1
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Ma HL, Bizet M, Soares Da Costa C, Murisier F, de Bony EJ, Wang MK, Yoshimi A, Lin KT, Riching KM, Wang X, Beckman JI, Arya S, Droin N, Calonne E, Hassabi B, Zhang QY, Li A, Putmans P, Malbec L, Hubert C, Lan J, Mies F, Yang Y, Solary E, Daniels DL, Gupta YK, Deplus R, Abdel-Wahab O, Yang YG, Fuks F. SRSF2 plays an unexpected role as reader of m 5C on mRNA, linking epitranscriptomics to cancer. Mol Cell 2023; 83:4239-4254.e10. [PMID: 38065062 DOI: 10.1016/j.molcel.2023.11.003] [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: 07/29/2022] [Revised: 09/06/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
A common mRNA modification is 5-methylcytosine (m5C), whose role in gene-transcript processing and cancer remains unclear. Here, we identify serine/arginine-rich splicing factor 2 (SRSF2) as a reader of m5C and impaired SRSF2 m5C binding as a potential contributor to leukemogenesis. Structurally, we identify residues involved in m5C recognition and the impact of the prevalent leukemia-associated mutation SRSF2P95H. We show that SRSF2 binding and m5C colocalize within transcripts. Furthermore, knocking down the m5C writer NSUN2 decreases mRNA m5C, reduces SRSF2 binding, and alters RNA splicing. We also show that the SRSF2P95H mutation impairs the ability of the protein to read m5C-marked mRNA, notably reducing its binding to key leukemia-related transcripts in leukemic cells. In leukemia patients, low NSUN2 expression leads to mRNA m5C hypomethylation and, combined with SRSF2P95H, predicts poor outcomes. Altogether, we highlight an unrecognized mechanistic link between epitranscriptomics and a key oncogenesis driver.
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Affiliation(s)
- Hai-Li Ma
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Christelle Soares Da Costa
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Frédéric Murisier
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Eric James de Bony
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Meng-Ke Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Akihide Yoshimi
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Xing Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - John I Beckman
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Shailee Arya
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Nathalie Droin
- Université Paris-Saclay, INSERM U1287, and Department of Hematology, Gustave Roussy Cancer Center, Villejuif 94800, France
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Bouchra Hassabi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Qing-Yang Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Ang Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Lionel Malbec
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Céline Hubert
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Jie Lan
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Frédérique Mies
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Eric Solary
- Université Paris-Saclay, INSERM U1287, and Department of Hematology, Gustave Roussy Cancer Center, Villejuif 94800, France
| | | | - Yogesh K Gupta
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China.
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium.
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2
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Dube G, Tiamiou A, Bizet M, Boumahd Y, Gasmi I, Crake R, Bellier J, Nokin MJ, Calonne E, Deplus R, Wissocq T, Peulen O, Castronovo V, Fuks F, Bellahcène A. Methylglyoxal: a novel upstream regulator of DNA methylation. J Exp Clin Cancer Res 2023; 42:78. [PMID: 36998085 PMCID: PMC10064647 DOI: 10.1186/s13046-023-02637-w] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/02/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Aerobic glycolysis, also known as the Warburg effect, is predominantly upregulated in a variety of solid tumors, including breast cancer. We have previously reported that methylglyoxal (MG), a very reactive by-product of glycolysis, unexpectedly enhanced the metastatic potential in triple negative breast cancer (TNBC) cells. MG and MG-derived glycation products have been associated with various diseases, such as diabetes, neurodegenerative disorders, and cancer. Glyoxalase 1 (GLO1) exerts an anti-glycation defense by detoxifying MG to D-lactate. METHODS Here, we used our validated model consisting of stable GLO1 depletion to induce MG stress in TNBC cells. Using genome-scale DNA methylation analysis, we report that this condition resulted in DNA hypermethylation in TNBC cells and xenografts. RESULTS GLO1-depleted breast cancer cells showed elevated expression of DNMT3B methyltransferase and significant loss of metastasis-related tumor suppressor genes, as assessed using integrated analysis of methylome and transcriptome data. Interestingly, MG scavengers revealed to be as potent as typical DNA demethylating agents at triggering the re-expression of representative silenced genes. Importantly, we delineated an epigenomic MG signature that effectively stratified TNBC patients based on survival. CONCLUSION This study emphasizes the importance of MG oncometabolite, occurring downstream of the Warburg effect, as a novel epigenetic regulator and proposes MG scavengers to reverse altered patterns of gene expression in TNBC.
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Affiliation(s)
- Gaurav Dube
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Assia Tiamiou
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Yasmine Boumahd
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Imène Gasmi
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Rebekah Crake
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Justine Bellier
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Marie-Julie Nokin
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Tom Wissocq
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Olivier Peulen
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - Vincent Castronovo
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
- WELBIO (Walloon Excellence in Lifesciences & Biotechnology), Brussels, Belgium
| | - Akeila Bellahcène
- Metastasis Research Laboratory, GIGA-Cancer, GIGA Institute, University of Liège, Liège, Belgium.
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3
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Jeschke J, Collignon E, Al Wardi C, Krayem M, Bizet M, Jia Y, Garaud S, Wimana Z, Calonne E, Hassabi B, Morandini R, Deplus R, Putmans P, Dube G, Singh NK, Koch A, Shostak K, Rizzotto L, Ross RL, Desmedt C, Bareche Y, Rothé F, Lehmann-Che J, Duterque-Coquillaud M, Leroy X, Menschaert G, Teixeira L, Guo M, Limbach PA, Close P, Chariot A, Leucci E, Ghanem G, Yuan BF, Willard-Gallo K, Sotiriou C, Marine JC, Fuks F. Downregulation of the FTO m 6A RNA demethylase promotes EMT-mediated progression of epithelial tumors and sensitivity to Wnt inhibitors. Nat Cancer 2021; 2:611-628. [PMID: 35121941 PMCID: PMC10734094 DOI: 10.1038/s43018-021-00223-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 05/17/2021] [Indexed: 02/05/2023]
Abstract
Post-transcriptional modifications of RNA constitute an emerging regulatory layer of gene expression. The demethylase fat mass- and obesity-associated protein (FTO), an eraser of N6-methyladenosine (m6A), has been shown to play a role in cancer, but its contribution to tumor progression and the underlying mechanisms remain unclear. Here, we report widespread FTO downregulation in epithelial cancers associated with increased invasion, metastasis and worse clinical outcome. Both in vitro and in vivo, FTO silencing promotes cancer growth, cell motility and invasion. In human-derived tumor xenografts (PDXs), FTO pharmacological inhibition favors tumorigenesis. Mechanistically, we demonstrate that FTO depletion elicits an epithelial-to-mesenchymal transition (EMT) program through increased m6A and altered 3'-end processing of key mRNAs along the Wnt signaling cascade. Accordingly, FTO knockdown acts via EMT to sensitize mouse xenografts to Wnt inhibition. We thus identify FTO as a key regulator, across epithelial cancers, of Wnt-triggered EMT and tumor progression and reveal a therapeutically exploitable vulnerability of FTO-low tumors.
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Affiliation(s)
- Jana Jeschke
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Evelyne Collignon
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Clémence Al Wardi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mohammad Krayem
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Yan Jia
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Soizic Garaud
- Molecular Immunology Laboratory, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Zéna Wimana
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium
- Department of Nuclear Medicine, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bouchra Hassabi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Renato Morandini
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Gaurav Dube
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Nitesh Kumar Singh
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Alexander Koch
- Department of Pathology, Maastricht UMC, Maastricht, the Netherlands
| | - Kateryna Shostak
- Laboratory of Medical Chemistry, GIGA Stem Cells, University of Liège, Liège, Belgium
| | - Lara Rizzotto
- Trace, LKI Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Robert L Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
| | - Yacine Bareche
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
| | - Françoise Rothé
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
| | - Jacqueline Lehmann-Che
- Pathophysiology of Breast Cancer Team, Université de Paris, INSERM U976, HIPI, Paris, France
- Breast Disease Unit and Molecular Oncology Unit, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Martine Duterque-Coquillaud
- Université Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-UMR-S 1277, CANTHER, Lille, France
| | - Xavier Leroy
- Université Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-UMR-S 1277, CANTHER, Lille, France
- Department of Pathology, CHU Lille, Université Lille, Lille, France
| | - Gerben Menschaert
- Biobix, Laboratory of Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium
| | - Luis Teixeira
- Pathophysiology of Breast Cancer Team, Université de Paris, INSERM U976, HIPI, Paris, France
- Breast Disease Unit and Molecular Oncology Unit, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Pierre Close
- Laboratory of Cancer Signaling, GIGA Stem Cells, University of Liège, Liège, Belgium
- WELBIO, University of Liège, Liège, Belgium
| | - Alain Chariot
- Laboratory of Medical Chemistry, GIGA Stem Cells, University of Liège, Liège, Belgium
- WELBIO, University of Liège, Liège, Belgium
| | - Eleonora Leucci
- Trace, LKI Leuven Cancer Institute, KU Leuven, Leuven, Belgium
- Laboratory of RNA Cancer Biology, Department of Oncology, LKI, KU Leuven, Leuven, Belgium
| | - Ghanem Ghanem
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Bi-Feng Yuan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Karen Willard-Gallo
- Molecular Immunology Laboratory, Institut Jules Bordet, ULB, Brussels, Belgium
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, U-CRC, ULB, Brussels, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB, KU Leuven, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium.
