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Radzisheuskaya A, Peña‐Rømer I, Lorenzini E, Koche R, Zhan Y, Shliaha PV, Cooper AJ, Fan Z, Shlyueva D, Johansen JV, Hendrickson RC, Helin K. An alternative NURF complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions. EMBO J 2023; 42:e114221. [PMID: 37987160 PMCID: PMC10711654 DOI: 10.15252/embj.2023114221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Efficient treatment of acute myeloid leukemia (AML) patients remains a challenge despite recent therapeutic advances. Here, using a CRISPRi screen targeting chromatin factors, we identified the nucleosome-remodeling factor (NURF) subunit BPTF as an essential regulator of AML cell survival. We demonstrate that BPTF forms an alternative NURF chromatin remodeling complex with SMARCA5 and BAP18, which regulates the accessibility of a large set of insulator regions in leukemic cells. This ensures efficient CTCF binding and boundary formation between topologically associated domains that is essential for maintaining the leukemic transcriptional programs. We also demonstrate that the well-studied PHD2-BROMO chromatin reader domains of BPTF, while contributing to complex recruitment to chromatin, are dispensable for leukemic cell growth. Taken together, our results uncover how the alternative NURF complex contributes to leukemia and provide a rationale for its targeting in AML.
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Affiliation(s)
- Aliaksandra Radzisheuskaya
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Isabel Peña‐Rømer
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Eugenia Lorenzini
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Richard Koche
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Yingqian Zhan
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Pavel V Shliaha
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | | | - Zheng Fan
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Daria Shlyueva
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Jens V Johansen
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
| | - Ronald C Hendrickson
- Microchemistry & Proteomics CoreMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Kristian Helin
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Biotech Research & Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
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Kampmeyer C, Johansen JV, Holmberg C, Karlson M, Gersing SK, Bordallo HN, Kragelund BB, Lerche MH, Jourdain I, Winther JR, Hartmann-Petersen R. Mutations in a Single Signaling Pathway Allow Cell Growth in Heavy Water. ACS Synth Biol 2020; 9:733-748. [PMID: 32142608 DOI: 10.1021/acssynbio.9b00376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Life is completely dependent on water. To analyze the role of water as a solvent in biology, we replaced water with heavy water (D2O) and investigated the biological effects by a wide range of techniques, using Schizosaccharomyces pombe as model organism. We show that high concentrations of D2O lead to altered glucose metabolism and growth retardation. After prolonged incubation in D2O, cells displayed gross morphological changes, thickened cell walls, and aberrant cytoskeletal organization. By transcriptomics and genetic screens, we show that the solvent replacement activates two signaling pathways: (1) the heat-shock response pathway and (2) the cell integrity pathway. Although the heat-shock response system upregulates various chaperones and other stress-relieving enzymes, we find that the activation of this pathway does not offer any fitness advantage to the cells under the solvent-replaced conditions. However, limiting the D2O-triggered activation of the cell integrity pathway allows cell growth when H2O is completely replaced with D2O. The isolated D2O-tolerant strains may aid biological production of deuterated biomolecules.
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Affiliation(s)
- Caroline Kampmeyer
- The Linderstrøm-Lang Center, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Jens V. Johansen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Christian Holmberg
- The Linderstrøm-Lang Center, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Magnus Karlson
- Technical University of Denmark, Department of Electrical Engineering, Ørsted Plads, Building 349, DK-2800 Kongens Lyngby, Denmark
| | - Sarah K. Gersing
- The Linderstrøm-Lang Center, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Heloisa N. Bordallo
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Birthe B. Kragelund
- The Linderstrøm-Lang Center, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
- The REPIN Center, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Mathilde H. Lerche
- Technical University of Denmark, Department of Electrical Engineering, Ørsted Plads, Building 349, DK-2800 Kongens Lyngby, Denmark
| | - Isabelle Jourdain
- College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Jakob R. Winther
- The Linderstrøm-Lang Center, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Center, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
- The REPIN Center, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
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Andersen MS, Hannezo E, Ulyanchenko S, Estrach S, Antoku Y, Pisano S, Boonekamp KE, Sendrup S, Maimets M, Pedersen MT, Johansen JV, Clement DL, Feral CC, Simons BD, Jensen KB. Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. Nat Cell Biol 2019; 21:924-932. [PMID: 31358966 PMCID: PMC6978139 DOI: 10.1038/s41556-019-0362-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 06/18/2019] [Indexed: 12/12/2022]
Abstract
The sebaceous gland (SG) is an essential component of the skin, and SG dysfunction is debilitating1,2. Yet, the cellular bases for its origin, development and subsequent maintenance remain poorly understood. Here, we apply large-scale quantitative fate mapping to define the patterns of cell fate behaviour during SG development and maintenance. We show that the SG develops from a defined number of lineage-restricted progenitors that undergo a programme of independent and stochastic cell fate decisions. Following an expansion phase, equipotent progenitors transition into a phase of homeostatic turnover, which is correlated with changes in the mechanical properties of the stroma and spatial restrictions on gland size. Expression of the oncogene KrasG12D results in a release from these constraints and unbridled gland expansion. Quantitative clonal fate analysis reveals that, during this phase, the primary effect of the Kras oncogene is to drive a constant fate bias with little effect on cell division rates. These findings provide insight into the developmental programme of the SG, as well as the mechanisms that drive tumour progression and gland dysfunction.
