1
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Lorusso G, Wyss CB, Kuonen F, Vannini N, Billottet C, Duffey N, Pineau R, Lan Q, Wirapati P, Barras D, Tancredi A, Lyck R, Lehr HA, Engelhardt B, Delorenzi M, Bikfalvi A, Rüegg C. Connexins orchestrate progression of breast cancer metastasis to the brain by promoting FAK activation. Sci Transl Med 2022; 14:eaax8933. [PMID: 36070364 DOI: 10.1126/scitranslmed.aax8933] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Brain metastasis is a complication of increasing incidence in patients with breast cancer at advanced disease stage. It is a severe condition characterized by a rapid decline in quality of life and poor prognosis. There is a critical clinical need to develop effective therapies to prevent and treat brain metastases. Here, we describe a unique and robust spontaneous preclinical model of breast cancer metastasis to the brain (4T1-BM2) in mice that has been instrumental in uncovering molecular mechanisms guiding metastatic dissemination and colonization of the brain. Key experimental findings were validated in the additional murine D2A1-BM2 model and in human MDA231-BrM2 model. Gene expression analyses and functional studies, coupled with clinical transcriptomic and histopathological investigations, identified connexins (Cxs) and focal adhesion kinase (FAK) as master molecules orchestrating breast cancer colonization of the brain. Cx31 promoted homotypic tumor cell adhesion, heterotypic tumor-astrocyte interaction, and FAK phosphorylation. FAK signaling prompted NF-κB activation inducing Lamc2 expression and laminin 332 (laminin 5) deposition, α6 integrin-mediated adhesion, and sustained survival and growth within brain parenchyma. In the MDA231-BrM2 model, the human homologous molecules CX43, LAMA4, and α3 integrin were involved. Systemic treatment with FAK inhibitors reduced brain metastasis progression. In conclusion, we report a spontaneous model of breast cancer metastasis to the brain and identified Cx-mediated FAK-NF-κB signaling as a mechanism promoting cell-autonomous and microenvironmentally controlled cell survival for brain colonization. Considering the limited therapeutic options for brain metastatic disease in cancer patients, we propose FAK as a therapeutic candidate to further pursue in the clinic.
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Affiliation(s)
- Girieca Lorusso
- Experimental and Translational Oncology, Pathology Unit, Department of Oncology Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg 1700, Switzerland.,Division of Experimental Oncology, Multidisciplinary Oncology Center (CePO), Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), Faculty of Biology and Medicine, Epalinges 1066, Switzerland.,National Center for Competence in Research (NCCR) Molecular Oncology, Swiss Institute of Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne (ISREC-EPFL), Lausanne 1015, Switzerland
| | - Christof B Wyss
- Experimental and Translational Oncology, Pathology Unit, Department of Oncology Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg 1700, Switzerland
| | - François Kuonen
- Division of Experimental Oncology, Multidisciplinary Oncology Center (CePO), Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), Faculty of Biology and Medicine, Epalinges 1066, Switzerland.,National Center for Competence in Research (NCCR) Molecular Oncology, Swiss Institute of Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne (ISREC-EPFL), Lausanne 1015, Switzerland
| | - Nicola Vannini
- Ludwig Institute for Cancer Research (LICR), Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), Epalinges 1066, Switzerland
| | | | - Nathalie Duffey
- Experimental and Translational Oncology, Pathology Unit, Department of Oncology Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg 1700, Switzerland
| | - Raphael Pineau
- INSERM U1029 and University of Bordeaux, Pessac Cedex 33615, France
| | - Qiang Lan
- Experimental and Translational Oncology, Pathology Unit, Department of Oncology Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg 1700, Switzerland.,Division of Experimental Oncology, Multidisciplinary Oncology Center (CePO), Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), Faculty of Biology and Medicine, Epalinges 1066, Switzerland.,National Center for Competence in Research (NCCR) Molecular Oncology, Swiss Institute of Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne (ISREC-EPFL), Lausanne 1015, Switzerland
| | - Pratyaksha Wirapati
- Bioinformatics Core Facility, Swiss Institute for Bioinformatics (SIB), Lausanne 1015, Switzerland
| | - David Barras
- Bioinformatics Core Facility, Swiss Institute for Bioinformatics (SIB), Lausanne 1015, Switzerland
| | - Alessandro Tancredi
- Experimental and Translational Oncology, Pathology Unit, Department of Oncology Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg 1700, Switzerland
| | - Ruth Lyck
- Theodor Kocher Institute, University of Bern (UNIBE), Bern 3012, Switzerland
| | - Hans-Anton Lehr
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), Lausanne 1011, Switzerland
| | - Britta Engelhardt
- Theodor Kocher Institute, University of Bern (UNIBE), Bern 3012, Switzerland
| | - Mauro Delorenzi
