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Rengifo Rojas C, Cercy J, Perillous S, Gonthier-Guéret C, Montibus B, Maupetit-Méhouas S, Espinadel A, Dupré M, Hong CC, Hata K, Nakabayashi K, Plagge A, Bouschet T, Arnaud P, Vaillant I, Court F. Biallelic non-productive enhancer-promoter interactions precede imprinted expression of Kcnk9 during mouse neural commitment. HGG Adv 2024; 5:100271. [PMID: 38297831 PMCID: PMC10869267 DOI: 10.1016/j.xhgg.2024.100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
It is only partially understood how constitutive allelic methylation at imprinting control regions (ICRs) interacts with other regulation levels to drive timely parental allele-specific expression along large imprinted domains. The Peg13-Kcnk9 domain is an imprinted domain with important brain functions. To gain insights into its regulation during neural commitment, we performed an integrative analysis of its allele-specific epigenetic, transcriptomic, and cis-spatial organization using a mouse stem cell-based corticogenesis model that recapitulates the control of imprinted gene expression during neurodevelopment. We found that, despite an allelic higher-order chromatin structure associated with the paternally CTCF-bound Peg13 ICR, enhancer-Kcnk9 promoter contacts occurred on both alleles, although they were productive only on the maternal allele. This observation challenges the canonical model in which CTCF binding isolates the enhancer and its target gene on either side and suggests a more nuanced role for allelic CTCF binding at some ICRs.
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Affiliation(s)
- Cecilia Rengifo Rojas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jil Cercy
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sophie Perillous
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Céline Gonthier-Guéret
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Bertille Montibus
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Stéphanie Maupetit-Méhouas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Astrid Espinadel
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Marylou Dupré
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan; Department of Human Molecular Genetics, Gunma University Graduate School of Medicine 3-39-22 Showa, Maebashi, Gunma 371-8511, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Antonius Plagge
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Philippe Arnaud
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Isabelle Vaillant
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Franck Court
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
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2
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Le Boiteux E, Guichet PO, Masliantsev K, Montibus B, Vaurs-Barriere C, Gonthier-Gueret C, Chautard E, Verrelle P, Karayan-Tapon L, Fogli A, Court F, Arnaud P. The Long Non-Coding RNA HOXA-AS2 Promotes Proliferation of Glioma Stem Cells and Modulates Their Inflammation Pathway Mainly through Post-Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094743. [PMID: 35563134 PMCID: PMC9102906 DOI: 10.3390/ijms23094743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 12/21/2022] Open
Abstract
Glioblastomas represent approximatively half of all gliomas and are the most deadly and aggressive form. Their therapeutic resistance and tumor relapse rely on a subpopulation of cells that are called Glioma Stem Cells (GSCs). Here, we investigated the role of the long non-coding RNA HOXA-AS2 in GSC biology using descriptive and functional analyses of glioma samples classified according to their isocitrate dehydrogenase (IDH) gene mutation status, and of GSC lines. We found that HOXA-AS2 is overexpressed only in aggressive (IDHwt) glioma and GSC lines. ShRNA-based depletion of HOXA-AS2 in GSCs decreased cell proliferation and altered the expression of several hundreds of genes. Integrative analysis revealed that these expression changes were not associated with changes in DNA methylation or chromatin signatures at the promoter of the majority of genes deregulated following HOXA-AS2 silencing in GSCs, suggesting a post-transcriptional regulation. In addition, transcription factor binding motif enrichment and correlation analyses indicated that HOXA-AS2 affects, directly or indirectly, the expression of key transcription factors implicated in GCS biology, including E2F8, E2F1, STAT1, and ATF3, thus contributing to GCS aggressiveness by promoting their proliferation and modulating the inflammation pathway.
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Affiliation(s)
- Elisa Le Boiteux
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Pierre-Olivier Guichet
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Konstantin Masliantsev
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Bertille Montibus
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Catherine Vaurs-Barriere
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Céline Gonthier-Gueret
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Emmanuel Chautard
- Pathology Department, Jean Perrin Center, F-63000 Clermont-Ferrand, France;
- INSERM, U1240 IMoST, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Pierre Verrelle
- CIMB, INSERM U1196 CNRS UMR9187, Curie Institute, F-91400 Orsay, France;
- Radiotherapy Department, Curie Institute, F-75248 Paris, France
- CNRS UMR 9187, INSERM U1196, Institut Curie, PSL Research University and Paris-Saclay University, F-91405 Orsay, France
| | - Lucie Karayan-Tapon
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Anne Fogli
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Radiation Oncology Department, Institut Curie, F-75005 Paris, France
| | - Franck Court
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Correspondence: (F.C.); (P.A.)
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Correspondence: (F.C.); (P.A.)
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3
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Pinson ME, Court F, Masson A, Renaud Y, Fantini A, Bacoeur-Ouzillou O, Barriere M, Pereira B, Guichet PO, Chautard E, Karayan-Tapon L, Verrelle P, Arnaud P, Vaurs-Barrière C. L1 chimeric transcripts are expressed in healthy brain and their deregulation in glioma follows that of their host locus. Hum Mol Genet 2022; 31:2606-2622. [PMID: 35298627 PMCID: PMC9396940 DOI: 10.1093/hmg/ddac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/18/2022] [Accepted: 03/03/2022] [Indexed: 11/30/2022] Open
Abstract
Besides the consequences of retrotransposition, long interspersed element 1 (L1) retrotransposons can affect the host genome through their antisense promoter. In addition to the sense promoter, the evolutionarily recent L1 retrotransposons, which are present in several thousand copies, also possess an anti-sense promoter that can produce L1 chimeric transcripts (LCT) composed of the L1 5′ UTR followed by the adjacent genomic sequence. The full extent to which LCT expression occurs in a given tissue and whether disruption of the defense mechanisms that normally control L1 retrotransposons affects their expression and function in cancer cells, remain to be established. By using CLIFinder, a dedicated bioinformatics tool, we found that LCT expression was widespread in normal brain and aggressive glioma samples, and that approximately 17% of recent L1 retrotransposons, from the L1PA1 to L1PA7 subfamilies, were involved in their production. Importantly, the transcriptional activities of the L1 antisense promoters and of their host loci were coupled. Accordingly, we detected LCT-producing L1 retrotransposons mainly in transcriptionally active genes and genomic loci. Moreover, changes in the host genomic locus expression level in glioma were associated with a similar change in LCT expression level, regardless of the L1 promoter methylation status. Our findings support a model in which the host genomic locus transcriptional activity is the main driving force of LCT expression. We hypothesize that this model is more applicable when host gene and LCT are transcribed from the same strand.