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Affiliation(s)
- Marianne Stemann Andersen
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Edouard Hannezo
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Svetlana Ulyanchenko
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Soline Estrach
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1081, Centre National de la Recherche Scientifique UMR 7284, Université Cote d'Azur, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
| | - Yasuko Antoku
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Sabrina Pisano
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1081, Centre National de la Recherche Scientifique UMR 7284, Université Cote d'Azur, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
| | - Kim E Boonekamp
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Sendrup
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Martti Maimets
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Terndrup Pedersen
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens V Johansen
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Ditte L Clement
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chloe C Feral
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1081, Centre National de la Recherche Scientifique UMR 7284, Université Cote d'Azur, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
| | - Benjamin D Simons
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- The Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - Kim B Jensen
- BRIC-Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Yui S, Azzolin L, Maimets M, Pedersen MT, Fordham RP, Hansen SL, Larsen HL, Guiu J, Alves MRP, Rundsten CF, Johansen JV, Li Y, Madsen CD, Nakamura T, Watanabe M, Nielsen OH, Schweiger PJ, Piccolo S, Jensen KB. YAP/TAZ-Dependent Reprogramming of Colonic Epithelium Links ECM Remodeling to Tissue Regeneration. Cell Stem Cell 2017; 22:35-49.e7. [PMID: 29249464 PMCID: PMC5766831 DOI: 10.1016/j.stem.2017.11.001] [Citation(s) in RCA: 370] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 09/25/2017] [Accepted: 10/31/2017] [Indexed: 12/23/2022]
Abstract
Tissue regeneration requires dynamic cellular adaptation to the wound environment. It is currently unclear how this is orchestrated at the cellular level and how cell fate is affected by severe tissue damage. Here we dissect cell fate transitions during colonic regeneration in a mouse dextran sulfate sodium (DSS) colitis model, and we demonstrate that the epithelium is transiently reprogrammed into a primitive state. This is characterized by de novo expression of fetal markers as well as suppression of markers for adult stem and differentiated cells. The fate change is orchestrated by remodeling the extracellular matrix (ECM), increased FAK/Src signaling, and ultimately YAP/TAZ activation. In a defined cell culture system recapitulating the extracellular matrix remodeling observed in vivo, we show that a collagen 3D matrix supplemented with Wnt ligands is sufficient to sustain endogenous YAP/TAZ and induce conversion of cell fate. This provides a simple model for tissue regeneration, implicating cellular reprogramming as an essential element. The repairing epithelium can be isolated based on Sca1 expression Markers upregulated during tissue repair are expressed in the fetal intestine Mechano-transduction via FAK, Src, and YAP/TAZ facilitate efficient tissue repair YAP/TAZ activation is required and sufficient to induce cellular reprogramming
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Affiliation(s)
- Shiro Yui
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Luca Azzolin
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy
| | - Martti Maimets
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Marianne Terndrup Pedersen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Robert P Fordham
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Stine L Hansen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Hjalte L Larsen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Jordi Guiu
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Mariana R P Alves
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Carsten F Rundsten
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Jens V Johansen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Yuan Li
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
| | - Chris D Madsen
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, 223 81 Lund, Sweden
| | - Tetsuya Nakamura
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8519, Japan
| | - Mamoru Watanabe
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8519, Japan
| | - Ole H Nielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730 Herlev, Denmark
| | - Pawel J Schweiger
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Stefano Piccolo
- Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy.
| | - Kim B Jensen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark; Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark.