- WELBIO, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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4
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De Dieuleveult M, Bizet M, Colin L, Calonne E, Bachman M, Li C, Stancheva I, Miotto B, Fuks F, Deplus R. The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome. Epigenetics 2021; 17:422-443. [PMID: 33960278 DOI: 10.1080/15592294.2021.1917152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ten-Eleven Translocation (TET) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) leading to a dynamic epigenetic state of DNA that can influence transcription and chromatin organization. While TET proteins interact with complexes involved in transcriptional repression and activation, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene expression still remains limited. Here, we show that TET proteins interact with the chromatin remodelling protein lymphoid-specific helicase (LSH/HELLS) in vivo and in vitro. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESCs) knock out of Lsh leads to a significant reduction of 5-hydroxymethylation amount in the DNA. Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh, some regions of the genome gain 5hmC while others lose it, with mild correlation with gene expression changes. We further show that differentially hydroxymethylated regions did not completely overlap with differentially methylated regions indicating that changes in 5hmC distribution upon Lsh knock-out are not a direct consequence of 5mC decrease. Altogether, our results suggest that LSH, which interacts with TET proteins, contributes to the regulation of 5hmC levels and distribution in MEFs and ESCs.
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Affiliation(s)
- Maud De Dieuleveult
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium.,Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Laurence Colin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Martin Bachman
- Medicines Discovery Catapult, Alderley Park, Macclesfield, UK
| | - Chao Li
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Irina Stancheva
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Benoit Miotto
- Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
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5
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Lan J, Rajan N, Bizet M, Penning A, Singh NK, Guallar D, Calonne E, Li Greci A, Bonvin E, Deplus R, Hsu PJ, Nachtergaele S, Ma C, Song R, Fuentes-Iglesias A, Hassabi B, Putmans P, Mies F, Menschaert G, Wong JJL, Wang J, Fidalgo M, Yuan B, Fuks F. Functional role of Tet-mediated RNA hydroxymethylcytosine in mouse ES cells and during differentiation. Nat Commun 2020; 11:4956. [PMID: 33009383 PMCID: PMC7532169 DOI: 10.1038/s41467-020-18729-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/01/2020] [Indexed: 12/23/2022] Open
Abstract
Tet-enzyme-mediated 5-hydroxymethylation of cytosines in DNA plays a crucial role in mouse embryonic stem cells (ESCs). In RNA also, 5-hydroxymethylcytosine (5hmC) has recently been evidenced, but its physiological roles are still largely unknown. Here we show the contribution and function of this mark in mouse ESCs and differentiating embryoid bodies. Transcriptome-wide mapping in ESCs reveals hundreds of messenger RNAs marked by 5hmC at sites characterized by a defined unique consensus sequence and particular features. During differentiation a large number of transcripts, including many encoding key pluripotency-related factors (such as Eed and Jarid2), show decreased cytosine hydroxymethylation. Using Tet-knockout ESCs, we find Tet enzymes to be partly responsible for deposition of 5hmC in mRNA. A transcriptome-wide search further reveals mRNA targets to which Tet1 and Tet2 bind, at sites showing a topology similar to that of 5hmC sites. Tet-mediated RNA hydroxymethylation is found to reduce the stability of crucial pluripotency-promoting transcripts. We propose that RNA cytosine 5-hydroxymethylation by Tets is a mark of transcriptome flexibility, inextricably linked to the balance between pluripotency and lineage commitment. TET mediated RNA-hydroxymethylation (5hmC) has been detected in mammals, but its physiological role remains unclear. Here the authors map 5hmC during embryonic stem cell (ESC) differentiation and find that Tet-mediated RNA hydroxymethylation reduces the stability of crucial pluripotency related transcripts.
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Affiliation(s)
- Jie Lan
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Nicholas Rajan
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Audrey Penning
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Nitesh K Singh
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Diana Guallar
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Andrea Li Greci
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Elise Bonvin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Phillip J Hsu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, and Howard Hughes Medical Institute, University of Chicago, Chicago, IL, 60637, USA
| | - Sigrid Nachtergaele
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, and Howard Hughes Medical Institute, University of Chicago, Chicago, IL, 60637, USA
| | - Chengjie Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, 430072, Wuhan, People's Republic of China
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Alejandro Fuentes-Iglesias
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Bouchra Hassabi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Frédérique Mies
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Gerben Menschaert
- Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Lab of Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium
| | - Justin J L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development (CCHD), Columbia University Irving Medical Center (CUIMC), New York, NY, 10032, USA
| | - Miguel Fidalgo
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Bifeng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, 430072, Wuhan, People's Republic of China
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium. .,WELBIO (Walloon Excellence in Lifesciences & Biotechnology), Brussels, Belgium.
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6
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Delliaux C, Tian TV, Bouchet M, Fradet A, Vanpouille N, Flourens A, Deplus R, Villers A, Leroy X, Clézardin P, de Launoit Y, Bonnelye E, Duterque-Coquillaud M. TMPRSS2:ERG gene fusion expression regulates bone markers and enhances the osteoblastic phenotype of prostate cancer bone metastases. Cancer Lett 2018; 438:32-43. [PMID: 30201302 DOI: 10.1016/j.canlet.2018.08.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 03/26/2018] [Revised: 07/31/2018] [Accepted: 08/26/2018] [Indexed: 12/11/2022]
Abstract
Prostate cancers have a strong propensity to metastasize to bone and promote osteoblastic lesions. TMPRSS2:ERG is the most frequent gene rearrangement identified in prostate cancer, but whether it is involved in prostate cancer bone metastases is largely unknown. We exploited an intratibial metastasis model to address this issue and we found that ectopic expression of the TMPRSS2:ERG fusion enhances the ability of prostate cancer cell lines to induce osteoblastic lesions by stimulating bone formation and inhibiting the osteolytic response. In line with these in vivo results, we demonstrate that the TMPRSS2:ERG fusion protein increases the expression of osteoblastic markers, including Collagen Type I Alpha 1 Chain and Alkaline Phosphatase, as well as Endothelin-1, a protein with a documented role in osteoblastic bone lesion formation. Moreover, we determined that the TMPRSS2:ERG fusion protein is bound to the regulatory regions of these genes in prostate cancer cell lines, and we report that the expression levels of these osteoblastic markers are correlated with the expression of the TMPRSS2:ERG fusion in patient metastasis samples. Taken together, our results reveal that the TMPRSS2:ERG gene fusion is involved in osteoblastic lesion formation induced by prostate cancer cells.
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Affiliation(s)
- Carine Delliaux
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - Mechanisms of Tumorigenesis and Target Therapies, F-59021, Lille, France; Montreal Clinical Research Institute (IRCM), QC H2W 1R7, Montreal, Canada
| | - Tian V Tian
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - Mechanisms of Tumorigenesis and Target Therapies, F-59021, Lille, France; Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, S-08003, Barcelona, Spain
| | - Mathilde Bouchet
- Unité INSERM U1033, F-69372, Lyon, France; Université Claude Bernard Lyon 1, F-69008, Lyon, France
| | - Anais Fradet
- Unité INSERM U1033, F-69372, Lyon, France; Université Claude Bernard Lyon 1, F-69008, Lyon, France
| | - Nathalie Vanpouille
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - Mechanisms of Tumorigenesis and Target Therapies, F-59021, Lille, France
| | - Anne Flourens
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - Mechanisms of Tumorigenesis and Target Therapies, F-59021, Lille, France
| | - Rachel Deplus
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - Mechanisms of Tumorigenesis and Target Therapies, F-59021, Lille, France
| | - Arnauld Villers
- Département d'Urologie, CHRU, Université de Lille, F-59037, Lille, France
| | - Xavier Leroy
- Institut de Pathologie-Centre de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire, F-59037, Lille, France
| | - Philippe Clézardin
- Unité INSERM U1033, F-69372, Lyon, France; Université Claude Bernard Lyon 1, F-69008, Lyon, France
| | - Yvan de Launoit
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - Mechanisms of Tumorigenesis and Target Therapies, F-59021, Lille, France
| | - Edith Bonnelye
- Unité INSERM U1033, F-69372, Lyon, France; Université Claude Bernard Lyon 1, F-69008, Lyon, France
| | - Martine Duterque-Coquillaud
- Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - Mechanisms of Tumorigenesis and Target Therapies, F-59021, Lille, France.