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Affiliation(s)
- Marie-Elisa Pinson
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | - Franck Court
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | - Aymeric Masson
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | - Yoan Renaud
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | - Allison Fantini
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | | | - Marie Barriere
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
| | - Bruno Pereira
- Biostatistics Department, Délégation à la Recherche Clinique et à l'Innovation, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | | | - Emmanuel Chautard
- Université Clermont Auvergne, INSERM, U1240 IMoST, Clermont-Ferrand 63011, France.,Pathology Department, Centre Jean PERRIN, Clermont-Ferrand 63011, France
| | - Lucie Karayan-Tapon
- Cancer Biology Department, CHU de Poitiers, Poitiers 86021, France.,INSERM, U1084, Poitiers 86021, France.,Université de Poitiers, Poitiers 86000, France
| | - Pierre Verrelle
- INSERM, U1196 CNRS UMR9187, Curie Institute, Orsay 91405, France.,Radiotherapy Department Curie Institute, Paris 75005, France.,Université Clermont Auvergne, Clermont-Ferrand 63000, France
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, iGReD, F-63000 Clermont-Ferrand, France
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4
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Le Boiteux E, Court F, Guichet PO, Vaurs-Barrière C, Vaillant I, Chautard E, Verrelle P, Costa BM, Karayan-Tapon L, Fogli A, Arnaud P. Widespread overexpression from the four DNA hypermethylated HOX clusters in aggressive (IDHwt) glioma is associated with H3K27me3 depletion and alternative promoter usage. Mol Oncol 2021; 15:1995-2010. [PMID: 33720519 PMCID: PMC8334257 DOI: 10.1002/1878-0261.12944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/17/2021] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
In human, the 39 coding HOX genes and 18 referenced noncoding antisense transcripts are arranged in four genomic clusters named HOXA, B, C, and D. This highly conserved family belongs to the homeobox class of genes that encode transcription factors required for normal development. Therefore, HOX gene deregulation might contribute to the development of many cancer types. Here, we study HOX gene deregulation in adult glioma, a common type of primary brain tumor. We performed extensive molecular analysis of tumor samples, classified according to their isocitrate dehydrogenase (IDH1) gene mutation status, and of glioma stem cells. We found widespread expression of sense and antisense HOX transcripts only in aggressive (IDHwt) glioma samples, although the four HOX clusters displayed DNA hypermethylation. Integrative analysis of expression, DNA methylation, and histone modification signatures along the clusters revealed that HOX gene upregulation relies on canonical and alternative bivalent CpG island promoters that escape hypermethylation. H3K27me3 loss at these promoters emerges as the main cause of widespread HOX gene upregulation in IDHwt glioma cell lines and tumors. Our study provides the first comprehensive description of the epigenetic changes at HOX clusters and their contribution to the transcriptional changes observed in adult glioma. It also identified putative 'master' HOX proteins that might contribute to the tumorigenic potential of glioma stem cells.
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Affiliation(s)
- Elisa Le Boiteux
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Franck Court
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pierre-Olivier Guichet
- INSERM-U1084, Poitiers, France.,Poitiers University, France.,Department of Cancer Biology, Poitiers Hospital, France
| | | | - Isabelle Vaillant
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Emmanuel Chautard
- Pathology Department, Jean Perrin Center, Clermont-Ferrand, France.,INSERM, U1240 IMoST, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pierre Verrelle
- CIMB, INSERM U1196 CNRS UMR9187, Curie Institute, Orsay, France.,Radiotherapy Department, Curie Institute, Paris, France.,Université Clermont Auvergne, Clermont-Ferrand, France
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Lucie Karayan-Tapon
- INSERM-U1084, Poitiers, France.,Poitiers University, France.,Department of Cancer Biology, Poitiers Hospital, France
| | - Anne Fogli
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France.,Biochemistry and Molecular Biology Department, Clermont-Ferrand Hospital, France
| | - Philippe Arnaud
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
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5
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Montibus B, Cercy J, Bouschet T, Charras A, Maupetit-Méhouas S, Nury D, Gonthier-Guéret C, Chauveau S, Allegre N, Chariau C, Hong CC, Vaillant I, Marques CJ, Court F, Arnaud P. TET3 controls the expression of the H3K27me3 demethylase Kdm6b during neural commitment. Cell Mol Life Sci 2021; 78:757-768. [PMID: 32405722 PMCID: PMC9644380 DOI: 10.1007/s00018-020-03541-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 01/03/2023]
Abstract
The acquisition of cell identity is associated with developmentally regulated changes in the cellular histone methylation signatures. For instance, commitment to neural differentiation relies on the tightly controlled gain or loss of H3K27me3, a hallmark of polycomb-mediated transcriptional gene silencing, at specific gene sets. The KDM6B demethylase, which removes H3K27me3 marks at defined promoters and enhancers, is a key factor in neurogenesis. Therefore, to better understand the epigenetic regulation of neural fate acquisition, it is important to determine how Kdm6b expression is regulated. Here, we investigated the molecular mechanisms involved in the induction of Kdm6b expression upon neural commitment of mouse embryonic stem cells. We found that the increase in Kdm6b expression is linked to a rearrangement between two 3D configurations defined by the promoter contact with two different regions in the Kdm6b locus. This is associated with changes in 5-hydroxymethylcytosine (5hmC) levels at these two regions, and requires a functional ten-eleven-translocation (TET) 3 protein. Altogether, our data support a model whereby Kdm6b induction upon neural commitment relies on an intronic enhancer the activity of which is defined by its TET3-mediated 5-hmC level. This original observation reveals an unexpected interplay between the 5-hmC and H3K27me3 pathways during neural lineage commitment in mammals. It also questions to which extent KDM6B-mediated changes in H3K27me3 level account for the TET-mediated effects on gene expression.
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Affiliation(s)
- Bertille Montibus
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
- King's College, London, UK
| | - Jil Cercy
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Amandine Charras
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
- Department of Women's and Children's Health, Institute of Lifecourse and Medical Sciences, Liverpool University, Liverpool, UK
| | | | - David Nury
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | | | - Sabine Chauveau
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - Nicolas Allegre
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - Caroline Chariau
- Nantes Université, CHU Nantes, SFR Santé, FED4203, Inserm UMS 016, CNRS UMS 3556, 44000, Nantes, France
| | - Charles C Hong
- Vanderbilt University School of Medicine Nashville, Nashville, USA
| | - Isabelle Vaillant
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - C Joana Marques
- Life and Health Sciences Research Institute (ICVS), University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
- Department of Genetics, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal
| | - Franck Court
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France.
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France.
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Court F, Le Boiteux E, Fogli A, Müller-Barthélémy M, Vaurs-Barrière C, Chautard E, Pereira B, Biau J, Kemeny JL, Khalil T, Karayan-Tapon L, Verrelle P, Arnaud P. Transcriptional alterations in glioma result primarily from DNA methylation-independent mechanisms. Genome Res 2019; 29:1605-1621. [PMID: 31533980 PMCID: PMC6771409 DOI: 10.1101/gr.249219.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
In cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution of DNA methylation–dependent and –independent mechanisms to transcriptional alterations at CpG island/promoter-associated genes in cancer, we studied 70 samples of adult glioma, a widespread type of brain tumor, classified according to their isocitrate dehydrogenase (IDH1) mutation status. We found that most transcriptional alterations in tumor samples were DNA methylation–independent. Instead, altered histone H3 trimethylation at lysine 27 (H3K27me3) was the predominant molecular defect at deregulated genes. Our results also suggest that the presence of a bivalent chromatin signature at CpG island promoters in stem cells predisposes not only to hypermethylation, as widely documented, but more generally to all types of transcriptional alterations in transformed cells. In addition, the gene expression strength in healthy brain cells influences the choice between DNA methylation- and H3K27me3-associated silencing in glioma. Highly expressed genes were more likely to be repressed by H3K27me3 than by DNA methylation. Our findings support a model in which altered H3K27me3 dynamics, more specifically defects in the interplay between polycomb protein complexes and the brain-specific transcriptional machinery, is the main cause of transcriptional alteration in glioma cells. Our study provides the first comprehensive description of epigenetic changes in glioma and their relative contribution to transcriptional changes. It may be useful for the design of drugs targeting cancer-related epigenetic defects.