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5
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Engelholm LH, Riaz A, Serra D, Dagnæs-Hansen F, Johansen JV, Santoni-Rugiu E, Hansen SH, Niola F, Frödin M. CRISPR/Cas9 Engineering of Adult Mouse Liver Demonstrates That the Dnajb1-Prkaca Gene Fusion Is Sufficient to Induce Tumors Resembling Fibrolamellar Hepatocellular Carcinoma. Gastroenterology 2017; 153:1662-1673.e10. [PMID: 28923495 PMCID: PMC5801691 DOI: 10.1053/j.gastro.2017.09.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/05/2017] [Accepted: 09/09/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS Fibrolamellar hepatocellular carcinoma (FL-HCC) is a primary liver cancer that predominantly affects children and young adults with no underlying liver disease. A somatic, 400 Kb deletion on chromosome 19 that fuses part of the DnaJ heat shock protein family (Hsp40) member B1 gene (DNAJB1) to the protein kinase cAMP-activated catalytic subunit alpha gene (PRKACA) has been repeatedly identified in patients with FL-HCC. However, the DNAJB1-PRKACA gene fusion has not been shown to induce liver tumorigenesis. We used the CRISPR/Cas9 technique to delete in mice the syntenic region on chromosome 8 to create a Dnajb1-Prkaca fusion and monitored the mice for liver tumor development. METHODS We delivered CRISPR/Cas9 vectors designed to juxtapose exon 1 of Dnajb1 with exon 2 of Prkaca to create the Dnajb1-Prkaca gene fusion associated with FL-HCC, or control Cas9 vector, via hydrodynamic tail vein injection to livers of 8-week-old female FVB/N mice. These mice did not have any other engineered genetic alterations and were not exposed to liver toxins or carcinogens. Liver tissues were collected 14 months after delivery; genomic DNA was analyzed by PCR to detect the Dnajb1-Prkaca fusion, and tissues were characterized by histology, immunohistochemistry, RNA sequencing, and whole-exome sequencing. RESULTS Livers from 12 of the 15 mice given the vectors to induce the Dnajb1-Prkaca gene fusion, but none of the 11 mice given the control vector, developed neoplasms. The tumors contained the Dnajb1-Prkaca gene fusion and had histologic and cytologic features of human FL-HCCs: large polygonal cells with granular, eosinophilic, and mitochondria-rich cytoplasm, prominent nucleoli, and markers of hepatocytes and cholangiocytes. In comparing expression levels of genes between the mouse tumor and non-tumor liver cells, we identified changes similar to those detected in human FL-HCC, which included genes that affect cell cycle and mitosis regulation. Genomic analysis of mouse neoplasms induced by the Dnajb1-Prkaca fusion revealed a lack of mutations in genes commonly associated with liver cancers, as observed in human FL-HCC. CONCLUSIONS Using CRISPR/Cas9 technology, we found generation of the Dnajb1-Prkaca fusion gene in wild-type mice to be sufficient to initiate formation of tumors that have many features of human FL-HCC. Strategies to block DNAJB1-PRKACA might be developed as therapeutics for this form of liver cancer.
