, Karolinska Institute, Stockholm, Sweden
| | - Shadab Abadpour
- Department of Transplant Medicine, Institute for Surgical Research, Oslo University Hospital, Oslo, Norway
- Hybrid Technology Hub, Centre of Excellence, University of Oslo, Oslo, Norway
| | - Elke Ericson
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - David M Smith
- Emerging Innovations Unit, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Ralph Knöll
- Research and Early Development Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Integrated Cardio Metabolic Centre, Karolinska Institute, Stockholm, Sweden
| | - Hanne Scholz
- Department of Transplant Medicine, Institute for Surgical Research, Oslo University Hospital, Oslo, Norway
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Björn Tyrberg
- Research and Early Development Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Althage
- Research and Early Development Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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Ali MM, Di Marco M, Mahale S, Jachimowicz D, Kosalai ST, Reischl S, Statello L, Mishra K, Darnfors C, Kanduri M, Kanduri C. LY6K-AS lncRNA is a lung adenocarcinoma prognostic biomarker and regulator of mitotic progression. Oncogene 2021; 40:2463-2478. [PMID: 33674747 DOI: 10.1038/s41388-021-01696-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 01/31/2023]
Abstract
Recent advances in genomics unraveled several actionable mutational drivers in lung cancer, leading to promising therapies such as tyrosine kinase inhibitors and immune checkpoint inhibitors. However, the tumors' acquired resistance to the newly-developed as well as existing therapies restricts life quality improvements. Therefore, we investigated the noncoding portion of the human transcriptome in search of alternative actionable targets. We identified an antisense transcript, LY6K-AS, with elevated expression in lung adenocarcinoma (LUAD) patients, and its higher expression in LUAD patients predicts poor survival outcomes. LY6K-AS abrogation interfered with the mitotic progression of lung cancer cells resulting in unfaithful chromosomal segregation. LY6K-AS interacts with and stabilizes 14-3-3 proteins to regulate the transcription of kinetochore and mitotic checkpoint proteins. We also show that LY6K-AS regulates the levels of histone H3 lysine 4 trimethylation (H3K4me3) at the promoters of kinetochore members. Cisplatin treatment and LY6K-AS silencing affect many common pathways enriched in cell cycle-related functions. LY6K-AS silencing affects the growth of xenografts derived from wildtype and cisplatin-resistant lung cancer cells. Collectively, these data indicate that LY6K-AS silencing is a promising therapeutic option for LUAD that inhibits oncogenic mitotic progression.
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Affiliation(s)
- Mohamad Moustafa Ali
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Mirco Di Marco
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sagar Mahale
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Jachimowicz
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Silke Reischl
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Luisa Statello
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Kankadeb Mishra
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Catarina Darnfors
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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Abstract
With the rapid revolution in RNA/DNA sequencing technologies, it is evident that mammalian genomes express tens of thousands of long noncoding RNAs (lncRNAs). Since a large majority of lncRNAs have been functionally implicated in cancer development and progression, there is an increasing appreciation for the use of antisense oligonucleotide (ASO)-based therapies targeting lncRNAs in several cancers. Despite their great potential in therapeutic applications, their use is still limited due to cellular toxicity and shortcomings in achieving required stability in biological fluids and tissue uptake. To overcome these limitations, major changes in ASO chemistry have been introduced to generate second and third generation ASOs, including locked nucleic acids (LNA) technology. Here we describe two different LNA-ASO delivery approaches, a peritumoral administration and a systemic delivery in xenograft models of lung adenocarcinoma, that significantly reduced tumor growth without inducing toxicity.
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Affiliation(s)
- Luisa Statello
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mohamad Moustafa Ali
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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9
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Athie A, Marchese FP, González J, Lozano T, Raimondi I, Juvvuna PK, Abad A, Marin-Bejar O, Serizay J, Martínez D, Ajona D, Pajares MJ, Sandoval J, Montuenga LM, Kanduri C, Lasarte JJ, Huarte M. Analysis of copy number alterations reveals the lncRNA ALAL-1 as a regulator of lung cancer immune evasion. J Cell Biol 2021; 219:152052. [PMID: 32858747 PMCID: PMC7480115 DOI: 10.1083/jcb.201908078] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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] [Revised: 12/12/2019] [Accepted: 06/05/2020] [Indexed: 12/31/2022] Open
Abstract
Cancer is characterized by genomic instability leading to deletion or amplification of oncogenes or tumor suppressors. However, most of the altered regions are devoid of known cancer drivers. Here, we identify lncRNAs frequently lost or amplified in cancer. Among them, we found amplified lncRNA associated with lung cancer-1 (ALAL-1) as frequently amplified in lung adenocarcinomas. ALAL-1 is also overexpressed in additional tumor types, such as lung squamous carcinoma. The RNA product of ALAL-1 is able to promote the proliferation and tumorigenicity of lung cancer cells. ALAL-1 is a TNFα- and NF-κB-induced cytoplasmic lncRNA that specifically interacts with SART3, regulating the subcellular localization of the protein deubiquitinase USP4 and, in turn, its function in the cell. Interestingly, ALAL-1 expression inversely correlates with the immune infiltration of lung squamous tumors, while tumors with ALAL-1 amplification show lower infiltration of several types of immune cells. We have thus unveiled a pro-oncogenic lncRNA that mediates cancer immune evasion, pointing to a new target for immune potentiation.
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Affiliation(s)
- Alejandro Athie
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Institute of Health Research of Navarra, Pamplona, Spain
| | - Francesco P Marchese
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Institute of Health Research of Navarra, Pamplona, Spain
| | - Jovanna González
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Institute of Health Research of Navarra, Pamplona, Spain
| | - Teresa Lozano
- Institute of Health Research of Navarra, Pamplona, Spain.,Department of Immunology and Immunotherapy, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Ivan Raimondi
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Institute of Health Research of Navarra, Pamplona, Spain
| | - Prasanna Kumar Juvvuna
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Amaya Abad
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Institute of Health Research of Navarra, Pamplona, Spain
| | - Oskar Marin-Bejar
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Institute of Health Research of Navarra, Pamplona, Spain
| | - Jacques Serizay
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Institute of Health Research of Navarra, Pamplona, Spain
| | - Dannys Martínez
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Institute of Health Research of Navarra, Pamplona, Spain
| | - Daniel Ajona
- Institute of Health Research of Navarra, Pamplona, Spain.,Department of Solid Tumors, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, University of Navarra and CIBERONC, Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Maria Jose Pajares
- Institute of Health Research of Navarra, Pamplona, Spain.,Department of Solid Tumors, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, University of Navarra and CIBERONC, Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Valencia, Spain.,Epigenomics Core Facility, Health Research Institute La Fe, Valencia, Spain
| | - Luis M Montuenga
- Institute of Health Research of Navarra, Pamplona, Spain.,Department of Solid Tumors, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, University of Navarra and CIBERONC, Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Juan J Lasarte
- Institute of Health Research of Navarra, Pamplona, Spain.,Department of Immunology and Immunotherapy, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain.,Institute of Health Research of Navarra, Pamplona, Spain
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10
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Mitra S, Muralidharan SV, Di Marco M, Juvvuna PK, Kosalai ST, Reischl S, Jachimowicz D, Subhash S, Raimondi I, Kurian L, Huarte M, Kogner P, Fischer M, Johnsen JI, Mondal T, Kanduri C. Subcellular Distribution of p53 by the p53-Responsive lncRNA NBAT1 Determines Chemotherapeutic Response in Neuroblastoma. Cancer Res 2021; 81:1457-1471. [PMID: 33372039 DOI: 10.1158/0008-5472.can-19-3499] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/03/2020] [Accepted: 12/16/2020] [Indexed: 11/16/2022]
Abstract
Neuroblastoma has a low mutation rate for the p53 gene. Alternative ways of p53 inactivation have been proposed in neuroblastoma, such as abnormal cytoplasmic accumulation of wild-type p53. However, mechanisms leading to p53 inactivation via cytoplasmic accumulation are not well investigated. Here we show that the neuroblastoma risk-associated locus 6p22.3-derived tumor suppressor NBAT1 is a p53-responsive lncRNA that regulates p53 subcellular levels. Low expression of NBAT1 provided resistance to genotoxic drugs by promoting p53 accumulation in cytoplasm and loss from mitochondrial and nuclear compartments. Depletion of NBAT1 altered CRM1 function and contributed to the loss of p53-dependent nuclear gene expression during genotoxic drug treatment. CRM1 inhibition rescued p53-dependent nuclear functions and sensitized NBAT1-depleted cells to genotoxic drugs. Combined inhibition of CRM1 and MDM2 was even more effective in sensitizing aggressive neuroblastoma cells with p53 cytoplasmic accumulation. Thus, our mechanistic studies uncover an NBAT1-dependent CRM1/MDM2-based potential combination therapy for patients with high-risk neuroblastoma. SIGNIFICANCE: This study shows how a p53-responsive lncRNA mediates chemotherapeutic response by modulating nuclear p53 pathways and identifies a potential treatment strategy for patients with high-risk neuroblastoma.
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Affiliation(s)
- Sanhita Mitra
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Sweden
| | | | - Mirco Di Marco
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Prasanna Kumar Juvvuna
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Sweden
| | | | - Silke Reischl
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Daniel Jachimowicz
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Ivan Raimondi
- Cima, University of Navarra, Pio XII, Pamplona, Spain
| | - Leo Kurian
- Center for Molecular Medicine Cologne, Institute for Neurophysiology, The Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany
| | - Maite Huarte
- Cima, University of Navarra, Pio XII, Pamplona, Spain
| | - Per Kogner
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Medical Faculty, Cologne, Germany
| | - John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Tanmoy Mondal
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Sweden.