- Bioinformatics Core Facility, Swiss Institute for Bioinformatics (SIB), Lausanne 1015, Switzerland
| | - Andreas Bikfalvi
- INSERM U1029 and University of Bordeaux, Pessac Cedex 33615, France
| | - Curzio Rüegg
- Experimental and Translational Oncology, Pathology Unit, Department of Oncology Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, Fribourg 1700, Switzerland.,Division of Experimental Oncology, Multidisciplinary Oncology Center (CePO), Centre Hospitalier Universitaire Vaudois (CHUV) and University of Lausanne (UNIL), Faculty of Biology and Medicine, Epalinges 1066, Switzerland.,National Center for Competence in Research (NCCR) Molecular Oncology, Swiss Institute of Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne (ISREC-EPFL), Lausanne 1015, Switzerland
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2
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Wu M, Karadoulama E, Lloret-Llinares M, Rouviere JO, Vaagensø CS, Moravec M, Li B, Wang J, Wu G, Gockert M, Pelechano V, Jensen TH, Sandelin A. The RNA exosome shapes the expression of key protein-coding genes. Nucleic Acids Res 2020; 48:8509-8528. [PMID: 32710631 PMCID: PMC7470964 DOI: 10.1093/nar/gkaa594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
The ribonucleolytic exosome complex is central for nuclear RNA degradation, primarily targeting non-coding RNAs. Still, the nuclear exosome could have protein-coding (pc) gene-specific regulatory activities. By depleting an exosome core component, or components of exosome adaptor complexes, we identify ∼2900 transcription start sites (TSSs) from within pc genes that produce exosome-sensitive transcripts. At least 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their transcripts share the annotated mRNA 3′ end. We identify two types of pc-genes, both employing a single, annotated TSS across cells, but the first type primarily produces full-length, exosome-sensitive transcripts, whereas the second primarily produces prematurely terminated transcripts. Genes within the former type often belong to immediate early response transcription factors, while genes within the latter are likely transcribed as a consequence of their proximity to upstream TSSs on the opposite strand. Conversely, when genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive transcripts typically do not contribute substantially to overall gene expression, and most such transcripts are prematurely terminated. Our results display a complex landscape of sense transcription within pc-genes and imply a direct role for nuclear RNA turnover in the regulation of a subset of pc-genes.
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Affiliation(s)
- Mengjun Wu
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Evdoxia Karadoulama
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Marta Lloret-Llinares
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark.,European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jerome Olivier Rouviere
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Christian Skov Vaagensø
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Martin Moravec
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Bingnan Li
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Guifen Wu
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Maria Gockert
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
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3
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Thodberg M, Thieffry A, Bornholdt J, Boyd M, Holmberg C, Azad A, Workman CT, Chen Y, Ekwall K, Nielsen O, Sandelin A. Comprehensive profiling of the fission yeast transcription start site activity during stress and media response. Nucleic Acids Res 2019; 47:1671-1691. [PMID: 30566651 PMCID: PMC6393241 DOI: 10.1093/nar/gky1227] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/09/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022] Open
Abstract
Fission yeast, Schizosaccharomyces pombe, is an attractive model organism for transcriptional and chromatin biology research. Such research is contingent on accurate annotation of transcription start sites (TSSs). However, comprehensive genome-wide maps of TSSs and their usage across commonly applied laboratory conditions and treatments for S. pombe are lacking. To this end, we profiled TSS activity genome-wide in S. pombe cultures exposed to heat shock, nitrogen starvation, hydrogen peroxide and two commonly applied media, YES and EMM2, using Cap Analysis of Gene Expression (CAGE). CAGE-based annotation of TSSs is substantially more accurate than existing PomBase annotation; on average, CAGE TSSs fall 50-75 bp downstream of PomBase TSSs and co-localize with nucleosome boundaries. In contrast to higher eukaryotes, dispersed TSS distributions are not common in S. pombe. Our data recapitulate known S. pombe stress expression response patterns and identify stress- and media-responsive alternative TSSs. Notably, alteration of growth medium induces changes of similar magnitude as some stressors. We show a link between nucleosome occupancy and genetic variation, and that the proximal promoter region is genetically diverse between S. pombe strains. Our detailed TSS map constitutes a central resource for S. pombe gene regulation research.