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Affiliation(s)
- Lars H Engelholm
- Finsen Laboratory, Rigshospitalet, Copenhagen Biocenter, Copenhagen, Denmark,Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anjum Riaz
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Denise Serra
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Jens V Johansen
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eric Santoni-Rugiu
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Steen H Hansen
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark,GI Cell Biology Research Laboratory, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Francesco Niola
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Morten Frödin
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Poulsen EG, Kampmeyer C, Kriegenburg F, Johansen JV, Hofmann K, Holmberg C, Hartmann-Petersen R. UBL/BAG-domain co-chaperones cause cellular stress upon overexpression through constitutive activation of Hsf1. Cell Stress Chaperones 2017; 22:143-154. [PMID: 27966061 PMCID: PMC5225068 DOI: 10.1007/s12192-016-0751-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 12/15/2022] Open
Abstract
As a result of exposure to stress conditions, mutations, or defects during synthesis, cellular proteins are prone to misfold. To cope with such partially denatured proteins, cells mount a regulated transcriptional response involving the Hsf1 transcription factor, which drives the synthesis of molecular chaperones and other stress-relieving proteins. Here, we show that the fission yeast Schizosaccharomyces pombe orthologues of human BAG-1, Bag101, and Bag102, are Hsp70 co-chaperones that associate with 26S proteasomes. Only a subgroup of Hsp70-type chaperones, including Ssa1, Ssa2, and Sks2, binds Bag101 and Bag102 and key residues in the Hsp70 ATPase domains, required for interaction with Bag101 and Bag102, were identified. In humans, BAG-1 overexpression is typically observed in cancers. Overexpression of bag101 and bag102 in fission yeast leads to a strong growth defect caused by triggering Hsp70 to release and activate the Hsf1 transcription factor. Accordingly, the bag101-linked growth defect is alleviated in strains containing a reduced amount of Hsf1 but aggravated in hsp70 deletion strains. In conclusion, we propose that the fission yeast UBL/BAG proteins release Hsf1 from Hsp70, leading to constitutive Hsf1 activation and growth defects.
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Affiliation(s)
- Esben G Poulsen
- The Linderstrøm-Land Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Caroline Kampmeyer
- The Linderstrøm-Land Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Franziska Kriegenburg
- The Linderstrøm-Land Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Jens V Johansen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, 50674, Cologne, Germany
| | - Christian Holmberg
- The Linderstrøm-Land Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Land Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark.
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7
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Poulsen EG, Nielsen SV, Pietras EJ, Johansen JV, Steinhauer C, Hartmann-Petersen R. High-Throughput siRNA Screening Applied to the Ubiquitin-Proteasome System. Methods Mol Biol 2016; 1449:421-439. [PMID: 27613054 DOI: 10.1007/978-1-4939-3756-1_28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The ubiquitin-proteasome system is the major pathway for intracellular protein degradation in eukaryotic cells. Due to the large number of genes dedicated to the ubiquitin-proteasome system, mapping degradation pathways for short lived proteins is a daunting task, in particular in mammalian cells that are not genetically tractable as, for instance, a yeast model system. Here, we describe a method relying on high-throughput cellular imaging of cells transfected with a targeted siRNA library to screen for components involved in degradation of a protein of interest. This method is a rapid and cost-effective tool which is also highly applicable for other studies on gene function.
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Affiliation(s)
- Esben G Poulsen
- Department of Biology, Section for Biomolecular Sciences, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark
| | - Sofie V Nielsen
- Department of Biology, Section for Biomolecular Sciences, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark
| | - Elin J Pietras
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark
| | - Jens V Johansen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark
| | - Cornelia Steinhauer
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, Section for Biomolecular Sciences, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark.
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8
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Feng Y, Vlassis A, Roques C, Lalonde ME, González-Aguilera C, Lambert JP, Lee SB, Zhao X, Alabert C, Johansen JV, Paquet E, Yang XJ, Gingras AC, Côté J, Groth A. BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation. EMBO J 2015; 35:176-92. [PMID: 26620551 DOI: 10.15252/embj.201591293] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [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: 02/16/2015] [Accepted: 11/03/2015] [Indexed: 12/23/2022] Open
Abstract
During DNA replication, thousands of replication origins are activated across the genome. Chromatin architecture contributes to origin specification and usage, yet it remains unclear which chromatin features impact on DNA replication. Here, we perform a RNAi screen for chromatin regulators implicated in replication control by measuring RPA accumulation upon replication stress. We identify six factors required for normal rates of DNA replication and characterize a function of the bromodomain and PHD finger-containing protein 3 (BRPF3) in replication initiation. BRPF3 forms a complex with HBO1 that specifically acetylates histone H3K14, and genomewide analysis shows high enrichment of BRPF3, HBO1 and H3K14ac at ORC1-binding sites and replication origins found in the vicinity of TSSs. Consistent with this, BRPF3 is necessary for H3K14ac at selected origins and efficient origin activation. CDC45 recruitment, but not MCM2-7 loading, is impaired in BRPF3-depleted cells, identifying a BRPF3-dependent function of HBO1 in origin activation that is complementary to its role in licencing. We thus propose that BRPF3-HBO1 acetylation of histone H3K14 around TSS facilitates efficient activation of nearby replication origins.