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11
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Statello L, Ali MM, Reischl S, Mahale S, Kosalai ST, Huarte M, Kanduri C. The DNA damage inducible lncRNA SCAT7 regulates genomic integrity and topoisomerase 1 turnover in lung adenocarcinoma. NAR Cancer 2021; 3:zcab002. [PMID: 34316698 PMCID: PMC8209975 DOI: 10.1093/narcan/zcab002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/26/2020] [Accepted: 01/06/2021] [Indexed: 12/15/2022] Open
Abstract
Despite the rapid improvements in unveiling the importance of lncRNAs in all aspects of cancer biology, there is still a void in mechanistic understanding of their role in the DNA damage response. Here we explored the potential role of the oncogenic lncRNA SCAT7 (ELF3-AS1) in the maintenance of genome integrity. We show that SCAT7 is upregulated in response to DNA-damaging drugs like cisplatin and camptothecin, where SCAT7 expression is required to promote cell survival. SCAT7 silencing leads to decreased proliferation of cisplatin-resistant cells in vitro and in vivo through interfering with cell cycle checkpoints and DNA repair molecular pathways. SCAT7 regulates ATR signaling, promoting homologous recombination. Importantly, SCAT7 also takes part in proteasome-mediated topoisomerase I (TOP1) degradation, and its depletion causes an accumulation of TOP1–cc structures responsible for the high levels of intrinsic DNA damage. Thus, our data demonstrate that SCAT7 is an important constituent of the DNA damage response pathway and serves as a potential therapeutic target for hard-to-treat drug resistant cancers.
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Affiliation(s)
- Luisa Statello
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Mohamad M Ali
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Silke Reischl
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Sagar Mahale
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona 31008, Spain
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
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12
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Subhash S, Kanduri M, Kanduri C. Sperm Originated Chromatin Imprints and LincRNAs in Organismal Development and Cancer. iScience 2020; 23:101165. [PMID: 32485645 PMCID: PMC7262563 DOI: 10.1016/j.isci.2020.101165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/04/2020] [Accepted: 05/08/2020] [Indexed: 01/17/2023] Open
Abstract
Importance of sperm-derived transcripts and chromatin imprints in organismal development is poorly investigated. Here using an integrative approach, we show that human sperm transcripts are equally important as oocyte. Sperm-specific and sperm-oocyte common transcripts carry distinct chromatin structures at their promoters correlating with corresponding transcript levels in sperm. Interestingly, sperm-specific H3K4me3 patterns at the lincRNA promoters are not maintained in the germ layers and somatic tissues. However, bivalent chromatin at the sperm-specific protein-coding gene promoters is maintained throughout the development. Sperm-specific transcripts reach their peak expression during zygotic genome activation, whereas sperm-oocyte common transcripts are present during early preimplantation development but decline at the onset of zygotic genome activation. Additionally, there is an inverse correlation between sperm-specific and sperm-oocyte lincRNAs throughout the development. Sperm-lincRNAs also show aberrant activation in tumors. Overall, our observations indicate that sperm transcripts carrying chromatin imprints may play an important role in human development and cancer. Sp-lincRNAs carry distinct chromatin structures correlating with transcript levels Sp-lincRNAs are active during ZGA in preimplantation developmental stages SpOc-lincRNAs are active in pre-ZGA and decline at the onset of ZGA Sp-lincRNAs are silent post implantation but show aberrant cancer-specific activation
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Affiliation(s)
- Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital 413 45, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden.
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13
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Mishra K, Kanduri C. Understanding Long Noncoding RNA and Chromatin Interactions: What We Know So Far. Noncoding RNA 2019; 5:ncrna5040054. [PMID: 31817041 PMCID: PMC6958424 DOI: 10.3390/ncrna5040054] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 12/12/2022] Open
Abstract
With the evolution of technologies that deal with global detection of RNAs to probing of lncRNA-chromatin interactions and lncRNA-chromatin structure regulation, we have been updated with a comprehensive repertoire of chromatin interacting lncRNAs, their genome-wide chromatin binding regions and mode of action. Evidence from these new technologies emphasize that chromatin targeting of lncRNAs is a prominent mechanism and that these chromatin targeted lncRNAs exert their functionality by fine tuning chromatin architecture resulting in an altered transcriptional readout. Currently, there are no unifying principles that define chromatin association of lncRNAs, however, evidence from a few chromatin-associated lncRNAs show presence of a short common sequence for chromatin targeting. In this article, we review how technological advancements contributed in characterizing chromatin associated lncRNAs, and discuss the potential mechanisms by which chromatin associated lncRNAs execute their functions.
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Affiliation(s)
- Kankadeb Mishra
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 40530 Gothenburg, Sweden;
- Department of Cell Biology, Memorial Sloan Kettering Cancer Centre, Rockefeller Research Laboratory, 430 East 67th Street, RRL 445, New York, NY 10065, USA
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 40530 Gothenburg, Sweden;
- Correspondence:
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14
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Kuo CC, Hänzelmann S, Sentürk Cetin N, Frank S, Zajzon B, Derks JP, Akhade VS, Ahuja G, Kanduri C, Grummt I, Kurian L, Costa IG. Detection of RNA-DNA binding sites in long noncoding RNAs. Nucleic Acids Res 2019; 47:e32. [PMID: 30698727 PMCID: PMC6451187 DOI: 10.1093/nar/gkz037] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [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: 09/04/2018] [Revised: 01/10/2019] [Accepted: 01/15/2019] [Indexed: 01/08/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) can act as scaffolds that promote the interaction of proteins, RNA, and DNA. There is increasing evidence of sequence-specific interactions of lncRNAs with DNA via triple-helix (triplex) formation. This process allows lncRNAs to recruit protein complexes to specific genomic regions and regulate gene expression. Here we propose a computational method called Triplex Domain Finder (TDF) to detect triplexes and characterize DNA-binding domains and DNA targets statistically. Case studies showed that this approach can detect the known domains of lncRNAs Fendrr, HOTAIR and MEG3. Moreover, we validated a novel DNA-binding domain in MEG3 by a genome-wide sequencing method. We used TDF to perform a systematic analysis of the triplex-forming potential of lncRNAs relevant to human cardiac differentiation. We demonstrated that the lncRNA with the highest triplex-forming potential, GATA6-AS, forms triple helices in the promoter of genes relevant to cardiac development. Moreover, down-regulation of GATA6-AS impairs GATA6 expression and cardiac development. These data indicate the unique ability of our computational tool to identify novel triplex-forming lncRNAs and their target genes.
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Affiliation(s)
- Chao-Chung Kuo
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen Medical Faculty, Aachen 52074, Germany
| | - Sonja Hänzelmann
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen Medical Faculty, Aachen 52074, Germany.,Klinik für Innere Medizin II, Universitätsklinikum Schleswig-Holstein, Kiel 24105, Germany
| | - Nevcin Sentürk Cetin
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg 69120, Germany
| | - Stefan Frank
- Center for Molecular Medicine Cologne, University of Cologne, Cologne 50923, Germany.,Institute for Neurophysiology, University of Cologne, Cologne 50923, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases, University of Cologne, Cologne 50923, Germany
| | - Barna Zajzon
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen Medical Faculty, Aachen 52074, Germany
| | - Jens-Peter Derks
- Center for Molecular Medicine Cologne, University of Cologne, Cologne 50923, Germany.,Institute for Neurophysiology, University of Cologne, Cologne 50923, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases, University of Cologne, Cologne 50923, Germany
| | - Vijay Suresh Akhade
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Gaurav Ahuja
- Center for Molecular Medicine Cologne, University of Cologne, Cologne 50923, Germany.,Institute for Neurophysiology, University of Cologne, Cologne 50923, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases, University of Cologne, Cologne 50923, Germany
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Ingrid Grummt
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg 69120, Germany
| | - Leo Kurian
- Center for Molecular Medicine Cologne, University of Cologne, Cologne 50923, Germany.,Institute for Neurophysiology, University of Cologne, Cologne 50923, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases, University of Cologne, Cologne 50923, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen Medical Faculty, Aachen 52074, Germany
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15
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Subhash S, Mishra K, Akhade VS, Kanduri M, Mondal T, Kanduri C. H3K4me2 and WDR5 enriched chromatin interacting long non-coding RNAs maintain transcriptionally competent chromatin at divergent transcriptional units. Nucleic Acids Res 2019; 46:9384-9400. [PMID: 30010961 PMCID: PMC6182144 DOI: 10.1093/nar/gky635] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 11/02/2017] [Accepted: 07/03/2018] [Indexed: 12/21/2022] Open
Abstract
Recently lncRNAs have been implicated in the sub-compartmentalization of eukaryotic genome via genomic targeting of chromatin remodelers. To explore the function of lncRNAs in the maintenance of active chromatin, we characterized lncRNAs from the chromatin enriched with H3K4me2 and WDR5 using chromatin RNA immunoprecipitation (ChRIP). Significant portion of these enriched lncRNAs were arranged in antisense orientation with respect to their protein coding partners. Among these, 209 lncRNAs, commonly enriched in H3K4me2 and WDR5 chromatin fractions, were named as active chromatin associated lncRNAs (active lncCARs). Interestingly, 43% of these active lncCARs map to divergent transcription units. Divergent transcription (XH) units were overrepresented in the active lncCARs as compared to the inactive lncCARs. ChIP-seq analysis revealed that active XH transcription units are enriched with H3K4me2, H3K4me3 and WDR5. WDR5 depletion resulted in the loss of H3K4me3 but not H3K4me2 at the XH promoters. Active XH CARs interact with and recruit WDR5 to XH promoters, and their depletion leads to decrease in the expression of the corresponding protein coding genes and loss of H3K4me2, H3K4me3 and WDR5 at the active XH promoters. This study unravels a new facet of chromatin-based regulation at the divergent XH transcription units by this newly identified class of H3K4me2/WDR5 chromatin enriched lncRNAs.