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7
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Deplus R, Delliaux C, Marchand N, Flourens A, Vanpouille N, Leroy X, de Launoit Y, Duterque-Coquillaud M. TMPRSS2-ERG fusion promotes prostate cancer metastases in bone. Oncotarget 2017; 8:11827-11840. [PMID: 28055969 PMCID: PMC5355307 DOI: 10.18632/oncotarget.14399] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 03/10/2016] [Accepted: 12/16/2016] [Indexed: 12/13/2022] Open
Abstract
Bone metastasis is the major deleterious event in prostate cancer (PCa). TMPRSS2-ERG fusion is one of the most common chromosomic rearrangements in PCa. However, its implication in bone metastasis development is still unclear. Since bone metastasis starts with the tropism of cancer cells to bone through specific migratory and invasive processes involving osteomimetic capabilities, it is crucial to better our understanding of the influence of TMPRSS2-ERG expression in the mechanisms underlying the bone tropism properties of PCa cells. We developed bioluminescent cell lines expressing the TMPRSS2-ERG fusion in order to assess its role in tumor growth and bone metastasis appearance in a mouse model. First, we showed that the TMPRSS2-ERG fusion increases cell migration and subcutaneous tumor size. Second, using intracardiac injection experiments in mice, we showed that the expression of TMPRSS2-ERG fusion increases the number of metastases in bone. Moreover, TMPRSS2-ERG affects the pattern of metastatic spread by increasing the incidence of tumors in hind limbs and spine, which are two of the most frequent sites of human PCa metastases. Finally, transcriptome analysis highlighted a series of genes regulated by the fusion and involved in the metastatic process. Altogether, our work indicates that TMPRSS2-ERG increases bone tropism of PCa cells and metastasis development.
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Affiliation(s)
- Rachel Deplus
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161 (M3T) Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
| | - Carine Delliaux
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161 (M3T) Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
| | - Nathalie Marchand
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161 (M3T) Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
| | - Anne Flourens
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161 (M3T) Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
| | - Nathalie Vanpouille
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161 (M3T) Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
| | - Xavier Leroy
- Institut de Pathologie Centre de Biologie Pathologie Centre Hospitalier Régional et Universitaire, F-59037 Lille, France
| | - Yvan de Launoit
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161 (M3T) Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
| | - Martine Duterque-Coquillaud
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161 (M3T) Mechanisms of Tumorigenesis and Target Therapies, F-59000 Lille, France
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Brenner C, Luciani J, Bizet M, Ndlovu M, Josseaux E, Dedeurwaerder S, Calonne E, Putmans P, Cartron PF, Defrance M, Fuks F, Deplus R. The interplay between the lysine demethylase KDM1A and DNA methyltransferases in cancer cells is cell cycle dependent. Oncotarget 2016; 7:58939-58952. [PMID: 27449289 PMCID: PMC5312287 DOI: 10.18632/oncotarget.10624] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 07/06/2016] [Indexed: 12/12/2022] Open
Abstract
DNA methylation and histone modifications are key epigenetic regulators of gene expression, and tight connections are known between the two. DNA methyltransferases are upregulated in several tumors and aberrant DNA methylation profiles are a cancer hallmark. On the other hand, histone demethylases are upregulated in cancer cells. Previous work on ES cells has shown that the lysine demethylase KDM1A binds to DNMT1, thereby affecting DNA methylation. In cancer cells, the occurrence of this interaction has not been explored. Here we demonstrate in several tumor cell lines an interaction between KDM1A and both DNMT1 and DNMT3B. Intriguingly and in contrast to what is observed in ES cells, KDM1A depletion in cancer cells was found not to trigger any reduction in the DNMT1 or DNMT3B protein level or any change in DNA methylation. In the S-phase, furthermore, KDM1A and DNMT1 were found, to co-localize within the heterochromatin. Using P-LISA, we revealed substantially increased binding of KDM1A to DNMT1 during the S-phase. Together, our findings propose a mechanistic link between KDM1A and DNA methyltransferases in cancer cells and suggest that the KDM1A/DNMT1 interaction may play a role during replication. Our work also strengthens the idea that DNMTs can exert functions unrelated to act on DNA methylation.
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Affiliation(s)
- Carmen Brenner
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Judith Luciani
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Matladi Ndlovu
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Eleonore Josseaux
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Sarah Dedeurwaerder
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Pierre-Francois Cartron
- Centre de Recherche en Cancérologie Nantes-Angers, INSERM, U892, Equipe Apoptose et Progression Tumorale, BP7021, 44007 Nantes, France
- Département de Recherche en Cancérologie, Faculté de Médecine, Université de Nantes, IFR26, F-4400, Nantes, France
- LaBCT, Institut de Cancérologie de l'Ouest, 44805 Nantes, Saint Herblain Cedex, France
| | - Matthieu Defrance
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre de Bruxelles, 1070 Brussels, Belgium
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Turpin A, Delliaux C, Tian T, Vanpouille N, Flourens A, Deplus R, Leroy X, de Launoit Y, Duterque-Coquillaud M. Abstract 694: Axon guidance neuropilin and plexin A2 genes are involved in ERG-associated prostate cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-694] [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: Bone metastases are frequent and severe complications of prostate cancer (PCa), the most common malignancy that affects men in Western countries. Recurrent gene fusions, involving the ERG gene and the androgen-regulated promoter of the TMPRSS2 gene, occur in over 50% of PCa. The abnormal over-expression of the ERG transcription factor disturbs prostate cell transcriptome. We previously identified a series of genes directly and positively regulated by the ERG-fusion in vitro and in vivo. Among them can be found Plexin A2 (PLXNA2), which is a semaphorin receptor family member involved in axon guidance and in many pathophysiological processes, including cancer and bone disorders. We showed that PLXNA2 is involved in TMPRSS2:ERG-mediated enhancements of PC3c cell migration and invasion. These results prompted us to look for genes functionally related to PLXNA2 and involved in ERG-associated PCa.
Methods: Using a PCa cell line (PC3c) stably over-expressing the TMPRSS2:ERG fusion, we first used Ingenuity Pathway Analysis® in silico studies to analyze transcriptomic results and identify axon guidance genes associated with ERG-fusion expression in PCa. Their expression was validated in stable clones by RT-PCR and Immunofluorescence. Secondly, using RNAs of a human PCa sample cohort, we performed qRT-PCR to detect and correlate candidate genes to fusion expression. Finally, to validate the relevance of the identified genes, using immunohistochemistry experiments, we studied the expression of these genes in tissue samples, including primary tumors and lymph nodes or bone metastases.
Results: Using transcriptomic analyzes and expression validation, we identified neuropilin (NRP1 and NRP2) genes, plexin and semaphorin genes deregulated by the ERG fusion expression in stable clones. In human samples, PLXNA2, NRP1 and NRP2 expression were strongly associated to PCa, and particularly to metastastic PCa. We established a significant correlation between both PLXNA2 and NRP1 gene expression and the presence of TMPRSS2-ERG fusion. At protein level, NRP1 and NRP2 were highly detected in human lymph nodes and bone metastasis samples. Since neuropilin proteins are known to interact with plexin to act as coreceptors for semaphorin ligands, protein colocalization in stable clones suggested a functional association of PLXNA2 and NRPs in tumor cells.
Conclusion: Taken together, our results reveal that TMPRSS2-ERG fusion gene expression is able to deregulate axon guidance genes such as NRP1 and PLXNA2 in PCa. Therefore, since the interaction between plexins and their NRP1 and 2 coreceptors often determines the functional specificity of their semaphorin ligand effects, we hypothesize that the ERG fusion expression imbalances the plexin/neuropilin/semaphorin signaling to contribute to PCa progression. These results reinforce the recent interest in targeting neuropilins for cancer therapy.