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Affiliation(s)
- Yunpeng Feng
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Arsenios Vlassis
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Céline Roques
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec Research Center, Quebec City, QC, Canada
| | - Marie-Eve Lalonde
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec Research Center, Quebec City, QC, Canada
| | - Cristina González-Aguilera
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | | | - Sung-Bau Lee
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Xiaobei Zhao
- Bioinformatics Centre Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Constance Alabert
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Jens V Johansen
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Eric Paquet
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec Research Center, Quebec City, QC, Canada
| | - Xiang-Jiao Yang
- Department of Medicine, McGill University Health Center, Montréal, QC, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Axis-CHU de Québec Research Center, Quebec City, QC, Canada
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC) and Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark
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9
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Rasmussen KD, Jia G, Johansen JV, Pedersen MT, Rapin N, Bagger FO, Porse BT, Bernard OA, Christensen J, Helin K. Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis. Genes Dev 2015; 29:910-22. [PMID: 25886910 PMCID: PMC4421980 DOI: 10.1101/gad.260174.115] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 03/30/2015] [Indexed: 11/25/2022]
Abstract
DNA methylation is tightly regulated throughout mammalian development, and altered DNA methylation patterns are a general hallmark of cancer. The methylcytosine dioxygenase TET2 is frequently mutated in hematological disorders, including acute myeloid leukemia (AML), and has been suggested to protect CG dinucleotide (CpG) islands and promoters from aberrant DNA methylation. In this study, we present a novel Tet2-dependent leukemia mouse model that closely recapitulates gene expression profiles and hallmarks of human AML1-ETO-induced AML. Using this model, we show that the primary effect of Tet2 loss in preleukemic hematopoietic cells is progressive and widespread DNA hypermethylation affecting up to 25% of active enhancer elements. In contrast, CpG island and promoter methylation does not change in a Tet2-dependent manner but increases relative to population doublings. We confirmed this specific enhancer hypermethylation phenotype in human AML patients with TET2 mutations. Analysis of immediate gene expression changes reveals rapid deregulation of a large number of genes implicated in tumorigenesis, including many down-regulated tumor suppressor genes. Hence, we propose that TET2 prevents leukemic transformation by protecting enhancers from aberrant DNA methylation and that it is the combined silencing of several tumor suppressor genes in TET2 mutated hematopoietic cells that contributes to increased stem cell proliferation and leukemogenesis.
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Affiliation(s)
- Kasper D Rasmussen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Guangshuai Jia
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens V Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Marianne T Pedersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nicolas Rapin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (Danstem), University of Copenhagen, 2200 Copenhagen, Denmark; Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Finsen Laboratory, Rigshospitalet, 2200 Copenhagen, Denmark
| | - Frederik O Bagger
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (Danstem), University of Copenhagen, 2200 Copenhagen, Denmark; Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Finsen Laboratory, Rigshospitalet, 2200 Copenhagen, Denmark
| | - Bo T Porse
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (Danstem), University of Copenhagen, 2200 Copenhagen, Denmark; Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Finsen Laboratory, Rigshospitalet, 2200 Copenhagen, Denmark
| | | | - Jesper Christensen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (Danstem), University of Copenhagen, 2200 Copenhagen, Denmark;
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10
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Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PAC, Rappsilber J, Helin K. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011; 473:343-8. [PMID: 21490601 DOI: 10.1038/nature10066] [Citation(s) in RCA: 773] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 03/28/2011] [Indexed: 01/04/2023]
Abstract
Enzymes catalysing the methylation of the 5-position of cytosine (mC) have essential roles in regulating gene expression and maintaining cellular identity. Recently, TET1 was found to hydroxylate the methyl group of mC, converting it to 5-hydroxymethyl cytosine (hmC). Here we show that TET1 binds throughout the genome of embryonic stem cells, with the majority of binding sites located at transcription start sites (TSSs) of CpG-rich promoters and within genes. The hmC modification is found in gene bodies and in contrast to mC is also enriched at CpG-rich TSSs. We provide evidence further that TET1 has a role in transcriptional repression. TET1 binds a significant proportion of Polycomb group target genes. Furthermore, TET1 associates and colocalizes with the SIN3A co-repressor complex. We propose that TET1 fine-tunes transcription, opposes aberrant DNA methylation at CpG-rich sequences and thereby contributes to the regulation of DNA methylation fidelity.