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Affiliation(s)
- Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
| | - Kankadeb Mishra
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
| | - Vijay Suresh Akhade
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Sweden
| | - Tanmoy Mondal
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 40530, Sweden
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16
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Wiel C, Le Gal K, Ibrahim MX, Jahangir CA, Kashif M, Yao H, Ziegler DV, Xu X, Ghosh T, Mondal T, Kanduri C, Lindahl P, Sayin VI, Bergo MO. BACH1 Stabilization by Antioxidants Stimulates Lung Cancer Metastasis. Cell 2019; 178:330-345.e22. [PMID: 31257027 DOI: 10.1016/j.cell.2019.06.005] [Citation(s) in RCA: 309] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 03/29/2019] [Accepted: 06/03/2019] [Indexed: 01/03/2023]
Abstract
For tumors to progress efficiently, cancer cells must overcome barriers of oxidative stress. Although dietary antioxidant supplementation or activation of endogenous antioxidants by NRF2 reduces oxidative stress and promotes early lung tumor progression, little is known about its effect on lung cancer metastasis. Here, we show that long-term supplementation with the antioxidants N-acetylcysteine and vitamin E promotes KRAS-driven lung cancer metastasis. The antioxidants stimulate metastasis by reducing levels of free heme and stabilizing the transcription factor BACH1. BACH1 activates transcription of Hexokinase 2 and Gapdh and increases glucose uptake, glycolysis rates, and lactate secretion, thereby stimulating glycolysis-dependent metastasis of mouse and human lung cancer cells. Targeting BACH1 normalized glycolysis and prevented antioxidant-induced metastasis, while increasing endogenous BACH1 expression stimulated glycolysis and promoted metastasis, also in the absence of antioxidants. We conclude that BACH1 stimulates glycolysis-dependent lung cancer metastasis and that BACH1 is activated under conditions of reduced oxidative stress.
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Affiliation(s)
- Clotilde Wiel
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden; Sahlgrenska Cancer Center, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Kristell Le Gal
- Sahlgrenska Cancer Center, Department of Surgery, Institute of Clinical Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Mohamed X Ibrahim
- Sahlgrenska Cancer Center, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | | | - Muhammad Kashif
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Haidong Yao
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Dorian V Ziegler
- Sahlgrenska Cancer Center, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Xiufeng Xu
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Tanushree Ghosh
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Tanmoy Mondal
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Per Lindahl
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Volkan I Sayin
- Sahlgrenska Cancer Center, Department of Surgery, Institute of Clinical Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden.
| | - Martin O Bergo
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden; Sahlgrenska Cancer Center, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden.
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17
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Kosalai ST, Morsy MHA, Papakonstantinou N, Mansouri L, Stavroyianni N, Kanduri C, Stamatopoulos K, Rosenquist R, Kanduri M. EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukaemia. Epigenetics 2019; 14:1125-1140. [PMID: 31216925 PMCID: PMC6773411 DOI: 10.1080/15592294.2019.1633867] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
EZH2 is overexpressed in poor-prognostic chronic lymphocytic leukaemia (CLL) cases, acting as an oncogene; however, thus far, the EZH2 target genes in CLL have not been disclosed. In this study, using ChIP-sequencing, we identified EZH2 and H3K27me3 target genes in two prognostic subgroups of CLL with distinct prognosis and outcome, i.e., cases with unmutated (U-CLL, n = 6) or mutated IGHV genes (M-CLL, n = 6). While the majority of oncogenic pathways were equally enriched for EZH2 target genes in both prognostic subgroups, PI3K pathway genes were differentially bound by EZH2 in U-CLL versus M-CLL. The occupancy of EZH2 for selected PI3K pathway target genes was validated in additional CLL samples (n = 16) and CLL cell lines using siRNA-mediated EZH2 downregulation and ChIP assays. Intriguingly, we found that EZH2 directly binds to the IGF1R promoter along with MYC and upregulates IGF1R expression in U-CLL, leading to downstream PI3K activation. By investigating an independent CLL cohort (n = 96), a positive correlation was observed between EZH2 and IGF1R expression with higher levels in U-CLL compared to M-CLL. Accordingly, siRNA-mediated downregulation of either EZH2, MYC or IGF1R and treatment with EZH2 and MYC pharmacological inhibitors in the HG3 CLL cell line induced a significant reduction in PI3K pathway activation. In conclusion, we characterize for the first time EZH2 target genes in CLL revealing a hitherto unknown implication of EZH2 in modulating the PI3K pathway in a non-canonical, PRC2-independent way, with potential therapeutic implications considering that PI3K inhibitors are effective therapeutic agents for CLL.
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Affiliation(s)
- Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | | | - Nikos Papakonstantinou
- Institute of Applied Biosciences, Center for Research and Technology Hellas , Thessaloniki , Greece
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet , Stockholm , Sweden
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital , Thessaloniki , Greece
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas , Thessaloniki , Greece
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet , Stockholm , Sweden
| | - Meena Kanduri
- Department of Clinical chemistry and Transfusion medicine, Sahlgrenska University Hospital , Gothenburg , Sweden
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18
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Frank S, Ahuja G, Bartsch D, Russ N, Yao W, Kuo JCC, Derks JP, Akhade VS, Kargapolova Y, Georgomanolis T, Messling JE, Gramm M, Brant L, Rehimi R, Vargas NE, Kuroczik A, Yang TP, Sahito RGA, Franzen J, Hescheler J, Sachinidis A, Peifer M, Rada-Iglesias A, Kanduri M, Costa IG, Kanduri C, Papantonis A, Kurian L. yylncT Defines a Class of Divergently Transcribed lncRNAs and Safeguards the T-mediated Mesodermal Commitment of Human PSCs. Cell Stem Cell 2019; 24:318-327.e8. [PMID: 30554961 DOI: 10.1016/j.stem.2018.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 02/26/2018] [Revised: 07/31/2018] [Accepted: 11/01/2018] [Indexed: 01/04/2023]
Abstract
Human protein-coding genes are often accompanied by divergently transcribed non-coding RNAs whose functions, especially in cell fate decisions, are poorly understood. Using an hESC-based cardiac differentiation model, we define a class of divergent lncRNAs, termed yin yang lncRNAs (yylncRNAs), that mirror the cell-type-specific expression pattern of their protein-coding counterparts. yylncRNAs are preferentially encoded from the genomic loci of key developmental cell fate regulators. Most yylncRNAs are spliced polyadenylated transcripts showing comparable expression patterns in vivo in mouse and in human embryos. Signifying their developmental function, the key mesoderm specifier BRACHYURY (T) is accompanied by yylncT, which localizes to the active T locus during mesoderm commitment. yylncT binds the de novo DNA methyltransferase DNMT3B, and its transcript is required for activation of the T locus, with yylncT depletion specifically abolishing mesodermal commitment. Collectively, we report a lncRNA-mediated regulatory layer safeguarding embryonic cell fate transitions.
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Affiliation(s)
- Stefan Frank
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Gaurav Ahuja
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Deniz Bartsch
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Nicole Russ
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Wenjie Yao
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Joseph Chao-Chung Kuo
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Jens-Peter Derks
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Vijay Suresh Akhade
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Yulia Kargapolova
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Department of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Theodore Georgomanolis
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Department of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jan-Erik Messling
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Marie Gramm
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Lilija Brant
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Department of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Rizwan Rehimi
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Natalia Emilse Vargas
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Alina Kuroczik
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Tsun-Po Yang
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | | | - Julia Franzen
- RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Juergen Hescheler
- Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Agapios Sachinidis
- Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Argyris Papantonis
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Department of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Leo Kurian
- Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Neurophysiology, University of Cologne, 50931 Cologne, Germany; CECAD, Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, 50931 Cologne, Germany.
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19
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Sukonina V, Ma H, Zhang W, Bartesaghi S, Subhash S, Heglind M, Foyn H, Betz MJ, Nilsson D, Lidell ME, Naumann J, Haufs-Brusberg S, Palmgren H, Mondal T, Beg M, Jedrychowski MP, Taskén K, Pfeifer A, Peng XR, Kanduri C, Enerbäck S. FOXK1 and FOXK2 regulate aerobic glycolysis. Nature 2019; 566:279-283. [PMID: 30700909 DOI: 10.1038/s41586-019-0900-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/17/2018] [Indexed: 12/17/2022]
Abstract
Adaptation to the environment and extraction of energy are essential for survival. Some species have found niches and specialized in using a particular source of energy, whereas others-including humans and several other mammals-have developed a high degree of flexibility1. A lot is known about the general metabolic fates of different substrates but we still lack a detailed mechanistic understanding of how cells adapt in their use of basic nutrients2. Here we show that the closely related fasting/starvation-induced forkhead transcription factors FOXK1 and FOXK2 induce aerobic glycolysis by upregulating the enzymatic machinery required for this (for example, hexokinase-2, phosphofructokinase, pyruvate kinase, and lactate dehydrogenase), while at the same time suppressing further oxidation of pyruvate in the mitochondria by increasing the activity of pyruvate dehydrogenase kinases 1 and 4. Together with suppression of the catalytic subunit of pyruvate dehydrogenase phosphatase 1 this leads to increased phosphorylation of the E1α regulatory subunit of the pyruvate dehydrogenase complex, which in turn inhibits further oxidation of pyruvate in the mitochondria-instead, pyruvate is reduced to lactate. Suppression of FOXK1 and FOXK2 induce the opposite phenotype. Both in vitro and in vivo experiments, including studies of primary human cells, show how FOXK1 and/or FOXK2 are likely to act as important regulators that reprogram cellular metabolism to induce aerobic glycolysis.