Citation Format: Anthony Turpin, Carine Delliaux, Tian Tian, Nathalie Vanpouille, Anne Flourens, Rachel Deplus, Xavier Leroy, Yvan de Launoit, Martine Duterque-Coquillaud. Axon guidance neuropilin and plexin A2 genes are involved in ERG-associated prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 694.
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Affiliation(s)
| | - Carine Delliaux
- 2Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France
| | - Tian Tian
- 3Center for Genomic Regulation, Barcelona, Spain
| | - Nathalie Vanpouille
- 2Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France
| | - Anne Flourens
- 2Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France
| | - Rachel Deplus
- 4Institut Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, Brussels, Belgium
| | | | - Yvan de Launoit
- 2Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France
| | - Martine Duterque-Coquillaud
- 2Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France
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Delliaux C, Tian TV, Bouchet M, Fradet A, Vanpouille N, Flourens A, Deplus R, Leroy X, de Launoit Y, Bonnelye E, Duterque-Coquillaud M. Abstract 1691: TMPRSS2:ERG fusion enhances osteoblastic phenotype of prostate cancer bone metastases. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-1691] [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: Bone metastases are the major cause of morbidity and mortality in prostate cancer (PCa) patients. Recently, TMPRSS2:ERG gene fusions produced by rearrangements along chromosome 21 was found in more than 50% of PCa samples, resulting in androgen-dependent aberrant expression of the functional ERG transcription factor. Interestingly, ERG transcription factor has been previously shown to be involved in bone development. This study is therefore focused on investigating whether TMPRSS2:ERG gene fusions are involved in PCa bone metastasis development.
Methods: We previously established cell clones overexpressing TMPRSS2:ERG from two PCa cell lines, PC3 and PC3c. We first studied induced bone lesion phenotype using in vivo intra-tibial injection models. Secondly, we analyzed transcriptional changes induced by ERG transcription factors in PC3c clones to identify potential target genes. Then, direct target genes were further validated and investigated in vitro using RT-qPCR, ELISA, siRNA and ChIP techniques. Importantly, using a cohort of prostate carcinoma samples, we validated the expression correlation between ERG and its target target genes expression in human pathology.
Results: Bone lesions induced in vivo by intra-tibial injections of PC3 or PC3c cells are known to be osteolytic or mixed (osteoblastic/osteolytic) respectively. Interestingly, intra-tibial injections of PC3c clones expressing the fusion showed a statistically significant increase of osteoblastic phenotype compared to control cells. Furthermore, intra-tibial injections of PC3 clones expressing the fusion showed a strong decrease of osteolytic phenotype, reinforcing our previous result in PC3c clones.
Among the genes identified by transcriptomic study and dysregulated in PC3c clones expressing the fusion, we have identified the ERG candidate target Endothelin-1 (ET-1), which is known to be involved in osteoblast proliferation and in osteoblastic metastasis formation in PCa. Indeed, we found that ET-1 expression was up-regulated in PC3c-TMPRSS2:ERG clones, and the up-regulation was dependent on ERG expression levels. Importantly, silencing of ERG resulted in decreased expression of ET-1. In silico analysis of the promoter of ET-1 revealed the presence of several potential binding sites of ERG. ChIP experiments followed by qPCR demonstrated a direct binding to one of them. Moreover, in human PCa samples, there was a significant expression correlation between ET-1 and fusion gene TMPRSS2:ERG, reinforcing the direct functional link between ET-1 and the fusion in PCa.
Conclusion: Taken together, these results strongly suggest that the TMPRSS2:ERG gene fusion contributes to the osteoblastic phenotype of PCa bone metastases and ET-1 is one of the involved factors, directly regulated by the transcription factor ERG.
Citation Format: Carine Delliaux, Tian V. Tian, Mathilde Bouchet, Anaïs Fradet, Nathalie Vanpouille, Anne Flourens, Rachel Deplus, Xavier Leroy, Yvan de Launoit, Edith Bonnelye, Martine Duterque-Coquillaud. TMPRSS2:ERG fusion enhances osteoblastic phenotype of prostate cancer bone metastases. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1691.
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Affiliation(s)
- Carine Delliaux
- 1Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France
| | - Tian V. Tian
- 2Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France; Center for Genomic Regulation, Barcelona, Spain
| | - Mathilde Bouchet
- 3Unité INSERM U1033; Université Claude Bernard Lyon 1, Lyon, France
| | - Anaïs Fradet
- 3Unité INSERM U1033; Université Claude Bernard Lyon 1, Lyon, France
| | - Nathalie Vanpouille
- 1Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France
| | - Anne Flourens
- 1Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France
| | - Rachel Deplus
- 4Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France; Institut Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, Brussels, Belgium
| | - Xavier Leroy
- 5Institut de Pathologie-Centre de Biologie-Pathologie-Centre Hospitalier Régional et Universitaire, Lille, France
| | - Yvan de Launoit
- 1Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France
| | - Edith Bonnelye
- 3Unité INSERM U1033; Université Claude Bernard Lyon 1, Lyon, France
| | - Martine Duterque-Coquillaud
- 1Univ. Lille, CNRS, Institut Pasteur de Lille, UMR 8161 - M3T – Mechanisms of Tumorigenesis and Target Therapies, Lille, France
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Delatte B, Wang F, Ngoc LV, Collignon E, Bonvin E, Deplus R, Calonne E, Hassabi B, Putmans P, Awe S, Wetzel C, Kreher J, Soin R, Creppe C, Limbach PA, Gueydan C, Kruys V, Brehm A, Minakhina S, Defrance M, Steward R, Fuks F. RNA biochemistry. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine. Science 2016; 351:282-5. [PMID: 26816380 DOI: 10.1126/science.aac5253] [Citation(s) in RCA: 289] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hydroxymethylcytosine, well described in DNA, occurs also in RNA. Here, we show that hydroxymethylcytosine preferentially marks polyadenylated RNAs and is deposited by Tet in Drosophila. We map the transcriptome-wide hydroxymethylation landscape, revealing hydroxymethylcytosine in the transcripts of many genes, notably in coding sequences, and identify consensus sites for hydroxymethylation. We found that RNA hydroxymethylation can favor mRNA translation. Tet and hydroxymethylated RNA are found to be most abundant in the Drosophila brain, and Tet-deficient fruitflies suffer impaired brain development, accompanied by decreased RNA hydroxymethylation. This study highlights the distribution, localization, and function of cytosine hydroxymethylation and identifies central roles for this modification in Drosophila.
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Affiliation(s)
- Benjamin Delatte
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Fei Wang
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Long Vo Ngoc
- Laboratory of Molecular Biology of the Gene, Faculty of Sciences, Université Libre de Bruxelles, Gosselies, Belgium
| | - Evelyne Collignon
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Elise Bonvin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bouchra Hassabi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Stephan Awe
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - Collin Wetzel
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Judith Kreher
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - Romuald Soin
- Laboratory of Molecular Biology of the Gene, Faculty of Sciences, Université Libre de Bruxelles, Gosselies, Belgium
| | - Catherine Creppe
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Cyril Gueydan
- Laboratory of Molecular Biology of the Gene, Faculty of Sciences, Université Libre de Bruxelles, Gosselies, Belgium
| | - Véronique Kruys
- Laboratory of Molecular Biology of the Gene, Faculty of Sciences, Université Libre de Bruxelles, Gosselies, Belgium
| | - Alexander Brehm
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - Svetlana Minakhina
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Matthieu Defrance
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ruth Steward
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium.
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Denis H, Van Grembergen O, Delatte B, Dedeurwaerder S, Putmans P, Calonne E, Rothé F, Sotiriou C, Fuks F, Deplus R. MicroRNAs regulate KDM5 histone demethylases in breast cancer cells. Mol BioSyst 2016; 12:404-13. [DOI: 10.1039/c5mb00513b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression.
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13
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Delatte B, Jeschke J, Defrance M, Bachman M, Creppe C, Calonne E, Bizet M, Deplus R, Marroquí L, Libin M, Ravichandran M, Mascart F, Eizirik DL, Murrell A, Jurkowski TP, Fuks F. Genome-wide hydroxymethylcytosine pattern changes in response to oxidative stress. Sci Rep 2015; 5:12714. [PMID: 26239807 PMCID: PMC4523844 DOI: 10.1038/srep12714] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [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: 12/30/2014] [Accepted: 07/01/2015] [Indexed: 12/21/2022] Open
Abstract
The TET enzymes convert methylcytosine to the newly discovered base hydroxymethylcytosine. While recent reports suggest that TETs may play a role in response to oxidative stress, this role remains uncertain, and results lackin vivomodels. Here we show a global decrease of hydroxymethylcytosine in cells treated with buthionine sulfoximine, and in mice depleted for the major antioxidant enzymesGPx1 and 2. Furthermore, genome-wide profiling revealed differentially hydroxymethylated regions in coding genes, and intriguingly in microRNA genes, both involved in response to oxidative stress. These results thus suggest a profound effect ofin vivooxidative stress on the global hydroxymethylome.