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Affiliation(s)
- Franck Court
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
| | - Elisa Le Boiteux
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
| | - Anne Fogli
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France.,Biochemistry and Molecular Biology Department, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Mélanie Müller-Barthélémy
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France.,Pathology Department, Jean Perrin Center, Clermont-Ferrand 63011, France
| | - Catherine Vaurs-Barrière
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
| | - Emmanuel Chautard
- Pathology Department, Jean Perrin Center, Clermont-Ferrand 63011, France.,Université Clermont Auvergne, INSERM, U1240 IMoST, Clermont-Ferrand 63011, France
| | - Bruno Pereira
- Biostatistics Department, Délégation à la Recherche Clinique et à l'Innovation, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Julian Biau
- Université Clermont Auvergne, INSERM, U1240 IMoST, Clermont-Ferrand 63011, France.,Radiotherapy Department, Jean Perrin Center, Clermont-Ferrand 63011, France
| | - Jean-Louis Kemeny
- Pathology Department, Université Clermont Auvergne and Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Toufic Khalil
- Department of Neurosurgery, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Lucie Karayan-Tapon
- INSERM, U1084, Poitiers 86021, France.,Poitiers University, Poitiers 86000, France.,Department of Cancer Biology, Poitiers Hospital, Poitiers 86021, France
| | - Pierre Verrelle
- INSERM, U1196 CNRS UMR9187, Curie Institute, Orsay 91405, France.,Radiotherapy Department Curie Institute, Paris 75005, France.,Université Clermont Auvergne, Clermont-Ferrand 63000, France
| | - Philippe Arnaud
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
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7
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Pinson ME, Pogorelcnik R, Court F, Arnaud P, Vaurs-Barrière C. CLIFinder: identification of LINE-1 chimeric transcripts in RNA-seq data. Bioinformatics 2019; 34:688-690. [PMID: 29069308 DOI: 10.1093/bioinformatics/btx671] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/19/2017] [Indexed: 11/12/2022] Open
Abstract
Summary L1 Chimeric Transcripts (LCTs) are initiated by repeated LINE-1 element antisense promoters and include the L1 5'UTR sequence in antisense orientation followed by the adjacent genomic region. LCTs have been characterized mainly using bioinformatics approaches to query dbEST. To take advantage of NGS data to unravel the transcriptome composition, we developed Chimeric LIne Finder (CLIFinder), a new bioinformatics tool. Using stranded paired-end RNA-seq data, we demonstrated that CLIFinder can identify genome-wide transcribed chimera sequences corresponding to potential LCTs. Moreover, CLIFinder can be adapted to study transcription from other repeat types. Availability and implementation The code is available at: https://github.com/GReD-Clermont/CLIFinder; and for Galaxy users, it is directly accessible in the tool shed at: https://toolshed.g2.bx.psu.edu/view/clifinder/clifinder/. Contact catherine.barriere@uca.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marie-Elisa Pinson
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Romain Pogorelcnik
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Franck Court
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Philippe Arnaud
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
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8
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Blane C, Chambers A, Vallence A, Massey E, Hunt R, Court F, Vestey S, Fowler C, Allak AA. A single centre experience with breast cancer patients aged over 80 years; what factors affect treatment options and what are the long-term outcomes? Eur J Surg Oncol 2019. [DOI: 10.1016/j.ejso.2018.10.335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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9
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Baudement MO, Cournac A, Court F, Seveno M, Parrinello H, Reynes C, Sabatier R, Bouschet T, Yi Z, Sallis S, Tancelin M, Rebouissou C, Cathala G, Lesne A, Mozziconacci J, Journot L, Forné T. High-salt-recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies. Genome Res 2018; 28:1733-1746. [PMID: 30287550 PMCID: PMC6211644 DOI: 10.1101/gr.237073.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/10/2018] [Indexed: 12/18/2022]
Abstract
The mammalian cell nucleus contains numerous discrete suborganelles named nuclear bodies. While recruitment of specific genomic regions into these large ribonucleoprotein (RNP) complexes critically contributes to higher-order functional chromatin organization, such regions remain ill-defined. We have developed the high-salt–recovered sequences-sequencing (HRS-seq) method, a straightforward genome-wide approach whereby we isolated and sequenced genomic regions associated with large high-salt insoluble RNP complexes. By using mouse embryonic stem cells (ESCs), we showed that these regions essentially correspond to the most highly expressed genes, and to cis-regulatory sequences like super-enhancers, that belong to the active A chromosomal compartment. They include both cell-type–specific genes, such as pluripotency genes in ESCs, and housekeeping genes associated with nuclear bodies, such as histone and snRNA genes that are central components of Histone Locus Bodies and Cajal bodies. We conclude that HRSs are associated with the active chromosomal compartment and with large RNP complexes including nuclear bodies. Association of such chromosomal regions with nuclear bodies is in agreement with the recently proposed phase separation model for transcription control and might thus play a central role in organizing the active chromosomal compartment in mammals.
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Affiliation(s)
| | | | - Franck Court
- IGMM, Université de Montpellier, CNRS, F-34293, Montpellier, France
| | - Marie Seveno
- IGMM, Université de Montpellier, CNRS, F-34293, Montpellier, France
| | - Hugues Parrinello
- MGX, Université de Montpellier, CNRS, INSERM, F-34094, Montpellier, France
| | - Christelle Reynes
- IGF, Université de Montpellier, CNRS, INSERM, F-34094, Montpellier, France
| | - Robert Sabatier
- IGF, Université de Montpellier, CNRS, INSERM, F-34094, Montpellier, France
| | - Tristan Bouschet
- IGF, Université de Montpellier, CNRS, INSERM, F-34094, Montpellier, France
| | - Zhou Yi
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, F-75252, Paris, France
| | - Sephora Sallis
- IGMM, Université de Montpellier, CNRS, F-34293, Montpellier, France
| | | | | | - Guy Cathala
- IGMM, Université de Montpellier, CNRS, F-34293, Montpellier, France
| | - Annick Lesne
- IGMM, Université de Montpellier, CNRS, F-34293, Montpellier, France.,Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, F-75252, Paris, France
| | - Julien Mozziconacci
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, F-75252, Paris, France
| | - Laurent Journot
- MGX, Université de Montpellier, CNRS, INSERM, F-34094, Montpellier, France.,IGF, Université de Montpellier, CNRS, INSERM, F-34094, Montpellier, France
| | - Thierry Forné
- IGMM, Université de Montpellier, CNRS, F-34293, Montpellier, France
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10
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Maupetit-Mehouas S, Court F, Bourgne C, Guerci-Bresler A, Cony-Makhoul P, Johnson H, Etienne G, Rousselot P, Guyotat D, Janel A, Hermet E, Saugues S, Berger J, Arnaud P, Berger MG. DNA methylation profiling reveals a pathological signature that contributes to transcriptional defects of CD34 + CD15 - cells in early chronic-phase chronic myeloid leukemia. Mol Oncol 2018; 12:814-829. [PMID: 29575763 PMCID: PMC5983208 DOI: 10.1002/1878-0261.12191] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 02/07/2018] [Accepted: 03/07/2018] [Indexed: 12/15/2022] Open
Abstract
Despite the high efficiency of tyrosine kinase inhibitors (TKI), some patients with chronic myeloid leukemia (CML) will display residual disease that can become resistant to treatment, indicating intraclonal heterogeneity in chronic‐phase CML (CP‐CML). To determine the basis of this heterogeneity, we conducted the first exhaustive characterization of the DNA methylation pattern of sorted CP‐CML CD34+CD15− (immature) and CD34−CD15+ (mature) cells at diagnosis (prior to any treatment) and compared it to that of CD34+CD15− and CD34−CD15+ cells isolated from healthy donors (HD). In both cell types, we identified several hundreds of differentially methylated regions (DMRs) showing DNA methylation changes between CP‐CML and HD samples, with only a subset of them in common between CD34+CD15− and CD34−CD15+ cells. This suggested DNA methylation variability within the same CML clone. We also identified 70 genes that could be aberrantly repressed upon hypermethylation and 171 genes that could be aberrantly expressed upon hypomethylation of some of these DMRs in CP‐CML cells, among which 18 and 81, respectively, were in CP‐CML CD34+CD15− cells only. We then validated the DNA methylation and expression defects of selected candidate genes. Specifically, we identified GAS2, a candidate oncogene, as a new example of gene the hypomethylation of which is associated with robust overexpression in CP‐CML cells. Altogether, we demonstrated that DNA methylation abnormalities exist at early stages of CML and can affect the transcriptional landscape of malignant cells. These observations could lead to the development of combination treatments with epigenetic drugs and TKI for CP‐CML.