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Affiliation(s)
- Valentina Sukonina
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Haixia Ma
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Wei Zhang
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Stefano Bartesaghi
- Diabetes Bioscience, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZenca, Gothenburg, Sweden
| | - Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Mikael Heglind
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Håvard Foyn
- Department of Cancer Immunology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Matthias J Betz
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Endocrinology, University Hospital Basel, Basel, Switzerland
| | - Daniel Nilsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Martin E Lidell
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Jennifer Naumann
- Institute of Pharmacology and Toxicology, University Hospital Bonn, Bonn, Germany.,PharmaCenter, University of Bonn, Bonn, Germany
| | - Saskia Haufs-Brusberg
- Institute of Pharmacology and Toxicology, University Hospital Bonn, Bonn, Germany.,PharmaCenter, University of Bonn, Bonn, Germany
| | - Henrik Palmgren
- Diabetes Bioscience, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZenca, Gothenburg, Sweden
| | - Tanmoy Mondal
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Muheeb Beg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Mark P Jedrychowski
- Department of Cell Biology, Harvard University Medical School, Boston, MA, USA
| | - Kjetil Taskén
- Department of Cancer Immunology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Alexander Pfeifer
- Institute of Pharmacology and Toxicology, University Hospital Bonn, Bonn, Germany.,PharmaCenter, University of Bonn, Bonn, Germany
| | - Xiao-Rong Peng
- Diabetes Bioscience, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZenca, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sven Enerbäck
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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20
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Wernig-Zorc S, Yadav MP, Kopparapu PK, Bemark M, Kristjansdottir HL, Andersson PO, Kanduri C, Kanduri M. Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia. Epigenetics Chromatin 2019; 12:4. [PMID: 30616658 PMCID: PMC6322269 DOI: 10.1186/s13072-018-0252-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/23/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis. RESULTS We show that naïve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n = 15) compared to naïve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to naïve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression. CONCLUSIONS Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.
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Affiliation(s)
- Sara Wernig-Zorc
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Mukesh Pratap Yadav
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Pradeep Kumar Kopparapu
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Hallgerdur Lind Kristjansdottir
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg University, Gothenburg, Sweden
| | - Per-Ola Andersson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg University, Gothenburg, Sweden.,Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden.
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21
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Mondal T, Kanduri C. LncRNAs join hands together to regulate neuroblastoma progression. Mol Cell Oncol 2018; 6:1553697. [PMID: 30788421 DOI: 10.1080/23723556.2018.1553697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/22/2018] [Accepted: 11/27/2018] [Indexed: 12/18/2022]
Abstract
Trait associated single nucleotide polymorphisms often overlap with noncoding transcripts but their contribution to disease phenotype is poorly investigated. Our study on neuroblastoma risk associated 6p22.3 locus derived long noncoding RNAs (lncRNAs) demonstrates that functional co-operation between sense-antisense CASC15 and NBAT1 lncRNAs control neuroblastoma progression via regulating SOX9-CHD7-USP36 regulatory axis.
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Affiliation(s)
- Tanmoy Mondal
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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22
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Subhash S, Ali MM, Kanduri C. S-phase cancer associated lncRNAs. Cell Cycle 2018; 17:2517-2519. [PMID: 30482083 DOI: 10.1080/15384101.2018.1553356] [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] [Indexed: 10/27/2022] Open
Abstract
Comment on: Ali MM, et al. Nature Communications 2018; 9:883.
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Affiliation(s)
- Santhilal Subhash
- a Department of Medical Biochemistry and cell Biology, The Sahlgrenska Academy, Institute of Biomedicine , University of Gothenburg , Gothenburg , Sweden
| | - Mohamad Moustafa Ali
- a Department of Medical Biochemistry and cell Biology, The Sahlgrenska Academy, Institute of Biomedicine , University of Gothenburg , Gothenburg , Sweden
| | - Chandrasekhar Kanduri
- a Department of Medical Biochemistry and cell Biology, The Sahlgrenska Academy, Institute of Biomedicine , University of Gothenburg , Gothenburg , Sweden
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23
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Mondal T, Juvvuna PK, Kirkeby A, Mitra S, Kosalai ST, Traxler L, Hertwig F, Wernig-Zorc S, Miranda C, Deland L, Volland R, Bartenhagen C, Bartsch D, Bandaru S, Engesser A, Subhash S, Martinsson T, Carén H, Akyürek LM, Kurian L, Kanduri M, Huarte M, Kogner P, Fischer M, Kanduri C. Sense-Antisense lncRNA Pair Encoded by Locus 6p22.3 Determines Neuroblastoma Susceptibility via the USP36-CHD7-SOX9 Regulatory Axis. Cancer Cell 2018. [PMID: 29533783 DOI: 10.1016/j.ccell.2018.01.020] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Trait-associated loci often map to genomic regions encoding long noncoding RNAs (lncRNAs), but the role of these lncRNAs in disease etiology is largely unexplored. We show that a pair of sense/antisense lncRNA (6p22lncRNAs) encoded by CASC15 and NBAT1 located at the neuroblastoma (NB) risk-associated 6p22.3 locus are tumor suppressors and show reduced expression in high-risk NBs. Loss of functional synergy between 6p22lncRNAs results in an undifferentiated state that is maintained by a gene-regulatory network, including SOX9 located on 17q, a region frequently gained in NB. 6p22lncRNAs regulate SOX9 expression by controlling CHD7 stability via modulating the cellular localization of USP36, encoded by another 17q gene. This regulatory nexus between 6p22.3 and 17q regions may lead to potential NB treatment strategies.
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Affiliation(s)
- Tanmoy Mondal
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Prasanna Kumar Juvvuna
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Agnete Kirkeby
- Wallenberg Neuroscience Center, Lund University, 22184 Lund, Sweden; Danish Stem Cell Center (DanStem), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sanhita Mitra
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Larissa Traxler
- Wallenberg Neuroscience Center, Lund University, 22184 Lund, Sweden
| | - Falk Hertwig
- Department of Experimental Pediatric Oncology, University Children's Hospital, and Center for Molecular Medicine (CMMC), Medical Faculty, University of Cologne, 50937 Cologne, Germany; Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Sara Wernig-Zorc
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Caroline Miranda
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Lily Deland
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Ruth Volland
- Department of Experimental Pediatric Oncology, University Children's Hospital, and Center for Molecular Medicine (CMMC), Medical Faculty, University of Cologne, 50937 Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital, and Center for Molecular Medicine (CMMC), Medical Faculty, University of Cologne, 50937 Cologne, Germany
| | - Deniz Bartsch
- Center for Molecular Medicine Cologne, Institute for Neurophysiology, The Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany
| | - Sashidhar Bandaru
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Anne Engesser
- Department of Experimental Pediatric Oncology, University Children's Hospital, and Center for Molecular Medicine (CMMC), Medical Faculty, University of Cologne, 50937 Cologne, Germany
| | - Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Tommy Martinsson
- Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Levent M Akyürek
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Leo Kurian
- Center for Molecular Medicine Cologne, Institute for Neurophysiology, The Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Maite Huarte
- Center for Applied Medical Research (CIMA), University of Navarra, Pio XII, 55, 31008 Pamplona, Spain
| | - Per Kogner
- Childhood Cancer Research Unit, Astrid Lindgren Children's Hospital, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital, and Center for Molecular Medicine (CMMC), Medical Faculty, University of Cologne, 50937 Cologne, Germany
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden.
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Ali MM, Akhade VS, Kosalai ST, Subhash S, Statello L, Meryet-Figuiere M, Abrahamsson J, Mondal T, Kanduri C. PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers. Nat Commun 2018; 9:883. [PMID: 29491376 PMCID: PMC5830406 DOI: 10.1038/s41467-018-03265-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 01/31/2018] [Indexed: 01/08/2023] Open
Abstract
Despite improvement in our understanding of long noncoding RNAs (lncRNAs) role in cancer, efforts to find clinically relevant cancer-associated lncRNAs are still lacking. Here, using nascent RNA capture sequencing, we identify 1145 temporally expressed S-phase-enriched lncRNAs. Among these, 570 lncRNAs show significant differential expression in at least one tumor type across TCGA data sets. Systematic clinical investigation of 14 Pan-Cancer data sets identified 633 independent prognostic markers. Silencing of the top differentially expressed and clinically relevant S-phase-enriched lncRNAs in several cancer models affects crucial cancer cell hallmarks. Mechanistic investigations on SCAT7 in multiple cancer types reveal that it interacts with hnRNPK/YBX1 complex and affects cancer cell hallmarks through the regulation of FGF/FGFR and its downstream PI3K/AKT and MAPK pathways. We also implement a LNA-antisense oligo-based strategy to treat cancer cell line and patient-derived tumor (PDX) xenografts. Thus, this study provides a comprehensive list of lncRNA-based oncogenic drivers with potential prognostic value. Although we know lncRNAs play a role in cancer, the identification of clinically relevant and functional lncRNAs is lacking. Here, the authors identify 633 prognostic markers, 570 S-phase cancer-associated lncRNAs, and show SCAT7 regulates FGF/FGFR and PI3K/AKT/MAPK pathways via interaction with hnRNPK/YBX1 complexes.
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Affiliation(s)
- Mohamad Moustafa Ali
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Vijay Suresh Akhade
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Luisa Statello
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Matthieu Meryet-Figuiere
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Jonas Abrahamsson
- Department of Pediatrics, Institution for Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Tanmoy Mondal
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 40530, Sweden.