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Affiliation(s)
- Benjamin Delatte
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Jana Jeschke
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Matthieu Defrance
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Martin Bachman
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Catherine Creppe
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Laura Marroquí
- ULB, Center for Diabetes Research, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Myriam Libin
- Laboratory of Vaccinology and Mucosal Immunity, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | | | - Françoise Mascart
- Laboratory of Vaccinology and Mucosal Immunity, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Decio L Eizirik
- ULB, Center for Diabetes Research, Faculty of Medicine, ULB, 1070 Brussels, Belgium
| | - Adele Murrell
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Tomasz P Jurkowski
- Institute of Biochemistry, Stuttgart University, 70569 Stuttgart, Germany
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB, 1070 Brussels, Belgium
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14
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Deplus R, Blanchon L, Rajavelu A, Boukaba A, Defrance M, Luciani J, Rothé F, Dedeurwaerder S, Denis H, Brinkman AB, Simmer F, Müller F, Bertin B, Berdasco M, Putmans P, Calonne E, Litchfield DW, de Launoit Y, Jurkowski TP, Stunnenberg HG, Bock C, Sotiriou C, Fraga MF, Esteller M, Jeltsch A, Fuks F. Regulation of DNA methylation patterns by CK2-mediated phosphorylation of Dnmt3a. Cell Rep 2014; 8:743-53. [PMID: 25066127 DOI: 10.1016/j.celrep.2014.06.048] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 05/06/2014] [Accepted: 06/23/2014] [Indexed: 11/30/2022] Open
Abstract
DNA methylation is a central epigenetic modification that is established by de novo DNA methyltransferases. The mechanisms underlying the generation of genomic methylation patterns are still poorly understood. Using mass spectrometry and a phosphospecific Dnmt3a antibody, we demonstrate that CK2 phosphorylates endogenous Dnmt3a at two key residues located near its PWWP domain, thereby downregulating the ability of Dnmt3a to methylate DNA. Genome-wide DNA methylation analysis shows that CK2 primarily modulates CpG methylation of several repeats, most notably of Alu SINEs. This modulation can be directly attributed to CK2-mediated phosphorylation of Dnmt3a. We also find that CK2-mediated phosphorylation is required for localization of Dnmt3a to heterochromatin. By revealing phosphorylation as a mode of regulation of de novo DNA methyltransferase function and by uncovering a mechanism for the regulation of methylation at repetitive elements, our results shed light on the origin of DNA methylation patterns.
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Affiliation(s)
- Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Loïc Blanchon
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Arumugam Rajavelu
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Abdelhalim Boukaba
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Matthieu Defrance
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Judith Luciani
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Françoise Rothé
- Breast Cancer Translational Research Laboratory J.C. Heuson, Jules Bordet Institute, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Sarah Dedeurwaerder
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Hélène Denis
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Arie B Brinkman
- Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands
| | - Femke Simmer
- Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands
| | - Fabian Müller
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Benjamin Bertin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Maria Berdasco
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08907, Catalonia, Spain
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - David W Litchfield
- Department of Biochemistry, Schulich School of Medicine & Dentistery, University of Western Ontario, London ON N6A 5C1, Canada
| | - Yvan de Launoit
- UMR 8161, CNRS, Institut Pasteur de Lille, Universités de Lille 1 et 2, Institut de Biologie de Lille, 1 rue Calmette, 59021 Lille, France
| | - Tomasz P Jurkowski
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Hendrik G Stunnenberg
- Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory J.C. Heuson, Jules Bordet Institute, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Mario F Fraga
- Centro Nacional de Biotecnología (CNB-CSIC) and Unidad de Epigenética del Cáncer, Instituto Universitario de Oncología del Principado de Asturias, 33006-Oviedo, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08907, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany.
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium.
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15
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Deplus R, Denis H, Putmans P, Calonne E, Fourrez M, Yamamoto K, Suzuki A, Fuks F. Citrullination of DNMT3A by PADI4 regulates its stability and controls DNA methylation. Nucleic Acids Res 2014; 42:8285-96. [PMID: 24957603 PMCID: PMC4117755 DOI: 10.1093/nar/gku522] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [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] [Indexed: 12/24/2022] Open
Abstract
DNA methylation is a central epigenetic modification in mammals, with essential roles in development and disease. De novo DNA methyltransferases establish DNA methylation patterns in specific regions within the genome by mechanisms that remain poorly understood. Here we show that protein citrullination by peptidylarginine deiminase 4 (PADI4) affects the function of the DNA methyltransferase DNMT3A. We found that DNMT3A and PADI4 interact, from overexpressed as well as untransfected cells, and associate with each other's enzymatic activity. Both in vitro and in vivo, PADI4 was shown to citrullinate DNMT3A. We identified a sequence upstream of the PWWP domain of DNMT3A as its primary region citrullinated by PADI4. Increasing the PADI4 level caused the DNMT3A protein level to increase as well, provided that the PADI4 was catalytically active, and RNAi targeting PADI4 caused reduced DNMT3A levels. Accordingly, pulse-chase experiments revealed stabilization of the DNMT3A protein by catalytically active PADI4. Citrullination and increased expression of native DNMT3A by PADI4 were confirmed in PADI4-knockout MEFs. Finally, we showed that PADI4 overexpression increases DNA methyltransferase activity in a catalytic-dependent manner and use bisulfite pyrosequencing to demonstrate that PADI4 knockdown causes significant reduction of CpG methylation at the p21 promoter, a known target of DNMT3A and PADI4. Protein citrullination by PADI4 thus emerges as a novel mechanism for controlling a de novo DNA methyltransferase. Our results shed new light on how post-translational modifications might contribute to shaping the genomic CpG methylation landscape.
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Affiliation(s)
- Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Hélène Denis
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Marie Fourrez
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune diseases, Center for Integrative Medical Science, The Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune diseases, Center for Integrative Medical Science, The Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, 808 route de Lennik, 1070 Brussels, Belgium
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16
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Abstract
Methylation of the fifth carbon of cytosine was the first epigenetic modification to be discovered in DNA. Recently, three new DNA modifications have come to light: hydroxymethylcytosine, formylcytosine, and carboxylcytosine, all generated by oxidation of methylcytosine by Ten Eleven Translocation (TET) enzymes. These modifications can initiate full DNA demethylation, but they are also likely to participate, like methylcytosine, in epigenetic signalling per se. A scenario is emerging in which coordinated regulation at multiple levels governs the participation of TETs in a wide range of physiological functions, sometimes via a mechanism unrelated to their enzymatic activity. Although still under construction, a sophisticated picture is rapidly forming where, according to the function to be performed, TETs ensure epigenetic marking to create specific landscapes, and whose improper build-up can lead to diseases such as cancer and neurodegenerative disorders.
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Affiliation(s)
- Benjamin Delatte
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
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17
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Deplus R, Delatte B, Schwinn MK, Defrance M, Méndez J, Murphy N, Dawson MA, Volkmar M, Putmans P, Calonne E, Shih AH, Levine RL, Bernard O, Mercher T, Solary E, Urh M, Daniels DL, Fuks F. TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS. EMBO J 2013; 32:645-55. [PMID: 23353889 PMCID: PMC3590984 DOI: 10.1038/emboj.2012.357] [Citation(s) in RCA: 371] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 12/21/2012] [Indexed: 12/31/2022] Open
Abstract
This paper identifies the N-acetylglucosamine transferase OGT as binding partner for TET2/3 proteins. Their genome-wide chromatin binding and the characterization of the Set1/COMPASS complex as OGT target implies coordinated gene regulation. TET proteins convert 5-methylcytosine to 5-hydroxymethylcytosine, an emerging dynamic epigenetic state of DNA that can influence transcription. Evidence has linked TET1 function to epigenetic repression complexes, yet mechanistic information, especially for the TET2 and TET3 proteins, remains limited. Here, we show a direct interaction of TET2 and TET3 with O-GlcNAc transferase (OGT). OGT does not appear to influence hmC activity, rather TET2 and TET3 promote OGT activity. TET2/3–OGT co-localize on chromatin at active promoters enriched for H3K4me3 and reduction of either TET2/3 or OGT activity results in a direct decrease in H3K4me3 and concomitant decreased transcription. Further, we show that Host Cell Factor 1 (HCF1), a component of the H3K4 methyltransferase SET1/COMPASS complex, is a specific GlcNAcylation target of TET2/3–OGT, and modification of HCF1 is important for the integrity of SET1/COMPASS. Additionally, we find both TET proteins and OGT activity promote binding of the SET1/COMPASS H3K4 methyltransferase, SETD1A, to chromatin. Finally, studies in Tet2 knockout mouse bone marrow tissue extend and support the data as decreases are observed of global GlcNAcylation and also of H3K4me3, notably at several key regulators of haematopoiesis. Together, our results unveil a step-wise model, involving TET–OGT interactions, promotion of GlcNAcylation, and influence on H3K4me3 via SET1/COMPASS, highlighting a novel means by which TETs may induce transcriptional activation.