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Affiliation(s)
- Malte Thodberg
- Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, University of Copenhagen, DK2100 Copenhagen N, Denmark
| | - Axel Thieffry
- Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, University of Copenhagen, DK2100 Copenhagen N, Denmark
| | - Jette Bornholdt
- Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, University of Copenhagen, DK2100 Copenhagen N, Denmark
| | - Mette Boyd
- Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, University of Copenhagen, DK2100 Copenhagen N, Denmark
| | - Christian Holmberg
- Department of Biology, Cell cycle and genome stability Group, University of Copenhagen, DK2100 Copenhagen N, Denmark
| | - Ajuna Azad
- Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, University of Copenhagen, DK2100 Copenhagen N, Denmark
| | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK2800 Kongens Lyngby, Denmark
| | - Yun Chen
- Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, University of Copenhagen, DK2100 Copenhagen N, Denmark
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institute, SE14183 Huddinge, Sweden
| | - Olaf Nielsen
- Department of Biology, Cell cycle and genome stability Group, University of Copenhagen, DK2100 Copenhagen N, Denmark
| | - Albin Sandelin
- Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, University of Copenhagen, DK2100 Copenhagen N, Denmark
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4
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Identification and Functional Analysis of Gene Regulatory Sequences Interacting with Colorectal Tumor Suppressors. Methods Mol Biol 2019; 1765:57-77. [PMID: 29589301 DOI: 10.1007/978-1-4939-7765-9_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Several tumor suppressors possess gene regulatory activity. Here, we describe how promoter and promoter/enhancer reporter assays can be used to characterize a colorectal tumor suppressor proteins' gene regulatory activity of possible target genes. In the first part, a bioinformatic approach to identify relevant gene regulatory regions of potential target genes is presented. In the second part, it is demonstrated how to prepare and carry out the functional assay.We explain how to clone the bioinformatically identified gene regulatory regions into luciferase reporter plasmids by the use of the quick and efficient In-Fusion cloning method, and how to carry out transient transfections of Caco-2 colon cancer cells with the produced luciferase reporter plasmids using polyethyleneimine (PEI). A plan describing how to set up and carry out the luciferase expression assay is presented. The luciferase/β-galactosidase (Dual Light) assay presented is a highly sensitive assay that can monitor small changes in the promoter/enhancer activity and includes an internal control monitoring transfection efficiency.
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5
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Lloret-Llinares M, Karadoulama E, Chen Y, Wojenski LA, Villafano GJ, Bornholdt J, Andersson R, Core L, Sandelin A, Jensen TH. The RNA exosome contributes to gene expression regulation during stem cell differentiation. Nucleic Acids Res 2018; 46:11502-11513. [PMID: 30212902 PMCID: PMC6265456 DOI: 10.1093/nar/gky817] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/29/2018] [Accepted: 09/09/2018] [Indexed: 12/27/2022] Open
Abstract
Gene expression programs change during cellular transitions. It is well established that a network of transcription factors and chromatin modifiers regulate RNA levels during embryonic stem cell (ESC) differentiation, but the full impact of post-transcriptional processes remains elusive. While cytoplasmic RNA turnover mechanisms have been implicated in differentiation, the contribution of nuclear RNA decay has not been investigated. Here, we differentiate mouse ESCs, depleted for the ribonucleolytic RNA exosome, into embryoid bodies to determine to which degree RNA abundance in the two states can be attributed to changes in transcription versus RNA decay by the exosome. As a general observation, we find that exosome depletion mainly leads to the stabilization of RNAs from lowly transcribed loci, including several protein-coding genes. Depletion of the nuclear exosome cofactor RBM7 leads to similar effects. In particular, transcripts that are differentially expressed between states tend to be more exosome sensitive in the state where expression is low. We conclude that the RNA exosome contributes to down-regulation of transcripts with disparate expression, often in conjunction with transcriptional down-regulation.