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Abstract
Researchers have recently had a growing interest in understanding the functional role of long noncoding RNAs (lncRNAs) in chromatin organization. Accumulated evidence suggests lncRNAs could act as interphase molecules between chromatin and chromatin remodelers to define the epigenetic code. However, it is not clear how lncRNAs target chromatin remodelers to specific chromosomal regions in order to establish a functionally distinct epigenetic state of chromatin. We developed and optimized chromatin RNA immunoprecipitation (ChRIP) technology to characterize the lncRNAs associated with active and inactive chromatin compartments. Use of ChRIP to identify chromatin-bound lncRNA will further improve our knowledge regarding the functional role of lncRNAs in establishing epigenetic modifications of chromatin.
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Affiliation(s)
- Tanmoy Mondal
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9A, Box 440, Gothenburg, 40530, Sweden
| | - Santhilal Subhash
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9A, Box 440, Gothenburg, 40530, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9A, Box 440, Gothenburg, 40530, Sweden.
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Kopparapu PK, Abdelrazak Morsy MH, Kanduri C, Kanduri M. Gene-body hypermethylation controlled cryptic promoter and miR26A1-dependent EZH2 regulation of TET1 gene activity in chronic lymphocytic leukemia. Oncotarget 2017; 8:77595-77608. [PMID: 29100411 PMCID: PMC5652802 DOI: 10.18632/oncotarget.20668] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/29/2017] [Indexed: 12/18/2022] Open
Abstract
The Ten-eleven-translocation 1 (TET1) protein is a member of dioxygenase protein family that catalyzes the oxidation of 5-methylcytosine to 5-hydroxymethylcytosine. TET1 is differentially expressed in many cancers, including leukemia. However, very little is known about mechanism behind TET1 deregulation. Previously, by characterizing global methylation patterns in CLL patients using MBD-seq, we found TET1 as one of the differentially methylated regions with gene-body hypermethylation. Herein, we characterize mechanisms that control TET1 gene activity at the transcriptional level. We show that treatment of CLL cell lines with 5-aza 2´-deoxycytidine (DAC) results in the activation of miR26A1, which causes decrease in both mRNA and protein levels of EZH2, which in turn results in the decreased occupancy of EZH2 over the TET1 promoter and consequently the loss of TET1 expression. In addition, DAC treatment also leads to the activation of antisense transcription overlapping the TET1 gene from a cryptic promoter, located in the hypermethylated intronic region. Increased expression of intronic transcripts correlates with decreased TET1 promoter activity through the loss of RNA Pol II occupancy. Thus, our data demonstrate that TET1 gene activation in CLL depends on miR26A1 regulated EZH2 binding at the TET1 promoter and silencing of novel cryptic promoter by gene-body hypermethylation.
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Affiliation(s)
- Pradeep Kumar Kopparapu
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Mohammad Hamdy Abdelrazak Morsy
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
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Milosevic J, Eissler N, Treis D, Wicktröm M, Fransson S, Sveinbjornsson B, Baryawno N, Kosalai S, Kanduri C, Sakaguchi K, Martinsson T, Johnsen JI, Kogner P. Abstract 1945: PPM1D/Wip1, promising new target in childhood cancers neuroblastoma and medulloblastoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:
The most common cytogenetic lesions in the embryonal neural tumors medulloblastoma (MB) and neuroblastoma (NB) affect chromosome 17, with 17q+ or isochromosome 17q, in approximately one-third of MB with these aberrations being a significant indicator of poor clinical outcome. Similarly, in NB gain of 17q is the most powerful genetic predictor of adverse clinical outcome. 17q+ correlates with poor survival in our population-based material where we found aberrations of chromosome 17 in 85% of primary neuroblastomas, specifically, gain of PPM1D/Wip1 at 17q23. Wip1 is a serine/threonine phosphatase encoded by the gene PPM1D, described as a gatekeeper in the Mdm2-p53 regulatory loop involved in genetic stability, inflammation and a potential oncogene contributing to carcinogenesis.
Methods:
Comparative genomic hybridization (CGH), immunostaining, mRNA arrays, qPCR, exome- and RNA-sequencing was used to examine PPM1D/Wip1 in neuroblastoma and medulloblastoma. Genetic and pharmacological inhibition was used to analyze the function of Wip1 in preclinical neuroblastoma and medulloblastoma models.
Results:
CGH-array analysis detected PPM1D/Wip1 extra copies in all tumors and cell lines containing 17q-gain. Expression arrays and immunostaining showed high expression of Wip1 in neuroblastoma corresponding to poor survival. RNA sequencing confirmed PPM1D-gain and revealed truncated isoforms with oncogenic potential. Exome-sequencing detected a mutation leading to constitutive PPM1D/Wip1 activation in an aggressive metastatic infant neuroblastoma. Wip1 knockdown experiments showed significant decrease of cell viability, proliferation and colony formation as well as substantial increase of DNA-damage response in neuroblastoma and medulloblastoma cells. Tumor neuroblastoma xenograft development was significantly delayed showing median tumor development (0.10 mL) to be more than doubled (median 15 days, vs. 33 days, p<0.001) after Wip1 downregulation compared to scrambled controls. A novel Wip1 inhibitor was highly potent in cytotoxic/cytostatic effect in neuroblastoma and medulloblastoma cell lines. Furthermore, this Wip1 inhibitor significantly inhibited growth of established human neuroblastomas and medulloblastomas in nude mice after treatment (P<0.01).
Conclusions:
Our results show that PPM1D/Wip1 is oncogenic in neuroblastoma and medulloblastoma development. We propose three different ways on how PPM1D/Wip1 is activated: due to chromosomal gain, alternative RNA-isoforms and/or DNA-mutation. PPM1D/Wip1 provides a novel therapeutic target in neuroblastoma and medulloblastoma.
Citation Format: Jelena Milosevic, Nina Eissler, Diana Treis, Malin Wicktröm, Susanne Fransson, Baldur Sveinbjornsson, Ninib Baryawno, Subazini Kosalai, Chandrasekhar Kanduri, Kazuyasu Sakaguchi, Tommy Martinsson, John Inge Johnsen, Per Kogner. PPM1D/Wip1, promising new target in childhood cancers neuroblastoma and medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1945. doi:10.1158/1538-7445.AM2017-1945
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Per Kogner
- 1Karolinska Institutet, Stockholm, Sweden
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Vizlin-Hodzic D, Zhai Q, Illes S, Södersten K, Truvé K, Parris TZ, Sobhan PK, Salmela S, Kosalai ST, Kanduri C, Strandberg J, Seth H, Bontell TO, Hanse E, Ågren H, Funa K. Early onset of inflammation during ontogeny of bipolar disorder: the NLRP2 inflammasome gene distinctly differentiates between patients and healthy controls in the transition between iPS cell and neural stem cell stages. Transl Psychiatry 2017; 7:e1010. [PMID: 28117838 PMCID: PMC5545741 DOI: 10.1038/tp.2016.284] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 11/27/2016] [Indexed: 01/09/2023] Open
Abstract
Neuro-inflammation and neuronal communication are considered as mis-regulated processes in the aetiology and pathology of bipolar disorder (BD). Which and when specific signal pathways become abnormal during the ontogeny of bipolar disorder patients is unknown. To address this question, we applied induced pluripotent stem cell (iPSC) technology followed by cortical neural differentiation on adipocyte-derived cells from BD type I patients (with psychotic episodes in psychiatric history) and healthy volunteers (controls). RNA sequencing in iPSC and cortical neural stem cell (NSC) lines were used to examine alterations between the transcriptomes from BD I and control samples during transition from the pluripotent stage towards the neural developmental stage. At the iPSC stage, the most highly significant differentially expressed gene (DEG) was the NLRP2 inflammasome (P=2.66 × 10-10). Also among 42 DEGs at the NSC stage, NLRP2 showed the strongest statistical significance (P=3.07 × 10-19). In addition, we have also identified several cytoskeleton-associated genes as DEGs from the NSC stage, such as TMP2, TAGLN and ACTA2; the former two genes are recognised for the first time to be associated with BD. Our results also suggest that iPSC-derived BD-cortical NSCs carry several abnormalities in dopamine and GABA receptor canonical pathways, underlining that our in vitro BD model reflects pathology in the central nervous system. This would indicate that mis-regulated gene expression of inflammatory, neurotransmitter and cytoskeletal signalling occurs during early fetal brain development of BD I patients.