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Affiliation(s)
- Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
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18
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Guenin S, Mouallif M, Deplus R, Lampe X, Krusy N, Calonne E, Delbecque K, Kridelka F, Fuks F, Ennaji MM, Delvenne P. Aberrant promoter methylation and expression of UTF1 during cervical carcinogenesis. PLoS One 2012; 7:e42704. [PMID: 22880087 PMCID: PMC3411846 DOI: 10.1371/journal.pone.0042704] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 07/10/2012] [Indexed: 01/09/2023] Open
Abstract
Promoter methylation profiles are proposed as potential prognosis and/or diagnosis biomarkers in cervical cancer. Up to now, little is known about the promoter methylation profile and expression pattern of stem cell (SC) markers during tumor development. In this study, we were interested to identify SC genes methylation profiles during cervical carcinogenesis. A genome-wide promoter methylation screening revealed a strong hypermethylation of Undifferentiated cell Transcription Factor 1 (UTF1) promoter in cervical cancer in comparison with normal ectocervix. By direct bisulfite pyrosequencing of DNA isolated from liquid-based cytological samples, we showed that UTF1 promoter methylation increases with lesion severity, the highest level of methylation being found in carcinoma. This hypermethylation was associated with increased UTF1 mRNA and protein expression. By using quantitative RT-PCR and Western Blot, we showed that both UTF1 mRNA and protein are present in epithelial cancer cell lines, even in the absence of its two main described regulators Oct4A and Sox2. Moreover, by immunofluorescence, we confirmed the nuclear localisation of UTF1 in cell lines. Surprisingly, direct bisulfite pyrosequencing revealed that the inhibition of DNA methyltransferase by 5-aza-2'-deoxycytidine was associated with decreased UTF1 gene methylation and expression in two cervical cancer cell lines of the four tested. These findings strongly suggest that UTF1 promoter methylation profile might be a useful biomarker for cervical cancer diagnosis and raise the questions of its role during epithelial carcinogenesis and of the mechanisms regulating its expression.
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MESH Headings
- Azacitidine/pharmacology
- Carcinoma, Ovarian Epithelial
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
- Cervix Uteri/drug effects
- Cervix Uteri/metabolism
- Cervix Uteri/pathology
- Cluster Analysis
- Cytological Techniques
- DNA Methylation/drug effects
- DNA Methylation/genetics
- DNA, Neoplasm/isolation & purification
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Genes, Neoplasm/genetics
- Humans
- Neoplasms, Glandular and Epithelial/genetics
- Neoplasms, Glandular and Epithelial/pathology
- Neoplastic Stem Cells/drug effects
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Octamer Transcription Factor-3/genetics
- Octamer Transcription Factor-3/metabolism
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/pathology
- Promoter Regions, Genetic
- SOXB1 Transcription Factors/genetics
- SOXB1 Transcription Factors/metabolism
- Sequence Analysis, DNA
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Uterine Cervical Neoplasms/genetics
- Uterine Cervical Neoplasms/pathology
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Affiliation(s)
- Samuel Guenin
- Laboratory of Experimental Pathology, Groupe Interdisciplinaire de Génoprotéomique Appliquée-Cancer, University of Liège, Liège, Belgium.
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19
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Volkmar M, Dedeurwaerder S, Cunha DA, Ndlovu MN, Defrance M, Deplus R, Calonne E, Volkmar U, Igoillo-Esteve M, Naamane N, Del Guerra S, Masini M, Bugliani M, Marchetti P, Cnop M, Eizirik DL, Fuks F. DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients. EMBO J 2012; 31:1405-26. [PMID: 22293752 PMCID: PMC3321176 DOI: 10.1038/emboj.2011.503] [Citation(s) in RCA: 289] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 12/12/2011] [Indexed: 12/17/2022] Open
Abstract
In addition to genetic predisposition, environmental and lifestyle factors contribute to the pathogenesis of type 2 diabetes (T2D). Epigenetic changes may provide the link for translating environmental exposures into pathological mechanisms. In this study, we performed the first comprehensive DNA methylation profiling in pancreatic islets from T2D and non-diabetic donors. We uncovered 276 CpG loci affiliated to promoters of 254 genes displaying significant differential DNA methylation in diabetic islets. These methylation changes were not present in blood cells from T2D individuals nor were they experimentally induced in non-diabetic islets by exposure to high glucose. For a subgroup of the differentially methylated genes, concordant transcriptional changes were present. Functional annotation of the aberrantly methylated genes and RNAi experiments highlighted pathways implicated in β-cell survival and function; some are implicated in cellular dysfunction while others facilitate adaptation to stressors. Together, our findings offer new insights into the intricate mechanisms of T2D pathogenesis, underscore the important involvement of epigenetic dysregulation in diabetic islets and may advance our understanding of T2D aetiology.
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Affiliation(s)
- Michael Volkmar
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
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20
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Dedeurwaerder S, Desmedt C, Calonne E, Singhal SK, Haibe-Kains B, Defrance M, Michiels S, Volkmar M, Deplus R, Luciani J, Lallemand F, Larsimont D, Toussaint J, Haussy S, Rothé F, Rouas G, Metzger O, Majjaj S, Saini K, Putmans P, Hames G, van Baren N, Coulie PG, Piccart M, Sotiriou C, Fuks F. DNA methylation profiling reveals a predominant immune component in breast cancers. EMBO Mol Med 2011; 3:726-41. [PMID: 21910250 PMCID: PMC3377115 DOI: 10.1002/emmm.201100801] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/01/2011] [Accepted: 09/05/2011] [Indexed: 12/25/2022] Open
Abstract
Breast cancer is a molecularly, biologically and clinically heterogeneous group of disorders. Understanding this diversity is essential to improving diagnosis and optimizing treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease are still poorly understood. By means of DNA methylation profiling of 248 breast tissues, we have highlighted the existence of previously unrecognized breast cancer groups that go beyond the currently known 'expression subtypes'. Interestingly, we showed that DNA methylation profiling can reflect the cell type composition of the tumour microenvironment, and in particular a T lymphocyte infiltration of the tumours. Further, we highlighted a set of immune genes having high prognostic value in specific tumour categories. The immune component uncovered here by DNA methylation profiles provides a new perspective for the importance of the microenvironment in breast cancer, holding implications for better management of breast cancer patients.
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Affiliation(s)
- Sarah Dedeurwaerder
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
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21
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Dedeurwaerder S, Desmedt C, Calonne E, Singhal SK, Haibe-Kains B, Defrance M, Michiels S, Volkmar M, Deplus R, Luciani J, Lallemand F, Larsimont D, Toussaint J, Haussy S, Rothé F, Rouas G, Metzger O, Majjaj S, Saini K, Putmans P, Hames G, van Baren N, Coulie PG, Piccart M, Sotiriou C, Fuks F. Abstract LB-180: Epigenetic portraits of human breast cancers. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-lb-180] [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:
Understanding the diversity of breast cancer is essential to improving diagnosis and optimising treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but information is scant on the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease. Our goal was to explore the DNA methylation landscapes of phenotypically heterogeneous tumours, to relate this diversity to landscape features, and extract biological and clinical meaningful information.
Methods:
We performed comprehensive DNA methylation profiling to assess the methylomes of two independent sets of frozen breast tissue samples: a “main set” of 123 samples (4 normal and 119 infiltrating ductal carcinomas, IDCs), and a “validation set” of 125 samples (8 normal and 117 IDCs). We used the recently developed Illumina's Infinium Methylation Assay, that allows to assess the methylation status of more than 27,000 CpGs corresponding to over 14,000 genes.