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Affiliation(s)
| | - Evdoxia Karadoulama
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Yun Chen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Luke A Wojenski
- Department of Molecular and Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Geno J Villafano
- Department of Molecular and Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Jette Bornholdt
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
| | - Leighton Core
- Department of Molecular and Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
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6
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Danielsen ET, Olsen AK, Coskun M, Nonboe AW, Larsen S, Dahlgaard K, Bennett EP, Mitchelmore C, Vogel LK, Troelsen JT. Intestinal regulation of suppression of tumorigenicity 14 (ST14) and serine peptidase inhibitor, Kunitz type -1 (SPINT1) by transcription factor CDX2. Sci Rep 2018; 8:11813. [PMID: 30087389 PMCID: PMC6081401 DOI: 10.1038/s41598-018-30216-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/23/2018] [Indexed: 12/14/2022] Open
Abstract
The type II membrane-anchored serine protease, matriptase, encoded by suppression of tumorgenicity-14 (ST14) regulates the integrity of the intestinal epithelial barrier in concert with its inhibitor, HAI-1 encoded by serine peptidase inhibitor, Kunitz type -1 (SPINT1). The balance of the protease/inhibitor gene expression ratio is vital in preventing the oncogenic potential of matriptase. The intestinal cell lineage is regulated by a transcriptional regulatory network where the tumor suppressor, Caudal homeobox 2 (CDX2) is considered to be an intestinal master transcription factor. In this study, we show that CDX2 has a dual function in regulating both ST14 and SPINT1, gene expression in intestinal cells. We find that CDX2 is not required for the basal ST14 and SPINT1 gene expression; however changes in CDX2 expression affects the ST14/SPINT1 mRNA ratio. Exploring CDX2 ChIP-seq data from intestinal cell lines, we identified genomic CDX2-enriched enhancer elements for both ST14 and SPINT1, which regulate their corresponding gene promoter activity. We show that CDX2 displays both repressive and enhancing regulatory abilities in a cell specific manner. Together, these data reveal new insight into transcriptional mechanisms controlling the intestinal matriptase/inhibitor balance.
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Affiliation(s)
- E Thomas Danielsen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.,Institute of Cellular and Molecular Medicine, the Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anders Krüger Olsen
- Institute of Cellular and Molecular Medicine, the Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Mehmet Coskun
- Department of Gastroenterology, University of Copenhagen, DK-2730, Herlev, Denmark
| | - Annika W Nonboe
- Institute of Cellular and Molecular Medicine, the Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Sylvester Larsen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.,Department of Clinical Immunology, Naestved Hospital, Naestved, Region Zealand, Denmark
| | - Katja Dahlgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Eric Paul Bennett
- Copenhagen Center for Glycomics, Department of Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cathy Mitchelmore
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Lotte Katrine Vogel
- Institute of Cellular and Molecular Medicine, the Panum Institute, University of Copenhagen, Copenhagen, Denmark
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7
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Boyd M, Thodberg M, Vitezic M, Bornholdt J, Vitting-Seerup K, Chen Y, Coskun M, Li Y, Lo BZS, Klausen P, Jan Schweiger P, Pedersen AG, Rapin N, Skovgaard K, Dahlgaard K, Andersson R, Terkelsen TB, Lilje B, Troelsen JT, Petersen AM, Jensen KB, Gögenur I, Thielsen P, Seidelin JB, Nielsen OH, Bjerrum JT, Sandelin A. Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies. Nat Commun 2018; 9:1661. [PMID: 29695774 PMCID: PMC5916929 DOI: 10.1038/s41467-018-03766-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/12/2018] [Indexed: 02/08/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic intestinal disorder, with two main types: Crohn’s disease (CD) and ulcerative colitis (UC), whose molecular pathology is not well understood. The majority of IBD-associated SNPs are located in non-coding regions and are hard to characterize since regulatory regions in IBD are not known. Here we profile transcription start sites (TSSs) and enhancers in the descending colon of 94 IBD patients and controls. IBD-upregulated promoters and enhancers are highly enriched for IBD-associated SNPs and are bound by the same transcription factors. IBD-specific TSSs are associated to genes with roles in both inflammatory cascades and gut epithelia while TSSs distinguishing UC and CD are associated to gut epithelia functions. We find that as few as 35 TSSs can distinguish active CD, UC, and controls with 85% accuracy in an independent cohort. Our data constitute a foundation for understanding the molecular pathology, gene regulation, and genetics of IBD. Many SNPs associated with inflammatory bowel disease are located in non-coding genomic regions. Here, the authors perform CAGE-sequencing on descending colon biopsies of Crohn’s disease and ulcerative colitis patients to map transcription start sites and enhancer activity for analysis of regulatory regions.