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Affiliation(s)
- D Vizlin-Hodzic
- Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Q Zhai
- Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - S Illes
- Institute of Neuroscience and Physiology, Department of Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Oncology Laboratory, Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - K Södersten
- Institute of Neuroscience and Physiology, Section of Psychiatry and Neurochemistry, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - K Truvé
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - T Z Parris
- Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - P K Sobhan
- Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - S Salmela
- Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - S T Kosalai
- Institute of Biomedicine, Department of Medical Genetics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - C Kanduri
- Institute of Biomedicine, Department of Medical Genetics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - J Strandberg
- Institute of Neuroscience and Physiology, Department of Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - H Seth
- Institute of Neuroscience and Physiology, Department of Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - T O Bontell
- Institute of Neuroscience and Physiology, Department of Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Department of Clinical Pathology and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - E Hanse
- Institute of Neuroscience and Physiology, Department of Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - H Ågren
- Institute of Neuroscience and Physiology, Section of Psychiatry and Neurochemistry, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Institute of Neuroscience and Physiology, Section of Psychiatry and Neurochemistry, Sahlgrenska Academy, University of Gothenburg, SE 405 30 Gothenburg, Sweden E-mail:
| | - K Funa
- Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Oncology Laboratory, Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden,Oncology Laboratory, Department of Pathology, Sahlgrenska University Hospital, SE 413 45 Gothenburg, Sweden. E-mail:
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Subhash S, Andersson PO, Kosalai ST, Kanduri C, Kanduri M. Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL. Clin Epigenetics 2016; 8:106. [PMID: 27777635 PMCID: PMC5062931 DOI: 10.1186/s13148-016-0274-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [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: 06/15/2016] [Accepted: 10/04/2016] [Indexed: 12/19/2022] Open
Abstract
Background Methyl-CpG-binding domain protein enriched genome-wide sequencing (MBD-Seq) is a robust and powerful method for analyzing methylated CpG-rich regions with complete genome-wide coverage. In chronic lymphocytic leukemia (CLL), the role of CpG methylated regions associated with transcribed long noncoding RNAs (lncRNA) and repetitive genomic elements are poorly understood. Based on MBD-Seq, we characterized the global methylation profile of high CpG-rich regions in different CLL prognostic subgroups based on IGHV mutational status. Results Our study identified 5800 hypermethylated and 12,570 hypomethylated CLL-specific differentially methylated genes (cllDMGs) compared to normal controls. From cllDMGs, 40 % of hypermethylated and 60 % of hypomethylated genes were mapped to noncoding RNAs. In addition, we found that the major repetitive elements such as short interspersed elements (SINE) and long interspersed elements (LINE) have a high percentage of cllDMRs (differentially methylated regions) in IGHV subgroups compared to normal controls. Finally, two novel lncRNAs (hypermethylated CRNDE and hypomethylated AC012065.7) were validated in an independent CLL sample cohort (48 samples) compared with 6 normal sorted B cell samples using quantitative pyrosequencing analysis. The methylation levels showed an inverse correlation to gene expression levels analyzed by real-time quantitative PCR. Notably, survival analysis revealed that hypermethylation of CRNDE and hypomethylation of AC012065.7 correlated with an inferior outcome. Conclusions Thus, our comprehensive methylation analysis by MBD-Seq provided novel hyper and hypomethylated long noncoding RNAs, repetitive elements, along with protein coding genes as potential epigenetic-based CLL-signature genes involved in disease pathogenesis and prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0274-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santhilal Subhash
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Per-Ola Andersson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden ; Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, S-413 45 Gothenburg, Sweden
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Subhash S, Kanduri C. GeneSCF: a real-time based functional enrichment tool with support for multiple organisms. BMC Bioinformatics 2016; 17:365. [PMID: 27618934 PMCID: PMC5020511 DOI: 10.1186/s12859-016-1250-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/08/2016] [Indexed: 12/19/2022] Open
Abstract
Background High-throughput technologies such as ChIP-sequencing, RNA-sequencing, DNA sequencing and quantitative metabolomics generate a huge volume of data. Researchers often rely on functional enrichment tools to interpret the biological significance of the affected genes from these high-throughput studies. However, currently available functional enrichment tools need to be updated frequently to adapt to new entries from the functional database repositories. Hence there is a need for a simplified tool that can perform functional enrichment analysis by using updated information directly from the source databases such as KEGG, Reactome or Gene Ontology etc. Results In this study, we focused on designing a command-line tool called GeneSCF (Gene Set Clustering based on Functional annotations), that can predict the functionally relevant biological information for a set of genes in a real-time updated manner. It is designed to handle information from more than 4000 organisms from freely available prominent functional databases like KEGG, Reactome and Gene Ontology. We successfully employed our tool on two of published datasets to predict the biologically relevant functional information. The core features of this tool were tested on Linux machines without the need for installation of more dependencies. Conclusions GeneSCF is more reliable compared to other enrichment tools because of its ability to use reference functional databases in real-time to perform enrichment analysis. It is an easy-to-integrate tool with other pipelines available for downstream analysis of high-throughput data. More importantly, GeneSCF can run multiple gene lists simultaneously on different organisms thereby saving time for the users. Since the tool is designed to be ready-to-use, there is no need for any complex compilation and installation procedures. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1250-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santhilal Subhash
- Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-40530, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-40530, Sweden.
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Meryet-Figuiere M, Alaei-Mahabadi B, Ali MM, Mitra S, Subhash S, Pandey GK, Larsson E, Kanduri C. Temporal separation of replication and transcription during S-phase progression. Cell Cycle 2015; 13:3241-8. [PMID: 25485504 DOI: 10.4161/15384101.2014.953876] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transcriptional events during S-phase are critical for cell cycle progression. Here, by using a nascent RNA capture assay coupled with high-throughput sequencing, we determined the temporal patterns of transcriptional events that occur during S-phase. We show that genes involved in critical S-phase-specific biological processes such as nucleosome assembly and DNA repair have temporal transcription patterns across S-phase that are not evident from total RNA levels. By comparing transcription timing with replication timing in S-phase, we show that early replicating genes show increased transcription late in S-phase whereas late replicating genes are predominantly transcribed early in S-phase. Global anti-correlation between replication and transcription timing was observed only based on nascent RNA but not total RNA. Our data provides a detailed view of ongoing transcriptional events during the S-phase of cell cycle, and supports that transcription and replication are temporally separated.
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Affiliation(s)
- Matthieu Meryet-Figuiere
- a Department of Medical Genetics; Institute of Biomedicine; The Sahlgrenska Academy ; University of Gothenburg ; Gothenburg , Sweden
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Kanduri C. Long noncoding RNAs: Lessons from genomic imprinting. Biochim Biophys Acta 2015; 1859:102-11. [PMID: 26004516 DOI: 10.1016/j.bbagrm.2015.05.006] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/12/2015] [Accepted: 05/15/2015] [Indexed: 12/17/2022]
Abstract
Genomic imprinting has been a great resource for studying transcriptional and post-transcriptional-based gene regulation by long noncoding RNAs (lncRNAs). In this article, I overview the functional role of intergenic lncRNAs (H19, IPW, and MEG3), antisense lncRNAs (Kcnq1ot1, Airn, Nespas, Ube3a-ATS), and enhancer lncRNAs (IG-DMR eRNAs) to understand the diverse mechanisms being employed by them in cis and/or trans to regulate the parent-of-origin-specific expression of target genes. Recent evidence suggests that some of the lncRNAs regulate imprinting by promoting intra-chromosomal higher-order chromatin compartmentalization, affecting replication timing and subnuclear positioning. Whereas others act via transcriptional occlusion or transcriptional collision-based mechanisms. By establishing genomic imprinting of target genes, the lncRNAs play a critical role in important biological functions, such as placental and embryonic growth, pluripotency maintenance, cell differentiation, and neural-related functions such as synaptic development and plasticity. An emerging consensus from the recent evidence is that the imprinted lncRNAs fine-tune gene expression of the protein-coding genes to maintain their dosage in cell. Hence, lncRNAs from imprinted clusters offer insights into their mode of action, and these mechanisms have been the basis for uncovering the mode of action of lncRNAs in several other biological contexts. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden.
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Kopparapu PK, Miranda C, Fogelstrand L, Mishra K, Andersson PO, Kanduri C, Kanduri M. MCPH1 maintains long-term epigenetic silencing of ANGPT2 in chronic lymphocytic leukemia. FEBS J 2015; 282:1939-52. [PMID: 25703238 DOI: 10.1111/febs.13245] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/27/2015] [Accepted: 02/17/2015] [Indexed: 12/15/2022]
Abstract
The microcephalin gene (MCPH1) [also known as inhibitor of human telomerase reverse transcriptase (hTERT) expression] is a tumor suppressor gene that is functionally involved in the DNA damage response. Angiopoietin 2 (ANGPT2) is a crucial factor regulating tumor angiopoiesis. Deregulation of angiogenesis is one of the hallmarks of many cancers, including chronic lymphocytic leukemia (CLL). In CLL, ANGPT2 is a well-studied potential prognostic marker. As MCPH1 overlaps with the ANGPT2 transcription unit on the same chromosome but in the opposite orientation, we wanted to study the functional role of MCPH1 in regulation of ANGPT2 in CLL. The mRNA expression levels of MCPH1 and ANGPT2, including the MCPH1 target gene hTERT, showed significant differences between two prognostic groups, i.e. IGHV-mutated and IGHV-unmutated (P = 0.007 for MCPH1, P = 0.0002 for ANGPT2, and P = 0.00001 for hTERT), in which the expression level of MCPH1 was inversely correlated with the expression levels of hTERT and ANGPT2. Downregulation of MCPH1 resulted in upregulation of ANGPT2, accompanied by loss of its promoter methylation. Using chromatin immunoprecipitation and coimmunoprecipitation assays, we found that MCPH1 binds to the ANGPT2 promoter and recruits DNA methyltransferases, thereby silencing ANGPT2. Thus, our data suggest a novel function for MCPH1 in regulating and maintaining ANGPT2 silencing in CLL through regulation of promoter DNA methylation.
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Affiliation(s)
- Pradeep Kumar Kopparapu
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Sweden
| | - Caroline Miranda
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Sweden
| | - Linda Fogelstrand
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Sweden
| | - Kankadeb Mishra
- Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Sweden
| | - Per-Ola Andersson
- Department of Internal Medicine and Oncology, Borås Hospital, Sweden.,Department of Medicine, Sahlgrenska Academy, Gothenburg University, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Sweden
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, Sweden
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Affiliation(s)
- Gaurav Kumar Pandey
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Pandey GK, Mitra S, Subhash S, Hertwig F, Kanduri M, Mishra K, Fransson S, Ganeshram A, Mondal T, Bandaru S, Ostensson M, Akyürek LM, Abrahamsson J, Pfeifer S, Larsson E, Shi L, Peng Z, Fischer M, Martinsson T, Hedborg F, Kogner P, Kanduri C. The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma progression by regulating cell proliferation and neuronal differentiation. Cancer Cell 2014; 26:722-37. [PMID: 25517750 DOI: 10.1016/j.ccell.2014.09.014] [Citation(s) in RCA: 252] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 04/08/2014] [Accepted: 09/25/2014] [Indexed: 02/08/2023]
Abstract
Neuroblastoma is an embryonal tumor of the sympathetic nervous system and the most common extracranial tumor of childhood. By sequencing transcriptomes of low- and high-risk neuroblastomas, we detected differentially expressed annotated and nonannotated long noncoding RNAs (lncRNAs). We identified a lncRNA neuroblastoma associated transcript-1 (NBAT-1) as a biomarker significantly predicting clinical outcome of neuroblastoma. CpG methylation and a high-risk neuroblastoma associated SNP on chromosome 6p22 functionally contribute to NBAT-1 differential expression. Loss of NBAT-1 increases cellular proliferation and invasion. It controls these processes via epigenetic silencing of target genes. NBAT-1 loss affects neuronal differentiation through activation of the neuronal-specific transcription factor NRSF/REST. Thus, loss of NBAT-1 contributes to aggressive neuroblastoma by increasing proliferation and impairing differentiation of neuronal precursors.