Results:
Firstly, it emerged that the two major phenotypes of breast cancers determined by ER status are widely epigenetically controlled. Secondly, we have distinguished, and validated in an independent set of tumours, 6 methylation-profile-based tumour groups, some coinciding with known “expression subtypes” but also new entities that may provide a meaningful basis for refining breast tumour taxonomy. Thirdly, we showed that DNA methylation profiling can reflect the cell type composition of the tumour microenvironment. Lastly, we highlighted an unexpectedly strong epigenetic component in the regulation of key immune pathways, revealing a set of immune genes having high prognostic value in specific tumour categories.
Conclusions:
In this study, we have generated the largest and most comprehensive DNA methylation data set for human breast tumor tissues. Several novel findings and original concepts for breast cancer emerge, that previous RNA expression profiling has not highlighted. By laying the ground for better understanding of breast cancer heterogeneity and improved tumor taxonomy, the precise epigenetic portraits drawn in our work should contribute to better management of breast cancer patients.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-180. doi:10.1158/1538-7445.AM2011-LB-180
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22
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Epsztejn-Litman S, Feldman N, Abu-Remaileh M, Shufaro Y, Gerson A, Ueda J, Deplus R, Fuks F, Shinkai Y, Cedar H, Bergman Y. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nat Struct Mol Biol 2008; 15:1176-1183. [PMID: 18953337 PMCID: PMC2581722 DOI: 10.1038/nsmb.1476] [Citation(s) in RCA: 323] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 07/15/2008] [Indexed: 12/17/2022]
Abstract
The pluripotency-determining gene Oct3/4 (also called Pou5f1) undergoes postimplantation silencing in a process mediated by the histone methyltransferase G9a. Microarray analysis now shows that this enzyme may operate as a master regulator that inactivates numerous early-embryonic genes by bringing about heterochromatinization of methylated histone H3K9 and de novo DNA methylation. Genetic studies in differentiating embryonic stem cells demonstrate that a point mutation in the G9a SET domain prevents heterochromatinization but still allows de novo methylation, whereas biochemical and functional studies indicate that G9a itself is capable of bringing about de novo methylation through its ankyrin domain, by recruiting Dnmt3a and Dnmt3b independently of its histone methyltransferase activity. These modifications seem to be programmed for carrying out two separate biological functions: histone methylation blocks target-gene reactivation in the absence of transcriptional repressors, whereas DNA methylation prevents reprogramming to the undifferentiated state.
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Affiliation(s)
- Silvina Epsztejn-Litman
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
| | - Nirit Feldman
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
| | - Monther Abu-Remaileh
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
| | - Yoel Shufaro
- IVF Unit, The Department of OB/GYN The Hadassah Human Embryonic Stem Cell Research Center Hadassah Hebrew University Medical Center Jerusalem, 91120 ISRAEL
| | - Ariela Gerson
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
| | - Jun Ueda
- Experimental Research Center for Infectious Disease Institute for Virus Research Kyoto University Sakyo-Ku, Kyoto 606-8507 JAPAN
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics Faculty of Medicine Free University of Brussels Brussels 1070 BELGIUM
| | - François Fuks
- Laboratory of Cancer Epigenetics Faculty of Medicine Free University of Brussels Brussels 1070 BELGIUM
| | - Yoichi Shinkai
- Experimental Research Center for Infectious Disease Institute for Virus Research Kyoto University Sakyo-Ku, Kyoto 606-8507 JAPAN
| | - Howard Cedar
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
| | - Yehudit Bergman
- Departments of Experimental Medicine and Cellular Biochemistry Hebrew University Medical School Ein Kerem Jerusalem, 91120 ISRAEL
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Lim C, Macaigne G, Boivin JF, Auriaul ML, Deplus R. Colite lymphocytaire associée à la prise de Stalevo®. ACTA ACUST UNITED AC 2008; 32:698-9. [DOI: 10.1016/j.gcb.2008.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 02/07/2008] [Accepted: 02/08/2008] [Indexed: 10/22/2022]
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Macaigne G, Al Jannoud A, Boivin JF, Auriault ML, Deplus R. Colite lymphocytaire associée à la prise d’Esberiven Fort®. ACTA ACUST UNITED AC 2008; 32:697-8. [DOI: 10.1016/j.gcb.2007.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Revised: 11/10/2007] [Accepted: 11/11/2007] [Indexed: 11/26/2022]
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Viré E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C, Morey L, Van Eynde A, Bernard D, Vanderwinden JM, Bollen M, Esteller M, Croce LD, de Launoit Y, Fuks F. Erratum: The Polycomb group protein EZH2 directly controls DNA methylation. Nature 2007. [DOI: 10.1038/nature05710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Viré E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C, Morey L, Van Eynde A, Bernard D, Vanderwinden JM, Bollen M, Esteller M, Di Croce L, de Launoit Y, Fuks F. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 2005; 439:871-4. [PMID: 16357870 DOI: 10.1038/nature04431] [Citation(s) in RCA: 1604] [Impact Index Per Article: 84.4] [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: 10/06/2005] [Accepted: 11/15/2005] [Indexed: 02/07/2023]
Abstract
The establishment and maintenance of epigenetic gene silencing is fundamental to cell determination and function. The essential epigenetic systems involved in heritable repression of gene activity are the Polycomb group (PcG) proteins and the DNA methylation systems. Here we show that the corresponding silencing pathways are mechanistically linked. We find that the PcG protein EZH2 (Enhancer of Zeste homolog 2) interacts-within the context of the Polycomb repressive complexes 2 and 3 (PRC2/3)-with DNA methyltransferases (DNMTs) and associates with DNMT activity in vivo. Chromatin immunoprecipitations indicate that binding of DNMTs to several EZH2-repressed genes depends on the presence of EZH2. Furthermore, we show by bisulphite genomic sequencing that EZH2 is required for DNA methylation of EZH2-target promoters. Our results suggest that EZH2 serves as a recruitment platform for DNA methyltransferases, thus highlighting a previously unrecognized direct connection between two key epigenetic repression systems.
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Affiliation(s)
- Emmanuelle Viré
- Free University of Brussels, Faculty of Medicine, Laboratory of Molecular Virology, 808 route de Lennik, 1070 Brussels, Belgium
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Brenner C, Deplus R, Didelot C, Loriot A, Viré E, De Smet C, Gutierrez A, Danovi D, Bernard D, Boon T, Giuseppe Pelicci P, Amati B, Kouzarides T, de Launoit Y, Di Croce L, Fuks F. Myc represses transcription through recruitment of DNA methyltransferase corepressor. EMBO J 2005; 24:336-46. [PMID: 15616584 PMCID: PMC545804 DOI: 10.1038/sj.emboj.7600509] [Citation(s) in RCA: 305] [Impact Index Per Article: 16.1] [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: 04/30/2004] [Accepted: 11/12/2004] [Indexed: 12/19/2022] Open
Abstract
The Myc transcription factor is an essential mediator of cell growth and proliferation through its ability to both positively and negatively regulate transcription. The mechanisms by which Myc silences gene expression are not well understood. The current model is that Myc represses transcription through functional interference with transcriptional activators. Here we show that Myc binds the corepressor Dnmt3a and associates with DNA methyltransferase activity in vivo. In cells with reduced Dnmt3a levels, we observe specific reactivation of the Myc-repressed p21Cip1 gene, whereas the expression of Myc-activated E-boxes genes is unchanged. In addition, we find that Myc can target Dnmt3a selectively to the promoter of p21Cip1. Myc is known to be recruited to the p21Cip1 promoter by the DNA-binding factor Miz-1. Consistent with this, we observe that Myc and Dnmt3a form a ternary complex with Miz-1 and that this complex can corepress the p21Cip1 promoter. Finally, we show that DNA methylation is required for Myc-mediated repression of p21Cip1. Our data identify a new mechanism by which Myc can silence gene expression not only by passive functional interference but also by active recruitment of corepressor proteins. Furthermore, these findings suggest that targeting of DNA methyltransferases by transcription factors is a wide and general mechanism for the generation of specific DNA methylation patterns within a cell.