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Affiliation(s)
- Stéphanie Maupetit-Mehouas
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont-Ferrand, France.,Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Franck Court
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont-Ferrand, France
| | - Céline Bourgne
- Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,Equipe d'Accueil 7453 CHELTER, Université Clermont Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Agnès Guerci-Bresler
- Hématologie Clinique, CHRU Nancy, Hôpitaux de Brabois, Vandoeuvre-lès-Nancy, France
| | | | - Hyacinthe Johnson
- Institut d'Hématologie de Basse Normandie, CHU de Caen, Caen Cedex 9, France
| | - Gabriel Etienne
- Hématologie Clinique, Institut Bergonié, Bordeaux Cedex, France
| | - Philippe Rousselot
- Centre Hospitalier de Versailles, service d'Hématologie et d'Oncologie, Le Chesney, France
| | - Denis Guyotat
- Département d'Hématologie, Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France
| | - Alexandre Janel
- Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,Equipe d'Accueil 7453 CHELTER, Université Clermont Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Eric Hermet
- Hématologie Clinique Adulte, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Sandrine Saugues
- Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,CRB-Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Juliette Berger
- Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,Equipe d'Accueil 7453 CHELTER, Université Clermont Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,CRB-Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
| | - Philippe Arnaud
- GReD, Université Clermont Auvergne, CNRS, INSERM, Clermont-Ferrand, France
| | - Marc G Berger
- Hématologie Biologique, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,Equipe d'Accueil 7453 CHELTER, Université Clermont Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France.,CRB-Auvergne, CHU Clermont-Ferrand, Hôpital Estaing, Clermont-Ferrand Cedex 1, France
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11
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Court F, Arnaud P. An annotated list of bivalent chromatin regions in human ES cells: a new tool for cancer epigenetic research. Oncotarget 2018; 8:4110-4124. [PMID: 27926531 PMCID: PMC5354816 DOI: 10.18632/oncotarget.13746] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/23/2016] [Indexed: 12/12/2022] Open
Abstract
CpG islands (CGI) marked by bivalent chromatin in stem cells are believed to be more prone to aberrant DNA methylation in tumor cells. The robustness and genome-wide extent of this instructive program in different cancer types remain to be determined. To address this issue we developed a user-friendly approach to integrate the stem cell chromatin signature in customized DNA methylation analyses. We used publicly available ChIP-sequencing datasets of several human embryonic stem cell (hESC) lines to determine the extent of bivalent chromatin genome-wide. We then created annotated lists of high-confidence bivalent, H3K4me3-only and H3K27me3-only chromatin regions. The main features of bivalent regions included localization in CGI/promoters, depletion in retroelements and enrichment in specific histone modifications, including the poorly characterized H3K23me2 mark. Moreover, bivalent promoters could be classified in three clusters based on PRC2 and PolII complexes occupancy. Genes with bivalent promoters of the PRC2-defined cluster displayed the lowest expression upon differentiation. As proof-of-concept, we assessed the DNA methylation pattern of eight types of tumors and confirmed that aberrant cancer-associated DNA hypermethylation preferentially targets CGI characterized by bivalent chromatin in hESCs. We also found that such aberrant DNA hypermethylation affected particularly bivalent CGI/promoters associated with genes that tend to remain repressed upon differentiation. Strikingly, bivalent CGI were the most affected by aberrant DNA hypermethylation in both CpG Island Methylator Phenotype-positive (CIMP+) and CIMP-negative tumors, suggesting that, besides transcriptional silencing in the pre-tumorigenic cells, the bivalent chromatin signature in hESCs is a key determinant of the instructive program for aberrant DNA methylation.
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Affiliation(s)
- Franck Court
- CNRS-UMR 6293, Clermont-Ferrand, 63001, France.,INSERM-U1103, Clermont-Ferrand, 63001, France.,Université Clermont Auvergne, GReD Laboratory, Clermont-Ferrand, 63000, France
| | - Philippe Arnaud
- CNRS-UMR 6293, Clermont-Ferrand, 63001, France.,INSERM-U1103, Clermont-Ferrand, 63001, France.,Université Clermont Auvergne, GReD Laboratory, Clermont-Ferrand, 63000, France
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12
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Monk D, Morales J, den Dunnen JT, Russo S, Court F, Prawitt D, Eggermann T, Beygo J, Buiting K, Tümer Z. Recommendations for a nomenclature system for reporting methylation aberrations in imprinted domains. Epigenetics 2018; 13:117-121. [PMID: 27911167 DOI: 10.1080/15592294.2016.1264561] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The analysis of DNA methylation has become routine in the pipeline for diagnosis of imprinting disorders, with many publications reporting aberrant methylation associated with imprinted differentially methylated regions (DMRs). However, comparisons between these studies are routinely hampered by the lack of consistency in reporting sites of methylation evaluated. To avoid confusion surrounding nomenclature, special care is needed to communicate results accurately, especially between scientists and other health care professionals. Within the European Network for Human Congenital Imprinting Disorders we have discussed these issues and designed a nomenclature for naming imprinted DMRs as well as for reporting methylation values. We apply these recommendations for imprinted DMRs that are commonly assayed in clinical laboratories and show how they support standardized database submission. The recommendations are in line with existing recommendations, most importantly the Human Genome Variation Society nomenclature, and should facilitate accurate reporting and data exchange among laboratories and thereby help to avoid future confusion.
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Affiliation(s)
- David Monk
- a Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Bellvitge Biomedical Research Institute , Barcelona , Spain
| | - Joannella Morales
- b European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge , UK
| | - Johan T den Dunnen
- c Human Genetics and Clinical Genetics, Leiden University Medical Center , Leiden , the Netherlands
| | - Silvia Russo
- d Laboratory of Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano , Milan , Italy
| | - Franck Court
- e Reproduction and Developmental Genetics , Centre National de la Recherche Scientifique , Clermont-Ferrand , France
| | - Dirk Prawitt
- f Center for Pediatrics and Adolescent Medicine, Johannes Gutenberg University Medical Center, Obere Zahlbacher , Mainz , Germany
| | - Thomas Eggermann
- g Institute of Human Genetics, Technical University of Aachen , Aachen , Germany
| | - Jasmin Beygo
- h Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen , Germany
| | - Karin Buiting
- h Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen , Germany
| | - Zeynep Tümer
- i Applied Human Molecular Genetics, Kennedy Centre, Copenhagen University Hospital, Rigshospitalet , Glostrup , Denmark
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13
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Alsina Casanova M, Monteagudo-Sánchez A, Rodiguez Guerineau L, Court F, Gazquez Serrano I, Martorell L, Rovira Zurriaga C, Moore GE, Ishida M, Castañon M, Moliner Calderon E, Monk D, Moreno Hernando J. Maternal mutations of FOXF1 cause alveolar capillary dysplasia despite not being imprinted. Hum Mutat 2017; 38:615-620. [PMID: 28256047 DOI: 10.1002/humu.23213] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 10/21/2016] [Revised: 02/07/2017] [Accepted: 02/23/2017] [Indexed: 11/06/2022]
Abstract
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare cause of pulmonary hypertension in newborns. Maternally inherited point mutations in Forkhead Box F1 gene (FOXF1), deletions of the gene, or its long-range enhancers on the maternal allele are responsible for this neonatal lethal disorder. Here, we describe monozygotic twins and one full-term newborn with ACD and gastrointestinal malformations caused by de novo mutations of FOXF1 on the maternal-inherited alleles. Since this parental transmission is consistent with genomic imprinting, the parent-of-origin specific monoallelic expression of genes, we have undertaken a detailed analysis of both allelic expression and DNA methylation. FOXF1 and its neighboring gene FENDRR were both biallelically expressed in a wide range of fetal tissues, including lung and intestine. Furthermore, detailed methylation screening within the 16q24.1 regions failed to identify regions of allelic methylation, suggesting that disrupted imprinting is not responsible for ACDMPV.