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Affiliation(s)
- Gaurav Kumar Pandey
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Sanhita Mitra
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Santhilal Subhash
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Falk Hertwig
- Department of Pediatric Hematology and Oncology, University Children's Hospital of Cologne, and Center for Molecular Medicine Cologne, University of Cologne, 50924 Cologne, Germany
| | - Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Kankadeb Mishra
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Susanne Fransson
- Department of Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Abiarchana Ganeshram
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Tanmoy Mondal
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Sashidhar Bandaru
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Malin Ostensson
- Department of Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Levent M Akyürek
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jonas Abrahamsson
- Department of Pediatrics, The Queen Silvia Children's Hospital, 416 85 Gothenburg, Sweden
| | - Susan Pfeifer
- Department of Women's and Children's Health, Uppsala University, Uppsala University Hospital, 751 85 Uppsala, Sweden
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Leming Shi
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Zhiyu Peng
- BGI-Guangzhou, Guangzhou 510006, China; BGI-Shenzhen, Shenzhen, GuangDong 518083, China
| | - Matthias Fischer
- Department of Pediatric Hematology and Oncology, University Children's Hospital of Cologne, and Center for Molecular Medicine Cologne, University of Cologne, 50924 Cologne, Germany
| | - Tommy Martinsson
- Department of Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Fredrik Hedborg
- Department of Women's and Children's Health, Uppsala University, Uppsala University Hospital, 751 85 Uppsala, Sweden; Centre for Research and Development, Uppsala University/County Council of Gävleborg, 801 88 Gävle, Sweden
| | - Per Kogner
- Department of Women's and Children's Health, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Chandrasekhar Kanduri
- Department of Medical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden.
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Abstract
Along the lines of established players like chromatin modifiers and transcription factors, noncoding RNA (ncRNA) are now widely accepted as one of the key regulatory molecules in epigenetic regulation of transcription. With increasing evidence of ncRNAs in the establishment of gene silencing through their ability to interact with major chromatin modifiers, in the current review, we discuss their prospective role in the area of inheritance and maintenance of these established silenced states which can be reversible or irreversible in nature. In addition, we attempt to understand and speculate how these RNA dependent or independent maintenance mechanisms differ between each other in a developmental stage, tissue, and gene-specific manner in different biological contexts by utilizing known/unknown regulatory factors.
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Affiliation(s)
- Tanmoy Mondal
- Department of Medical Genetics, Institute of Biomedicine, The Sahlgrenska Academy, Gothenburg University, Medicinaregatan 9A, 40530, Gothenburg, Sweden
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Kanduri M, Sander B, Ntoufa S, Papakonstantinou N, Sutton LA, Stamatopoulos K, Kanduri C, Rosenquist R. A key role for EZH2 in epigenetic silencing of HOX genes in mantle cell lymphoma. Epigenetics 2013; 8:1280-8. [PMID: 24107828 DOI: 10.4161/epi.26546] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The chromatin modifier EZH2 is overexpressed and associated with inferior outcome in mantle cell lymphoma (MCL). Recently, we demonstrated preferential DNA methylation of HOX genes in MCL compared with chronic lymphocytic leukemia (CLL), despite these genes not being expressed in either entity. Since EZH2 has been shown to regulate HOX gene expression, to gain further insight into its possible role in differential silencing of HOX genes in MCL vs. CLL, we performed detailed epigenetic characterization using representative cell lines and primary samples. We observed significant overexpression of EZH2 in MCL vs. CLL. Chromatin immune precipitation (ChIP) assays revealed that EZH2 catalyzed repressive H3 lysine 27 trimethylation (H3K27me3), which was sufficient to silence HOX genes in CLL, whereas in MCL H3K27me3 is accompanied by DNA methylation for a more stable repression. More importantly, hypermethylation of the HOX genes in MCL resulted from EZH2 overexpression and subsequent recruitment of the DNA methylation machinery onto HOX gene promoters. The importance of EZH2 upregulation in this process was further underscored by siRNA transfection and EZH2 inhibitor experiments. Altogether, these observations implicate EZH2 in the long-term silencing of HOX genes in MCL, and allude to its potential as a therapeutic target with clinical impact.
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Affiliation(s)
- Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; Gothenburg University; Gothenburg, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine; Division of Pathology; Karolinska Institutet and Karolinska University Hospital; Huddinge, Sweden
| | - Stavroula Ntoufa
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Nikos Papakonstantinou
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology; Uppsala University; Uppsala, Sweden
| | - Kostas Stamatopoulos
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Chandrasekhar Kanduri
- Department of Medical and Clinical Genetics; Department of Biomedicine; The Sahlgrenska Academy; Gothenburg University; Gothenburg, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology; Uppsala University; Uppsala, Sweden
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Abstract
The catalogue of genes expressed at different levels in the two sexes is growing, and the mechanisms underlying sex differences in regulation of the mammalian transcriptomes are being explored. Here we report that the expression of the imprinted non-protein-coding maternally expressed gene H19 was female-biased specifically in the female mouse eye (1.9-fold, p = 3.0E−6) while not being sex-biased in other somatic tissues. The female-to-male expression fold-change of H19 fell in the range expected from an effect of biallelic versus monoallelic expression. Recently, the possibility of sex-specific parent-of-origin allelic expression has been debated. This led us to hypothesize that H19 might express biallelically in the female mouse eye, thus escape its silencing imprint on the paternal allele specifically in this tissue. We therefore performed a sex-specific imprinting assay of H19 in female and male eye derived from a cross between Mus musculus and Mus spretus. However, this analysis demonstrated that H19 was exclusively expressed from the maternal gene copy, disproving the escape hypothesis. Instead, this supports that the female-biased expression of H19 is the result of upregulation of the single maternal. Furthermore, if H19 would have been expressed from both gene copies in the female eye, an associated downregulation of Insulin-like growth factor 2 (Igf2) was expected, since H19 and Igf2 compete for a common enhancer element located in the H19/Igf2 imprinted domain. On the contrary we found that also Igf2 was significantly upregulated in its expression in the female eye (1.2-fold, p = 6.1E−3), in further agreement with the conclusion that H19 is monoallelically elevated in females. The female-biased expression of H19 and Igf2 specifically in the eye may contribute to our understanding of sex differences in normal as well as abnormal eye physiology and processes.
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Affiliation(s)
- Björn Reinius
- Institute of Biomedicine, Department of Medical and Clinical Genetics, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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Abstract
The Genome of a eukaryotic cell harbors genetic material in the form of DNA which carries the hereditary information encoded in their bases. Nucleotide bases of DNA are transcribed into complimentary RNA bases which are further translated into protein, performing defined set of functions. The central dogma of life ensures sequential flow of genetic information among these biopolymers. Noncoding RNAs (ncRNAs) serve as exceptions for this principle as they do not code for any protein. Nevertheless, a major portion of the human transcriptome comprises noncoding RNAs. These RNAs vary in size, as well as they vary in the spatio-temporal distribution. These ncRnAs are functional and are shown to be involved in diverse cellular activities. Precise location and expression of ncRNA is essential for the cellular homeostasis. Failures of these events ultimately results in numerous disease conditions including cancer. The present review lists out the various classes of ncRNAs with a special emphasis on their role in chromatin organization and transcription regulation.
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Affiliation(s)
- Karthigeyan Dhanasekaran
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore, 560064, India
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Akhtar M, Holmgren C, Göndör A, Vesterlund M, Kanduri C, Larsson C, Ekström TJ. Cell type and context-specific function of PLAG1 for IGF2 P3 promoter activity. Int J Oncol 2012; 41:1959-66. [PMID: 23023303 PMCID: PMC3583874 DOI: 10.3892/ijo.2012.1641] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [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: 06/15/2012] [Accepted: 08/14/2012] [Indexed: 12/23/2022] Open
Abstract
The fetal transcription factor PLAG1 is found to be overexpressed in cancers, and has been suggested to bind the insulin like growth factor 2 (IGF2) P3 promoter, and to activate the IGF2 gene. The expression of IGF2 has partly been linked to loss of CTCF-dependent chromatin insulator function at the H19 imprinting control region (ICR). We investigated the role of PLAG1 for IGF2 regulation in Hep3B and JEG-3 cell lines. Chromatin immunoprecipitation revealed cell type-specific binding of PLAG1 to the IGF2 P3 promoter, which was substantially insensitive to recombinant PLAG1 overexpression in the endogenous context. We hypothesized that the H19 chromatin insulator may be involved in the cell type-specific PLAG1 response. By using a GFP reporter gene/insulator assay plasmid construct with and without the H19 ICR and/or an SV40 enhancer, we confirm that the effect of the insulator is specifically associated with the activity of the IGF2 P3 promoter in the GFP reporter system, and furthermore, that the reporter insulator is functional in JEG-3 but not in Hep3B cells. FACS analysis was used to assess the function of PLAG1 in low endogenously expressing, but Zn-inducible stable PLAG1 expressing JEG-3 cell clones. Considerable increase in IGF2 expression upon PLAG1 induction with a partial insulator overriding activity was found using the reporter constructs. This is in contrast to the effect of the endogenous IGF2 gene which was insensitive to PLAG1 expression in JEG-3, while modestly induced the already highly expressed IGF2 gene in Hep3B cells. We suggest that the PLAG1 binding to the IGF2 P3 promoter and IGF2 expression is cell type-specific, and that the PLAG1 transcription factor acts as a transcriptional facilitator that partially overrides the insulation by the H19 ICR.