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Affiliation(s)
- Kristine Williams
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
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11
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Doehn U, Hauge C, Frank SR, Jensen CJ, Duda K, Nielsen JV, Cohen MS, Johansen JV, Winther BR, Lund LR, Winther O, Taunton J, Hansen SH, Frödin M. RSK is a principal effector of the RAS-ERK pathway for eliciting a coordinate promotile/invasive gene program and phenotype in epithelial cells. Mol Cell 2009; 35:511-22. [PMID: 19716794 DOI: 10.1016/j.molcel.2009.08.002] [Citation(s) in RCA: 175] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 05/18/2009] [Accepted: 08/07/2009] [Indexed: 10/20/2022]
Abstract
The RAS-stimulated RAF-MEK-ERK pathway confers epithelial cells with critical motile and invasive capacities during development, tissue regeneration, and carcinoma progression, often via promoting the epithelial-mesenchymal transition (EMT). Many mechanisms by which ERK exerts this control remain elusive. We demonstrate that the ERK-activated kinase RSK is necessary to induce mesenchymal motility and invasive capacities in nontransformed epithelial and carcinoma cells. RSK is sufficient to induce certain motile responses. Expression profiling analysis revealed that a primary role of RSK is to induce transcription of a potent promotile/invasive gene program by FRA1-dependent and -independent mechanisms. The program enables RSK to coordinately modulate the extracellular environment, the intracellular motility apparatus, and receptors mediating communication between these compartments to stimulate motility and invasion. These findings uncover a mechanism whereby the RAS-ERK pathway controls epithelial cell motility by identifying RSK as a key effector, from which emanate multiple highly coordinate transcription-dependent mechanisms for stimulation of motility and invasive properties.
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Affiliation(s)
- Ulrik Doehn
- Biotech Research & Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen N, Denmark
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12
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Schaller S, Henriksen K, Sveigaard C, Heegaard AM, Hélix N, Stahlhut M, Ovejero MC, Johansen JV, Solberg H, Andersen TL, Hougaard D, Berryman M, Shiødt CB, Sørensen BH, Lichtenberg J, Christophersen P, Foged NT, Delaissé JM, Engsig MT, Karsdal MA. The chloride channel inhibitor NS3736 [corrected] prevents bone resorption in ovariectomized rats without changing bone formation. J Bone Miner Res 2004; 19:1144-53. [PMID: 15176998 DOI: 10.1359/jbmr.040302] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [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: 10/28/2003] [Revised: 01/26/2004] [Accepted: 02/26/2004] [Indexed: 01/21/2023]
Abstract
UNLABELLED Chloride channel activity is essential for osteoclast function. Consequently, inhibition of the osteoclastic chloride channel should prevent bone resorption. Accordingly, we tested a chloride channel inhibitor on bone turnover and found that it inhibits bone resorption without affecting bone formation. This study indicates that chloride channel inhibitors are highly promising for treatment of osteoporosis. INTRODUCTION The chloride channel inhibitor, NS3736, blocked osteoclastic acidification and resorption in vitro with an IC50 value of 30 microM. When tested in the rat ovariectomy model for osteoporosis, daily treatment with 30 mg/kg orally protected bone strength and BMD by approximately 50% 6 weeks after surgery. Most interestingly, bone formation assessed by osteocalcin, mineral apposition rate, and mineralized surface index was not inhibited. MATERIALS AND METHODS Analysis of chloride channels in human osteoclasts revealed that ClC-7 and CLIC1 were highly expressed. Furthermore, by electrophysiology, we detected a volume-activated anion channel on human osteoclasts. Screening 50 different human tissues showed a broad expression for CLIC1 and a restricted immunoreactivity for ClC-7, appearing mainly in osteoclasts, ovaries, appendix, and Purkinje cells. This highly selective distribution predicts that inhibition of ClC-7 should specifically target osteoclasts in vivo. We suggest that NS3736 is inhibiting ClC-7, leading to a bone-specific effect in vivo. RESULTS AND CONCLUSION In conclusion, we show for the first time that chloride channel inhibitors can be used for prevention of ovariectomy-induced bone loss without impeding bone formation. We speculate that the coupling of bone resorption to bone formation is linked to the acidification of the resorption lacunae, thereby enabling compounds that directly interfere with this process to be able to positive uncouple this process resulting in a net bone gain.
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