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Affiliation(s)
- Miguel Alsina Casanova
- Department of Neonatology, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Ana Monteagudo-Sánchez
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Bellvitge Biomedical Research Institute, Hospital Duran & Reynals, Barcelona, Spain
| | | | - Franck Court
- Genetics, Reproduction and Development laboratories (GreD), CNRS, UMR6247, Clermont Université, INSERM U931, Clermont-Ferrand, France
| | - Isabel Gazquez Serrano
- Department of Neonatology, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Loreto Martorell
- Laboratory of Molecular Genètics, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Carlota Rovira Zurriaga
- Department of Pathology, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Gudrun E Moore
- Genetics and Genomic Medicine Programme, Institute of Child Health, University College London, London, UK
| | - Miho Ishida
- Genetics and Genomic Medicine Programme, Institute of Child Health, University College London, London, UK
| | - Montserrat Castañon
- Department of Surgery, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | | | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Bellvitge Biomedical Research Institute, Hospital Duran & Reynals, Barcelona, Spain
| | - Julio Moreno Hernando
- Department of Neonatology, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
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14
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Sanchez-Delgado M, Court F, Vidal E, Medrano J, Monteagudo-Sánchez A, Martin-Trujillo A, Tayama C, Iglesias-Platas I, Kondova I, Bontrop R, Poo-Llanillo ME, Marques-Bonet T, Nakabayashi K, Simón C, Monk D. Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting. PLoS Genet 2016; 12:e1006427. [PMID: 27835649 PMCID: PMC5106035 DOI: 10.1371/journal.pgen.1006427] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [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: 06/22/2016] [Accepted: 10/14/2016] [Indexed: 01/23/2023] Open
Abstract
Thousands of regions in gametes have opposing methylation profiles that are largely resolved during the post-fertilization epigenetic reprogramming. However some specific sequences associated with imprinted loci survive this demethylation process. Here we present the data describing the fate of germline-derived methylation in humans. With the exception of a few known paternally methylated germline differentially methylated regions (DMRs) associated with known imprinted domains, we demonstrate that sperm-derived methylation is reprogrammed by the blastocyst stage of development. In contrast a large number of oocyte-derived methylation differences survive to the blastocyst stage and uniquely persist as transiently methylated DMRs only in the placenta. Furthermore, we demonstrate that this phenomenon is exclusive to primates, since no placenta-specific maternal methylation was observed in mouse. Utilizing single cell RNA-seq datasets from human preimplantation embryos we show that following embryonic genome activation the maternally methylated transient DMRs can orchestrate imprinted expression. However despite showing widespread imprinted expression of genes in placenta, allele-specific transcriptional profiling revealed that not all placenta-specific DMRs coordinate imprinted expression and that this maternal methylation may be absent in a minority of samples, suggestive of polymorphic imprinted methylation. Differences in gamete DNA methylation is subject to genome-wide reprogramming during preimplantation development to establish an embryo with an epigenetic state compatible with totipotency. DNA sequences associated with imprinted differentially methylated regions (DMRs) are largely protected from this process, retaining their parent-of-origin epigenetic marks. By comparing the methylation profiles of human oocytes, sperm, blastocysts and various somatic tissues including placenta, we observe hundreds of CpG island sequences that maintain methylation on their maternal allele in blastocysts and placenta indicative of incomplete reprogramming. In some cases this maternal methylation influence transcription of nearby genes, revealing transient imprinting in embryos after genome-activation and in placenta. Strikingly, these placenta-specific DMRs are polymorphic between placenta samples with a minority of samples being robustly unmethylated on both alleles.
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Affiliation(s)
- Marta Sanchez-Delgado
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Franck Court
- Laboratoire GReD, CNRS, UMR6293, Clermont-Ferrand, France
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jose Medrano
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - Ana Monteagudo-Sánchez
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Alex Martin-Trujillo
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Isabel Iglesias-Platas
- Neonatal service, Hospital Sant Joan de Déu, BCNatal Hospital Sant Joan de Déu i Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Maria Eugenia Poo-Llanillo
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institute of Research and Advanced Studies, (ICREA), Passeig de Lluís Companys, Barcelona, Spain
- Centro Nacional de Analisis Genomico (CRG-CNAG), Barcelona, Spain
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Carlos Simón
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
- * E-mail:
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15
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Martín DH, Court F, Rello-Varona S, Sáinz-Jaspeado M, Buj R, Morán S, García-Monclús S, Huertas-Martínez J, Mora J, Peinado MA, Alonso J, de Álava E, Esteller M, Tirado OM. Epigenetic profiling identifies MIR10A-5 p as a putative tumor suppresor in Ewing sarcoma and rhabdomyosarcoma. Klin Padiatr 2016. [DOI: 10.1055/s-0036-1582504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Herrero-Martin D, Court F, Rello-Varona S, Sainz-Jaspeado M, Buj R, Moran S, Garcia-Monclus S, Huertas-Martinez J, Mora J, Peinado MA, Alonso J, Alava ED, Monk D, Esteller M, Tirado OM. Abstract A40: Epigenomic profiling identifies NCRNAs as novel tumor suppressors in developmental tumors. Cancer Res 2016. [DOI: 10.1158/1538-7445.nonrna15-a40] [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
Pediatric sarcomas represent a diverse group of rare bone and soft tissue malignancies. Although the molecular mechanisms that propel the development of these cancers are not well understood, identification of tumor-specific translocations in many sarcomas has provided significant insight into their tumorigenesis. Besides of acting as a direct modulator of transcription, fusion proteins appear to exert its oncogenic functions by epigenetic modifications on the transcriptome. Aberrant DNA methylations are thought to be closely related to the development of cancer. Therefore, the identification of specific DNA methylation markers would be helpful for understanding the pathogenetic mechanism as well as for developing new therapeutic strategies. By using the Illumina Infinium HumanMethylation450, we analyze the methylome of Ewing Sarcoma (ES) and Rhabdomyosarcoma (RMS) tumors and cell lines as developmental tumors in comparison to a significant number of normal tissues and cells as a reference. Our results uncover one miRNA with tumor suppressive activities in both tumor entities. Molecular mechanisms associated to these activities are further explored.
Citation Format: David Herrero-Martin, Franck Court, Santiago Rello-Varona, Miguel Sainz-Jaspeado, Raquel Buj, Sebastian Moran, Silvia Garcia-Monclus, Juan Huertas-Martinez, Jaume Mora, Miquel Angel Peinado, Javier Alonso, Enrique de Alava, Dave Monk, Manel Esteller, Oscar M. Tirado. Epigenomic profiling identifies NCRNAs as novel tumor suppressors in developmental tumors. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A40.