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Affiliation(s)
- Carmen Brenner
- Free University of Brussels, Faculty of Medicine, Laboratory of Molecular Virology, Brussels, Belgium
| | - Rachel Deplus
- Free University of Brussels, Faculty of Medicine, Laboratory of Molecular Virology, Brussels, Belgium
| | - Céline Didelot
- Free University of Brussels, Faculty of Medicine, Laboratory of Molecular Virology, Brussels, Belgium
| | - Axelle Loriot
- Ludwig Institute For Cancer Research, UCL, Brussels, Belgium
| | - Emmanuelle Viré
- Free University of Brussels, Faculty of Medicine, Laboratory of Molecular Virology, Brussels, Belgium
| | - Charles De Smet
- Ludwig Institute For Cancer Research, UCL, Brussels, Belgium
| | | | - Davide Danovi
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - David Bernard
- Free University of Brussels, Faculty of Medicine, Laboratory of Molecular Virology, Brussels, Belgium
| | - Thierry Boon
- Ludwig Institute For Cancer Research, UCL, Brussels, Belgium
| | | | - Bruno Amati
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Tony Kouzarides
- Wellcome/Cancer Research UK Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - Yvan de Launoit
- Free University of Brussels, Faculty of Medicine, Laboratory of Molecular Virology, Brussels, Belgium
- UMR 8117, CNRS Institut Pasteur de Lille, Université de Lille 1, Institut de Biologie de Lille, Lille, Cedex, France
| | - Luciano Di Croce
- ICREA and Center for Genomic Regulation, Barcelona, Spain
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - François Fuks
- Free University of Brussels, Faculty of Medicine, Laboratory of Molecular Virology, Brussels, Belgium
- Wellcome/Cancer Research UK Institute and Department of Pathology, University of Cambridge, Cambridge, UK
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Laduron S, Deplus R, Zhou S, Kholmanskikh O, Godelaine D, De Smet C, Hayward SD, Fuks F, Boon T, De Plaen E. MAGE-A1 interacts with adaptor SKIP and the deacetylase HDAC1 to repress transcription. Nucleic Acids Res 2004; 32:4340-50. [PMID: 15316101 PMCID: PMC514365 DOI: 10.1093/nar/gkh735] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
MAGE-A1 belongs to a family of 12 genes that are active in various types of tumors and silent in normal tissues except in male germ-line cells. The MAGE-encoded antigens recognized by T cells are highly tumor-specific targets for T cell-oriented cancer immunotherapy. The function of MAGE-A1 is currently unknown. To analyze it, we attempted to identify protein partners of MAGE-A1. Using yeast two-hybrid screening, we detected an interaction between MAGE-A1 and Ski Interacting Protein (SKIP). SKIP is a transcriptional regulator that connects DNA-binding proteins to proteins that either activate or repress transcription. We show that MAGE-A1 inhibits the activity of a SKIP-interacting transactivator, namely the intracellular part of Notch1. Deletion analysis indicated that this inhibition requires the binding of MAGE-A1 to SKIP. Moreover, MAGE-A1 was found to actively repress transcription by binding and recruiting histone deacetylase 1 (HDAC1). Our results indicate that by binding to SKIP and by recruiting HDACs, MAGE-A1 can act as a potent transcriptional repressor. MAGE-A1 could therefore participate in the setting of specific gene expression patterns for tumor cell growth or spermatogenesis.
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Affiliation(s)
- Sandra Laduron
- Ludwig Institute for Cancer Research, Brussels branch, and Cellular Genetics Unit, Université Catholique de Louvain, Brussels B1200, Belgium
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Fuks F, Hurd PJ, Deplus R, Kouzarides T. The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res 2003; 31:2305-12. [PMID: 12711675 PMCID: PMC154218 DOI: 10.1093/nar/gkg332] [Citation(s) in RCA: 520] [Impact Index Per Article: 24.8] [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: 02/04/2003] [Revised: 03/04/2003] [Accepted: 03/04/2003] [Indexed: 02/03/2023] Open
Abstract
The DNA methyltransferases, Dnmts, are the enzymes responsible for methylating DNA in mammals, which leads to gene silencing. Repression by DNA methylation is mediated partly by recruitment of the methyl-CpG-binding protein MeCP2. Recently, MeCP2 was shown to associate and facilitate histone methylation at Lys9 of H3, which is a key epigenetic modification involved in gene silencing. Here, we show that endogenous Dnmt3a associates primarily with histone H3-K9 methyltransferase activity as well as, to a lesser extent, with H3-K4 enzymatic activity. The association with enzymatic activity is mediated by the conserved PHD-like motif of Dnmt3a. The H3-K9 histone methyltransferase that binds Dnmt3a is likely the H3-K9 specific SUV39H1 enzyme since we find that it interacts both in vitro and in vivo with Dnmt3a, using its PHD-like motif. We find that SUV39H1 also binds to Dnmt1 and, consistent with these interactions, SUV39H1 can purify DNA methyltransferase activity from nuclear extracts. In addition, we show that HP1beta, a SUV39H1-interacting partner, binds directly to Dnmt1 and Dnmt3a and that native HP1beta associates with DNA methyltransferase activity. Our data show a direct connection between the enzymes responsible for DNA methylation and histone methylation. These results further substantiate the notion of a self-reinforcing repressive chromatin state through the interplay between these two global epigenetic modifications.
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Affiliation(s)
- François Fuks
- Wellcome Trust/CR UK Institute and Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QR, UK
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Deplus R, Brenner C, Burgers WA, Putmans P, Kouzarides T, de Launoit Y, Fuks F. Dnmt3L is a transcriptional repressor that recruits histone deacetylase. Nucleic Acids Res 2002; 30:3831-8. [PMID: 12202768 PMCID: PMC137431 DOI: 10.1093/nar/gkf509] [Citation(s) in RCA: 133] [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] [Indexed: 11/14/2022] Open
Abstract
The Dnmt3L protein belongs to the Dnmt3 family of DNA methyltransferases by virtue of its sequence homology in the plant homeodomain (PHD)-like motif. Dnmt3L is essential for the establishment of maternal genomic imprints and, given its lack of key methyltransferase motifs, is more likely to act as a regulator of methylation rather than as an enzyme that methylates DNA. Here, we show that Dnmt3L, like Dnmt3a and Dnmt3b, interacts both in vitro and in vivo with the histone deacetylase HDAC1. Consistent with the binding to a deacetylase, Dnmt3L purifies histone deacetylase activity from nuclear extracts. We find that Dnmt3L can repress transcription and that this repression is dependent on HDAC1 and is relieved by treatment with the HDAC inhibitor trichostatin A. Binding of Dnmt3L to HDAC1 as well as its repressive function require the PHD-like motif. Our results indicate that Dnmt3L plays a role in transcriptional regulation and that recruitment of the HDAC repressive machinery is a shared and conserved feature of the Dnmt3 family. The fact that, despite the absence of a methyltransferase domain, Dnmt3L retains the capacity to contact deacetylase further substantiates the notion that the Dnmts can repress transcription independently of their methylating activities.
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Affiliation(s)
- Rachel Deplus
- Free University of Brussels, Faculty of Medicine, Laboratory of Molecular Virology, 808 route de Lennik, 1070 Brussels, Belgium
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Macaigne G, David F, Boivin JF, Cheiab S, Chayette C, Deplus R. [Colorectal spirochetosis, a possible but unusual cause of chronic diarrhea?]. Presse Med 2002; 31:458-61. [PMID: 11933749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
INTRODUCTION Human intestinal spirochetosis has been known since the end of the nineteenth century. OBSERVATION We report one case of intestinal spirochetosis revealed by chronic diarrhoea and diagnosed on colonic biopsies. The chronic diarrhoea disappeared with antibiotherapy. COMMENTARIES The prevalence of intestinal spirochetosis in rectal and colonic biopsies, among patients with digestive disorders, varies in occidental countries from 2% to 7%. Presently, the pathogenic role of intestinal spirochetosis is controversial.
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Macaigne G, Boivin JF, Simon P, Chayette C, Cheaib S, Deplus R. [Lansoprazole-associated collagenous colitis]. Gastroenterol Clin Biol 2001; 25:1030. [PMID: 11845059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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Macaigne G, Boivin JF, Colombu JP, Desbiez JP, Chayette C, Cheaib S, Deplus R. [Stromal tumor with skenoid fibers of small bowel manifesting as intestinal bleeding]. Gastroenterol Clin Biol 2001; 25:717-9. [PMID: 11673742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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34
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Macaigne G, Boivin JF, Chayette C, Chaieb S, Deplus R. [Small-cell carcinoma o the esophagus: presentation of a case and review of the literature]. Gastroenterol Clin Biol 1999; 23:988-90. [PMID: 10533152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
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