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Affiliation(s)
- Monira Akhtar
- Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
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Mohammad F, Pandey GK, Mondal T, Enroth S, Redrup L, Gyllensten U, Kanduri C. Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing. J Cell Sci 2012. [DOI: 10.1242/jcs.116681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Mohammad F, Pandey GK, Mondal T, Enroth S, Redrup L, Gyllensten U, Kanduri C. Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing. Development 2012; 139:2792-803. [PMID: 22721776 DOI: 10.1242/dev.079566] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Establishment of silencing by noncoding RNAs (ncRNAs) via targeting of chromatin remodelers is relatively well investigated; however, their role in the maintenance of silencing is poorly understood. Here, we explored the functional role of the long ncRNA Kcnq1ot1 in the maintenance of transcriptional gene silencing in the one mega-base Kcnq1 imprinted domain in a transgenic mouse model. By conditionally deleting the Kcnq1ot1 ncRNA at different stages of mouse development, we suggest that Kcnq1ot1 ncRNA is required for the maintenance of the silencing of ubiquitously imprinted genes (UIGs) at all developmental stages. In addition, Kcnq1ot1 ncRNA is also involved in guiding and maintaining the CpG methylation at somatic differentially methylated regions flanking the UIGs, which is a hitherto unknown role for a long ncRNA. On the other hand, silencing of some of the placental-specific imprinted genes (PIGs) is maintained independently of Kcnq1ot1 ncRNA. Interestingly, the non-imprinted genes (NIGs) that escape RNA-mediated silencing are enriched with enhancer-specific modifications. Taken together, this study illustrates the gene-specific maintenance mechanisms operational at the Kcnq1 locus for tissue-specific transcriptional gene silencing and activation.
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Affiliation(s)
- Faizaan Mohammad
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Dag Hammarskjölds Väg 20, Uppsala University, Uppsala, Sweden
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Affiliation(s)
- Tanmoy Mondal
- From the Department of Medical and Clinical Genetics (T.M., C.K.), Institute of Biomedicine, The Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- From the Department of Medical and Clinical Genetics (T.M., C.K.), Institute of Biomedicine, The Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
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Chiesa N, De Crescenzo A, Mishra K, Perone L, Carella M, Palumbo O, Mussa A, Sparago A, Cerrato F, Russo S, Lapi E, Cubellis MV, Kanduri C, Cirillo Silengo M, Riccio A, Ferrero GB. The KCNQ1OT1 imprinting control region and non-coding RNA: new properties derived from the study of Beckwith-Wiedemann syndrome and Silver-Russell syndrome cases. Hum Mol Genet 2011; 21:10-25. [PMID: 21920939 PMCID: PMC3235007 DOI: 10.1093/hmg/ddr419] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A cluster of imprinted genes at chromosome 11p15.5 is associated with the growth disorders, Silver–Russell syndrome (SRS) and Beckwith–Wiedemann syndrome (BWS). The cluster is divided into two domains with independent imprinting control regions (ICRs). We describe two maternal 11p15.5 microduplications with contrasting phenotypes. The first is an inverted and in cis duplication of the entire 11p15.5 cluster associated with the maintenance of genomic imprinting and with the SRS phenotype. The second is a 160 kb duplication also inverted and in cis, but resulting in the imprinting alteration of the centromeric domain. It includes the centromeric ICR (ICR2) and the most 5′ 20 kb of the non-coding KCNQ1OT1 gene. Its maternal transmission is associated with ICR2 hypomethylation and the BWS phenotype. By excluding epigenetic mosaicism, cell clones analysis indicated that the two closely located ICR2 sequences resulting from the 160 kb duplication carried discordant DNA methylation on the maternal chromosome and supported the hypothesis that the ICR2 sequence is not sufficient for establishing imprinted methylation and some other property, possibly orientation-dependent, is needed. Furthermore, the 1.2 Mb duplication demonstrated that all features are present for correct imprinting at ICR2 when this is duplicated and inverted within the entire cluster. In the individuals maternally inheriting the 160 kb duplication, ICR2 hypomethylation led to the expression of a truncated KCNQ1OT1 transcript and to down-regulation of CDKN1C. We demonstrated by chromatin RNA immunopurification that the KCNQ1OT1 RNA interacts with chromatin through its most 5′ 20 kb sequence, providing a mechanism likely mediating the silencing activity of this long non-coding RNA.
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Affiliation(s)
- Nicoletta Chiesa
- Dipartimento di Scienze Pediatriche e dell’Adolescenza, Università di Torino, Torino, Italy
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Mohammad F, Mondal T, Guseva N, Pandey GK, Kanduri C. Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development 2010; 137:2493-9. [PMID: 20573698 DOI: 10.1242/dev.048181] [Citation(s) in RCA: 207] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A long noncoding RNA, Kcnq1ot1, regulates the expression of both ubiquitously and tissue-specific imprinted genes within the Kcnq1 domain. However, the functional sequences of the Kcnq1ot1 RNA that mediate lineage-specific imprinting are unknown. Here, we have generated a knockout mouse with a deletion encompassing an 890-bp silencing domain (Delta890) downstream of the Kcnq1ot1 promoter. Maternal transmission of the Delta890 allele has no effect on imprinting, whereas paternal inheritance of the deletion leads to selective relaxation of the imprinting of ubiquitously imprinted genes to a variable extent in a tissue-specific manner. Interestingly, the deletion affects DNA methylation at somatically acquired differentially methylated regions (DMRs), but does not affect the histone modifications of the ubiquitously imprinted genes. Importantly, we found that Kcnq1ot1 recruits Dnmt1 to somatic DMRs by interacting with Dnmt1, and that this interaction was significantly reduced in the Delta890 mice. Thus, the ubiquitous and placental-specific imprinting of genes within the Kcnq1 domain might be mediated by distinct mechanisms, and Kcnq1ot1 RNA might mediate the silencing of ubiquitously imprinted genes by maintaining allele-specific methylation through its interactions with Dnmt1.
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Affiliation(s)
- Faizaan Mohammad
- Department of Genetics and Pathology, Dag Hammarskjölds Väg 20, 75185 Rudbeck Laboratory, Uppsala University, Uppsala 75185, Sweden
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Abstract
Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harboring CARs. The intronic and intergenic CARs show significant conservation across 44 species of placental mammals. Functional characterization of one of the intergenic CARs, Intergenic10, revealed that it regulates gene expression of neighboring genes through modulating the chromatin structure in cis. Our data suggest that ncRNA is an integral component of chromatin and that it may regulate various biological functions through fine-tuning of the chromatin architecture.
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Affiliation(s)
- Tanmoy Mondal
- Department of Genetics and Pathology, Uppsala University, Uppsala S-75185, Sweden
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Mohammad F, Mondal T, Kanduri C. Epigenetics of imprinted long noncoding RNAs. Epigenetics 2009; 4:277-286. [PMID: 19617707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
It is becoming increasingly evident that noncoding RNA (ncRNA) constitutes an important component of chromatin and that ncRNA has a critical role in organizing the chromatin architecture and epigenetic memory by acting as an interface with the chromatin modifying machinery. Xist is the only RNA that has been shown to regulate gene expression by modulating chromatin structure using a multilayered silencing pathway. Recent emerging evidence indicates that long ncRNAs such as Kcnq1ot1 and Air which map to the Kcnq1 and Igf2r imprinted gene clusters, respectively, mediate the transcriptional silencing of multiple genes by interacting with chromatin and recruiting the chromatin modifying machinery. Though there are some parallels in the mechanistic actions of Kcnq1ot1 and Air, they seem to differ greatly in the way they achieve the silencing of overlapping and nonoverlapping genes. By reviewing the latest available evidence, we propose that Kcnq1ot1 RNA itself seems to play a critical role in the bidirectional silencing of genes in the Kcnq1 domain, thus resembling the Xist RNA; whereas in the case of Air, the act of transcription plays a critical role in the silencing of the overlapping gene, whilst Air RNA itself mediates the silencing of nonoverlapping genes in a fashion similar to Kcnq1ot1 and Xist RNAs.
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Affiliation(s)
- Faizaan Mohammad
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Kanduri C, Whitehead J, Mohammad F. The long and the short of it: RNA-directed chromatin asymmetry in mammalian X-chromosome inactivation. FEBS Lett 2009; 583:857-64. [PMID: 19302783 DOI: 10.1016/j.febslet.2009.02.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 02/01/2009] [Accepted: 02/02/2009] [Indexed: 01/07/2023]
Abstract
Mammalian X-chromosome inactivation is controlled by a multilayered silencing pathway involving both short and long non-coding RNAs, which differentially recruit the epigenetic machinery to establish chromatin asymmetries. In response to developmentally regulated small RNAs, dicer, a key effector of RNA interference, locally silences Xist on the active X-chromosome and establishes the heterochromatin conformation along the silent X-chromosome. The 1.6 kb RepA RNA initiates silencing by targeting the PRC2 polycomb complex to the inactive X-chromosome. In addition, the nuclear microenvironment is implicated in the initiation and maintenance of X-chromosome asymmetries. Here we review new findings involving these various RNA species in terms of understanding Xist gene regulation and the establishment of X-chromosome inactivation.
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Affiliation(s)
- Chandrasekhar Kanduri
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
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