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Affiliation(s)
| | - Franck Court
- 2PEBC, IDIBELL, Hospitalet De Llobregat, State, Spain,
| | | | | | | | | | | | | | - Jaume Mora
- 4Hospital Sant Joan de Deu, Barcelona, Spain,
| | | | | | | | - Dave Monk
- 2PEBC, IDIBELL, Hospitalet De Llobregat, State, Spain,
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17
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Fogli A, Chautard E, Vaurs-Barrière C, Pereira B, Müller-Barthélémy M, Court F, Biau J, Pinto AA, Kémény JL, Khalil T, Karayan-Tapon L, Verrelle P, Costa BM, Arnaud P. The tumoral A genotype of the MGMT rs34180180 single-nucleotide polymorphism in aggressive gliomas is associated with shorter patients' survival. Carcinogenesis 2015; 37:169-176. [PMID: 26717998 DOI: 10.1093/carcin/bgv251] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/19/2015] [Indexed: 01/09/2023] Open
Abstract
Malignant gliomas are the most common primary brain tumors. Grade III and IV gliomas harboring wild-type IDH1/2 are the most aggressive. In addition to surgery and radiotherapy, concomitant and adjuvant chemotherapy with temozolomide (TMZ) significantly improves overall survival (OS). The methylation status of the O(6)-methylguanine-DNA methyltransferase (MGMT) promoter is predictive of TMZ response and a prognostic marker of cancer outcome. However, the promoter regions the methylation of which correlates best with survival in aggressive glioma and whether the promoter methylation status predictive value could be refined or improved by other MGMT-associated molecular markers are not precisely known. In a cohort of 87 malignant gliomas treated with radiotherapy and TMZ-based chemotherapy, we retrospectively determined the MGMT promoter methylation status, genotyped single nucleotide polymorphisms (SNPs) in the promoter region and quantified MGMT mRNA expression level. Each of these variables was correlated with each other and with the patients' OS. We found that methylation of the CpG sites within MGMT exon 1 best correlated with OS and MGMT expression levels, and confirmed MGMT methylation as a stronger independent prognostic factor compared to MGMT transcription levels. Our main finding is that the presence of only the A allele at the rs34180180 SNP in the tumor was significantly associated with shorter OS, independently of the MGMT methylation status. In conclusion, in the clinic, rs34180180 SNP genotyping could improve the prognostic value of the MGMT promoter methylation assay in patients with aggressive glioma treated with TMZ.
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Affiliation(s)
- Anne Fogli
- INSERM-U1103 and.,CNRS-UMR 6293, Clermont-Ferrand 63001, France.,GReD Laboratory, Clermont Auvergne University, Clermont-Ferrand 63000, France.,Biochemistry and Molecular Biology Department, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Emmanuel Chautard
- Clermont Auvergne University, EA 7283 CREaT, Clermont-Ferrand 63000, France.,Radiotherapy Department, Jean Perrin Center, Clermont-Ferrand 63011, France
| | - Catherine Vaurs-Barrière
- INSERM-U1103 and.,CNRS-UMR 6293, Clermont-Ferrand 63001, France.,GReD Laboratory, Clermont Auvergne University, Clermont-Ferrand 63000, France
| | - Bruno Pereira
- Biostatistics Department , DRCI, Clermont-Ferrand Hospital , Clermont-Ferrand 63003 , France
| | | | - Franck Court
- INSERM-U1103 and.,CNRS-UMR 6293, Clermont-Ferrand 63001, France.,GReD Laboratory, Clermont Auvergne University, Clermont-Ferrand 63000, France
| | - Julian Biau
- Clermont Auvergne University, EA 7283 CREaT, Clermont-Ferrand 63000, France.,Radiotherapy Department, Jean Perrin Center, Clermont-Ferrand 63011, France
| | - Afonso Almeida Pinto
- Department of Neurosurgery , Braga Hospital , Braga 4710-243 São Victor , Portugal
| | - Jean-Louis Kémény
- Department of Anatomopathology , Clermont-Ferrand Hospital , Clermont-Ferrand 63003 , France
| | - Toufic Khalil
- Department of Neurosurgery, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France.,Clermont Auvergne University, EA 7282 IGCNC, Clermont-Ferrand 63000, France
| | - Lucie Karayan-Tapon
- INSERM-U935, Poitiers 86021, France.,Poitiers University, Poitiers 86000, France.,Cancer Biology Laboratory, Poitiers Hospital, Poitiers 86021, France
| | - Pierre Verrelle
- Clermont Auvergne University, EA 7283 CREaT, Clermont-Ferrand 63000, France.,Radiotherapy Department, Jean Perrin Center, Clermont-Ferrand 63011, France.,INSERM U2021 CNRS UMR3347, Curie Institute, Orsay 91405, France
| | - Bruno Marques Costa
- School of Health Sciences, Life and Health Sciences Research Institute (ICVS), Braga 4710-057, Portugal and.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Braga 4710-057, Portugal
| | - Philippe Arnaud
- INSERM-U1103 and.,CNRS-UMR 6293, Clermont-Ferrand 63001, France.,GReD Laboratory, Clermont Auvergne University, Clermont-Ferrand 63000, France
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18
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Maupetit-Méhouas S, Montibus B, Nury D, Tayama C, Wassef M, Kota SK, Fogli A, Cerqueira Campos F, Hata K, Feil R, Margueron R, Nakabayashi K, Court F, Arnaud P. Imprinting control regions (ICRs) are marked by mono-allelic bivalent chromatin when transcriptionally inactive. Nucleic Acids Res 2015; 44:621-35. [PMID: 26400168 PMCID: PMC4737186 DOI: 10.1093/nar/gkv960] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [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: 05/21/2015] [Accepted: 09/12/2015] [Indexed: 01/10/2023] Open
Abstract
Parental allele-specific expression of imprinted genes is mediated by imprinting control regions (ICRs) that are constitutively marked by DNA methylation imprints on the maternal or paternal allele. Mono-allelic DNA methylation is strictly required for the process of imprinting and has to be faithfully maintained during the entire life-span. While the regulation of DNA methylation itself is well understood, the mechanisms whereby the opposite allele remains unmethylated are unclear. Here, we show that in the mouse, at maternally methylated ICRs, the paternal allele, which is constitutively associated with H3K4me2/3, is marked by default by H3K27me3 when these ICRs are transcriptionally inactive, leading to the formation of a bivalent chromatin signature. Our data suggest that at ICRs, chromatin bivalency has a protective role by ensuring that DNA on the paternal allele remains unmethylated and protected against spurious and unscheduled gene expression. Moreover, they provide the proof of concept that, beside pluripotent cells, chromatin bivalency is the default state of transcriptionally inactive CpG island promoters, regardless of the developmental stage, thereby contributing to protect cell identity.
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Affiliation(s)
- Stéphanie Maupetit-Méhouas
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Bertille Montibus
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - David Nury
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Michel Wassef
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Satya K Kota
- Institute of Molecular Genetics, CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Anne Fogli
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Fabiana Cerqueira Campos
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Robert Feil
- Institute of Molecular Genetics, CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Raphael Margueron
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Franck Court
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Philippe Arnaud
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
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Court F, Tayama C, Romanelli V, Martin-Trujillo A, Iglesias-Platas I, Okamura K, Sugahara N, Simón C, Moore H, Harness JV, Keirstead H, Sanchez-Mut JV, Kaneki E, Lapunzina P, Soejima H, Wake N, Esteller M, Ogata T, Hata K, Nakabayashi K, Monk D. Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment. Genome Res 2014; 24:554-69. [PMID: 24402520 PMCID: PMC3975056 DOI: 10.1101/gr.164913.113] [Citation(s) in RCA: 247] [Impact Index Per Article: 24.7] [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: 08/09/2013] [Accepted: 12/26/2013] [Indexed: 12/16/2022]
Abstract
Differential methylation between the two alleles of a gene has been observed in imprinted regions, where the methylation of one allele occurs on a parent-of-origin basis, the inactive X-chromosome in females, and at those loci whose methylation is driven by genetic variants. We have extensively characterized imprinted methylation in a substantial range of normal human tissues, reciprocal genome-wide uniparental disomies, and hydatidiform moles, using a combination of whole-genome bisulfite sequencing and high-density methylation microarrays. This approach allowed us to define methylation profiles at known imprinted domains at base-pair resolution, as well as to identify 21 novel loci harboring parent-of-origin methylation, 15 of which are restricted to the placenta. We observe that the extent of imprinted differentially methylated regions (DMRs) is extremely similar between tissues, with the exception of the placenta. This extra-embryonic tissue often adopts a different methylation profile compared to somatic tissues. Further, we profiled all imprinted DMRs in sperm and embryonic stem cells derived from parthenogenetically activated oocytes, individual blastomeres, and blastocysts, in order to identify primary DMRs and reveal the extent of reprogramming during preimplantation development. Intriguingly, we find that in contrast to ubiquitous imprints, the majority of placenta-specific imprinted DMRs are unmethylated in sperm and all human embryonic stem cells. Therefore, placental-specific imprinting provides evidence for an inheritable epigenetic state that is independent of DNA methylation and the existence of a novel imprinting mechanism at these loci.