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Affiliation(s)
- Mette Boyd
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Malte Thodberg
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Morana Vitezic
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Jette Bornholdt
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Kristoffer Vitting-Seerup
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Yun Chen
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Mehmet Coskun
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Yuan Li
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark
| | - Bobby Zhao Sheng Lo
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark.,Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark
| | - Pia Klausen
- Department of Gastroenterology, Surgical Section, Herlev Hospital, 2730, Herlev, Denmark
| | - Pawel Jan Schweiger
- Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | | | - Nicolas Rapin
- Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark.,The Finsen Laboratory, Rigshospitalet, University of Copenhagen, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Katja Dahlgaard
- Department of Science and Environment (INM), Roskilde University, 4000, Roskilde, Denmark
| | - Robin Andersson
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Thilde Bagger Terkelsen
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Berit Lilje
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | | | - Andreas Munk Petersen
- Hvidovre Hospital, Gastrounit Medical Division, University of Copenhagen, 2650, Hvidovre, Denmark.,Hvidovre Hospital, Department of Clinical Microbiology, University of Copenhagen, 2650, Hvidovre, Denmark
| | - Kim Bak Jensen
- Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Ismail Gögenur
- Centre for Surgical Science, Department of Surgery, Zealand University Hospital, 4600, Koege, Denmark
| | - Peter Thielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark
| | - Jakob Benedict Seidelin
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark
| | - Jacob Tveiten Bjerrum
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark.
| | - Albin Sandelin
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark. .,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark.
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8
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Cortijo S, Charoensawan V, Brestovitsky A, Buning R, Ravarani C, Rhodes D, van Noort J, Jaeger KE, Wigge PA. Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis. MOLECULAR PLANT 2017; 10:1258-1273. [PMID: 28893714 PMCID: PMC6175055 DOI: 10.1016/j.molp.2017.08.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/21/2017] [Accepted: 08/24/2017] [Indexed: 05/18/2023]
Abstract
Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors (HSFs), have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade of Arabidopsis HSFs, which cause a rapid and dynamic eviction of H2A.Z nucleosomes at target genes. A transcriptional cascade results in the activation of multiple downstream stress-responsive transcription factors, triggering large-scale changes to the transcriptome in response to elevated temperature. H2A.Z nucleosomes are enriched at temperature-responsive genes at non-inducible temperature, and thus likely confer inducibility of gene expression and higher responsive dynamics. We propose that the antagonistic effects of H2A.Z and HSF1 provide a mechanism to activate gene expression rapidly and precisely in response to temperature, while preventing leaky transcription in the absence of an activation signal.
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Affiliation(s)
- Sandra Cortijo
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Varodom Charoensawan
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK; Department of Biochemistry, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi District, Bangkok 10400, Thailand; Integrative Computational BioScience (ICBS) Center, Mahidol University, 999 Phuttamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand.
| | - Anna Brestovitsky
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Ruth Buning
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands
| | - Charles Ravarani
- Medical Research Council Laboratory for Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Daniela Rhodes
- Medical Research Council Laboratory for Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Structural Biology, Nanyang Technical University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, the Netherlands
| | - Katja E Jaeger
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Philip A Wigge
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.