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Affiliation(s)
- Franck Court
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Valeria Romanelli
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Alex Martin-Trujillo
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Isabel Iglesias-Platas
- Servicio de Neonatología, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, 08950 Barcelona, Spain
| | - Kohji Okamura
- Department of Systems Biomedicine, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Naoko Sugahara
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Carlos Simón
- Fundación IVI-Instituto Universitario IVI-Universidad de Valencia, INCLIVA, 46980 Paterna, Valencia, Spain
| | - Harry Moore
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Julie V. Harness
- Reeve-Irvine Research Centre, Sue and Bill Gross Stem Cell Research Center, Department of Anatomy and Neurobiology, School of Medicine, University of California at Irvine, Irvine, California 92697, USA
| | - Hans Keirstead
- Reeve-Irvine Research Centre, Sue and Bill Gross Stem Cell Research Center, Department of Anatomy and Neurobiology, School of Medicine, University of California at Irvine, Irvine, California 92697, USA
| | - Jose Vicente Sanchez-Mut
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Eisuke Kaneki
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kyushu University, Fukuoka 812-8582, Japan
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular, CIBERER, IDIPAZ-Hospital Universitario La Paz, Universidad Autónoma de Madrid, 28046 Madrid, Spain
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Norio Wake
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kyushu University, Fukuoka 812-8582, Japan
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
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Court F, Camprubi C, Garcia CV, Guillaumet-Adkins A, Sparago A, Seruggia D, Sandoval J, Esteller M, Martin-Trujillo A, Riccio A, Montoliu L, Monk D. The PEG13-DMR and brain-specific enhancers dictate imprinted expression within the 8q24 intellectual disability risk locus. Epigenetics Chromatin 2014; 7:5. [PMID: 24667089 PMCID: PMC3986935 DOI: 10.1186/1756-8935-7-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 03/05/2014] [Indexed: 12/16/2022] Open
Abstract
Background Genomic imprinting is the epigenetic marking of genes that results in parent-of-origin monoallelic expression. Most imprinted domains are associated with differentially DNA methylated regions (DMRs) that originate in the gametes, and are maintained in somatic tissues after fertilization. This allelic methylation profile is associated with a plethora of histone tail modifications that orchestrates higher order chromatin interactions. The mouse chromosome 15 imprinted cluster contains multiple brain-specific maternally expressed transcripts including Ago2, Chrac1, Trappc9 and Kcnk9 and a paternally expressed gene, Peg13. The promoter of Peg13 is methylated on the maternal allele and is the sole DMR within the locus. To determine the extent of imprinting within the human orthologous region on chromosome 8q24, a region associated with autosomal recessive intellectual disability, Birk-Barel mental retardation and dysmorphism syndrome, we have undertaken a systematic analysis of allelic expression and DNA methylation of genes mapping within an approximately 2 Mb region around TRAPPC9. Results Utilizing allele-specific RT-PCR, bisulphite sequencing, chromatin immunoprecipitation and chromosome conformation capture (3C) we show the reciprocal expression of the novel, paternally expressed, PEG13 non-coding RNA and maternally expressed KCNK9 genes in brain, and the biallelic expression of flanking transcripts in a range of tissues. We identify a tandem-repeat region overlapping the PEG13 transcript that is methylated on the maternal allele, which binds CTCF-cohesin in chromatin immunoprecipitation experiments and possesses enhancer-blocker activity. Using 3C, we identify mutually exclusive approximately 58 and 500 kb chromatin loops in adult frontal cortex between a novel brain-specific enhancer, marked by H3K4me1 and H3K27ac, with the KCNK9 and PEG13 promoters which we propose regulates brain-specific expression. Conclusions We have characterised the molecular mechanism responsible for reciprocal allelic expression of the PEG13 and KCNK9 transcripts. Therefore, our observations may have important implications for identifying the cause of intellectual disabilities associated with the 8q24 locus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08907, Spain.
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Romanelli V, Nakabayashi K, Vizoso M, Moran S, Iglesias-Platas I, Sugahara N, Simón C, Hata K, Esteller M, Court F, Monk D. Variable maternal methylation overlapping the nc886/vtRNA2-1 locus is locked between hypermethylated repeats and is frequently altered in cancer. Epigenetics 2014; 9:783-90. [PMID: 24589629 PMCID: PMC4063837 DOI: 10.4161/epi.28323] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Cancer is as much an epigenetic disease as a genetic one; however, the interplay between these two processes is unclear. Recently, it has been shown that a large proportion of DNA methylation variability can be explained by allele-specific methylation (ASM), either at classical imprinted loci or those regulated by underlying genetic variants. During a recent screen for imprinted differentially methylated regions, we identified the genomic interval overlapping the non-coding nc886 RNA (previously known as vtRNA2-1) as an atypical ASM that shows variable levels of methylation, predominantly on the maternal allele in many tissues. Here we show that the nc886 interval is the first example of a polymorphic imprinted DMR in humans. Further analysis of the region suggests that the interval subjected to ASM is approximately 2 kb in size and somatically acquired. An in depth analysis of this region in primary cancer samples with matching normal adjacent tissue from the Cancer Genome Atlas revealed that aberrant methylation in bladder, breast, colon and lung tumors occurred in approximately 27% of cases. Hypermethylation occurred more frequently than hypomethylation. Using additional normal-tumor paired samples we show that on rare occasions the aberrant methylation profile is due to loss-of-heterozygosity. This work therefore suggests that the nc886 locus is subject to variable allelic methylation that undergoes cancer-associated epigenetic changes in solid tumors.
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Affiliation(s)
- Valeria Romanelli
- Imprinting and Cancer Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology and Department of Molecular Endocrinology; National Research Institute for Child Health and Development; Tokyo, Japan
| | - Miguel Vizoso
- Cancer Epigenetics Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain
| | - Sebastián Moran
- Cancer Epigenetics Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain
| | - Isabel Iglesias-Platas
- Servicio de Neonatología; Hospital Sant Joan de Déu; Fundació Sant Joan de Déu; Barcelona, Spain
| | - Naoko Sugahara
- Department of Maternal-Fetal Biology and Department of Molecular Endocrinology; National Research Institute for Child Health and Development; Tokyo, Japan
| | - Carlos Simón
- Fundación IVI; Instituto Universitario IVI; Universidad de Valencia; INCLIVA; Valencia, Spain
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology and Department of Molecular Endocrinology; National Research Institute for Child Health and Development; Tokyo, Japan
| | - Manel Esteller
- Cancer Epigenetics Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain; Department of Physiological Sciences II; School of Medicine; University of Barcelona; Barcelona, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA); Barcelona, Spain
| | - Franck Court
- Imprinting and Cancer Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain
| | - David Monk
- Imprinting and Cancer Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain
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Liang J, Lacroix L, Gamot A, Cuddapah S, Queille S, Lhoumaud P, Lepetit P, Martin PGP, Vogelmann J, Court F, Hennion M, Micas G, Urbach S, Bouchez O, Nöllmann M, Zhao K, Emberly E, Cuvier O. Chromatin immunoprecipitation indirect peaks highlight long-range interactions of insulator proteins and Pol II pausing. Mol Cell 2014; 53:672-81. [PMID: 24486021 DOI: 10.1016/j.molcel.2013.12.029] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 08/21/2013] [Accepted: 12/27/2013] [Indexed: 11/15/2022]
Abstract
Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify "indirect peaks" of multiple IBPs that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common cofactors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions.