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9
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Bornholdt J, Saber AT, Lilje B, Boyd M, Jørgensen M, Chen Y, Vitezic M, Jacobsen NR, Poulsen SS, Berthing T, Bressendorff S, Vitting-Seerup K, Andersson R, Hougaard KS, Yauk CL, Halappanavar S, Wallin H, Vogel U, Sandelin A. Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo. ACS NANO 2017; 11:3597-3613. [PMID: 28345861 DOI: 10.1021/acsnano.6b07533] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Increased use of nanomaterials in industry, medicine, and consumer products has raised concerns over their toxicity. To ensure safe use of nanomaterials, understanding their biological effects at the molecular level is crucial. In particular, the regulatory mechanisms responsible for the cascade of genes activated by nanomaterial exposure are not well-characterized. To this end, we profiled the genome-wide usage of gene transcription start sites and linked active enhancer regions in lungs of C57BL/6 mice 24 h after intratracheal instillation of a single dose of the multiwalled carbon nanotube (MWCNT) Mitsui-7. Our results revealed a massive gene regulatory response, where expression of key inflammatory genes (e.g., Csf3, Il24, and Fgf23) was increased >100-fold 24 h after Mitsui-7 exposure. Many of the Mitsui-7-responsive transcription start sites were alternative transcription start sites for known genes, and the number of alternative transcription start sites used in a given gene was correlated with overall Mitsui-7 response. Strikingly, genes that were up-regulated after Mitsui-7 exposure only through their main annotated transcription start site were linked to inflammatory and defense responses, while genes up-regulated only through alternative transcription start sites were functionally heterogeneous and not inflammation-associated. Furthermore, we identified almost 12 000 active enhancers, many of which were Mitsui-7-responsive, and we identified similarly responding putative target genes. Overall, our study provides the location and activity of Mitsui-7-induced enhancers and transcription start sites, providing a useful resource for targeted experiments elucidating the biological effects of nanomaterials and the identification of biomarkers for early detection of MWCNT-induced inflammation.
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Affiliation(s)
- Jette Bornholdt
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Berit Lilje
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Mette Boyd
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Mette Jørgensen
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Yun Chen
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Morana Vitezic
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Sarah Søs Poulsen
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
| | - Trine Berthing
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
| | - Simon Bressendorff
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
| | - Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Carole L Yauk
- Environmental and Radiation Health Sciences Directorate, Health Canada , Ottawa, Ontario K1A 0K9, Canada
| | - Sabina Halappanavar
- Environmental and Radiation Health Sciences Directorate, Health Canada , Ottawa, Ontario K1A 0K9, Canada
| | - Håkan Wallin
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
- Department of Public Health, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
- Department of Micro and Nanotechnology, Technical University of Denmark , 2800 Kongens Lyngby, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
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10
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Coskun M, Soendergaard C, Joergensen S, Dahlgaard K, Riis LB, Nielsen OH, Sandelin A, Troelsen JT. Regulation of Laminin γ2 Expression by CDX2 in Colonic Epithelial Cells Is Impaired During Active Inflammation. J Cell Biochem 2016; 118:298-307. [DOI: 10.1002/jcb.25636] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/21/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Mehmet Coskun
- Department of Gastroenterology, Medical Section; Herlev Hospital; University of Copenhagen; Herlev DK-2730 Denmark
- The Bioinformatics Centre; Department of Biology and Biotech Research and Innovation Centre (BRIC); University of Copenhagen; Copenhagen DK-2200 Denmark
| | - Christoffer Soendergaard
- Department of Gastroenterology, Medical Section; Herlev Hospital; University of Copenhagen; Herlev DK-2730 Denmark
| | - Steffen Joergensen
- Department of Science, Systems and Models; Roskilde University; Roskilde DK-4000 Denmark
| | - Katja Dahlgaard
- Department of Science, Systems and Models; Roskilde University; Roskilde DK-4000 Denmark
| | - Lene Buhl Riis
- Department of Pathology; Herlev Hospital; University of Copenhagen; Herlev DK-2730 Denmark
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Medical Section; Herlev Hospital; University of Copenhagen; Herlev DK-2730 Denmark
| | - Albin Sandelin
- The Bioinformatics Centre; Department of Biology and Biotech Research and Innovation Centre (BRIC); University of Copenhagen; Copenhagen DK-2200 Denmark
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