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Affiliation(s)
- Jun Liang
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France
| | - Laurent Lacroix
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France
| | - Adrien Gamot
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France
| | - Suresh Cuddapah
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health (NIH), Bethesda, MD 20824, USA
| | - Sophie Queille
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France
| | - Priscillia Lhoumaud
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France
| | - Pierre Lepetit
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France
| | - Pascal G P Martin
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France; INRA, UMR444- GeT-PlaGe, Genotoul, 31326 Toulouse, France
| | - Jutta Vogelmann
- Centre de Biochimie Structurale, CNRS, 34090 Montpellier, France
| | - Franck Court
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France
| | - Magali Hennion
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France
| | - Gaël Micas
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France
| | - Serge Urbach
- Platform Proteomic Fonctionnelle, IGF, CNRS, 34060 Montpellier, France
| | | | - Marcelo Nöllmann
- Centre de Biochimie Structurale, CNRS, 34090 Montpellier, France
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health (NIH), Bethesda, MD 20824, USA
| | - Eldon Emberly
- Physics Department, Simon Fraser University (SFU), Burnaby, BC V5A 1S6, Canada
| | - Olivier Cuvier
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France.
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23
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Guillaumet-Adkins A, Richter J, Odero MD, Sandoval J, Agirre X, Catala A, Esteller M, Prósper F, Calasanz MJ, Buño I, Kwon M, Court F, Siebert R, Monk D. Hypermethylation of the alternative AWT1 promoter in hematological malignancies is a highly specific marker for acute myeloid leukemias despite high expression levels. J Hematol Oncol 2014; 7:4. [PMID: 24405639 PMCID: PMC3900738 DOI: 10.1186/1756-8722-7-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/19/2013] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Wilms tumor 1 (WT1) is over-expressed in numerous cancers with respect to normal cells, and has either a tumor suppressor or oncogenic role depending on cellular context. This gene is associated with numerous alternatively spliced transcripts, which initiate from two different unique first exons within the WT1 and the alternative (A)WT1 promoter intervals. Within the hematological system, WT1 expression is restricted to CD34+/CD38- cells and is undetectable after differentiation. Detectable expression of this gene is an excellent marker for minimal residual disease in acute myeloid leukemia (AML), but the underlying epigenetic alterations are unknown. METHODS To determine the changes in the underlying epigenetic landscape responsible for this expression, we characterized expression, DNA methylation and histone modification profiles in 28 hematological cancer cell lines and confirmed the methylation signature in 356 cytogenetically well-characterized primary hematological malignancies. RESULTS Despite high expression of WT1 and AWT1 transcripts in AML-derived cell lines, we observe robust hypermethylation of the AWT1 promoter and an epigenetic switch from a permissive to repressive chromatin structure between normal cells and AML cell lines. Subsequent methylation analysis in our primary leukemia and lymphoma cohort revealed that the epigenetic signature identified in cell lines is specific to myeloid-lineage malignancies, irrespective of underlying mutational status or translocation. In addition to being a highly specific marker for AML diagnosis (positive predictive value 100%; sensitivity 86.1%; negative predictive value 89.4%), we show that AWT1 hypermethylation also discriminates patients that relapse from those achieving complete remission after hematopoietic stem cell transplantation, with similar efficiency to WT1 expression profiling. CONCLUSIONS We describe a methylation signature of the AWT1 promoter CpG island that is a promising marker for classifying myeloid-derived leukemias. In addition AWT1 hypermethylation is ideally suited to monitor the recurrence of disease during remission in patients undergoing allogeneic stem cell transfer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Av, Gran Via de L'Hospotalet 199-203, 08907 L'Hospitalet de Llobregat, Barcelona, Spain.
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24
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Camprubí C, Iglesias-Platas I, Martin-Trujillo A, Salvador-Alarcon C, Rodriguez MA, Barredo DR, Court F, Monk D. Stability of genomic imprinting and gestational-age dynamic methylation in complicated pregnancies conceived following assisted reproductive technologies. Biol Reprod 2013; 89:50. [PMID: 23884645 DOI: 10.1095/biolreprod.113.108456] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
For the past three decades, assisted reproductive technologies (ART) have revolutionized infertility treatments. The use of ART is thought to be safe. However, early investigations suggested that children born as a result of ART had higher risk of diseases with epigenetic etiologies, including imprinting disorders caused by a lack of maternal methylation at imprinting control elements. In addition, large epidemiology studies have highlighted an increased risk of obstetric complications, including severe intrauterine growth restriction (IUGR) in babies conceived using ART. It is plausible that the increased frequency of IUGR may be due to abnormal imprinting because these transcripts are key for normal fetal growth and development. To address this, we have collected a large cohort of placenta and cord blood samples from ART conceptions and compared the imprinting status with appropriate non-ART population. Using a custom DNA methylation array that simultaneously quantifies 25 imprinted differentially methylated regions, we observed similar epigenetic profiles between groups. A multiplex Sequenom iPLEX allelic expression assay revealed monoallelic expression for 11 imprinted transcripts in our placenta cohort. We also observe appropriate gestational age-dependent methylation dynamics at retrotransposable elements and promoters associated with growth genes in ART placental biopsies. This study confirms that children conceived by ART do not show variability in imprinted regulation and that loss-of-imprinting is not commonly associated with nonsyndromic IUGR or prematurity.
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Affiliation(s)
- Cristina Camprubí
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program, Bellvitge Institute for Biomedical Research, L'Hospitalet de Llobregat, Barcelona, Spain
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25
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Salem T, Gomard T, Court F, Moquet-Torcy G, Brockly F, Forné T, Piechaczyk M. Chromatin loop organization of the junb locus in mouse dendritic cells. Nucleic Acids Res 2013; 41:8908-25. [PMID: 23921639 PMCID: PMC3799436 DOI: 10.1093/nar/gkt669] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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] [Indexed: 12/22/2022] Open
Abstract
The junb gene behaves as an immediate early gene in bacterial lipopolysaccharide (LPS)-stimulated dendritic cells (DCs), where its transient transcriptional activation is necessary for the induction of inflammatory cytokines. junb is a short gene and its transcriptional activation by LPS depends on the binding of NF-κB to an enhancer located just downstream of its 3′ UTR. Here, we have addressed the mechanisms underlying the transcriptional hyper-reactivity of junb. Using transfection and pharmacological assays to complement chromatin immunoprecipitation analyses addressing the localization of histones, polymerase II, negative elongation factor (NELF)-, DRB sensitivity-inducing factor (DSIF)- and Positive Transcription Factor b complexes, we demonstrate that junb is a RNA Pol II-paused gene where Pol II is loaded in the transcription start site domain but poorly active. Moreover, High salt-Recovered Sequence, chromosome conformation capture (3C)- and gene transfer experiments show that (i) junb is organized in a nuclear chromatin loop bringing into close spatial proximity the upstream promoter region and the downstream enhancer and (ii) this configuration permits immediate Pol II release on the junb body on binding of LPS-activated NF-κB to the enhancer. Thus, our work unveils a novel topological framework underlying fast junb transcriptional response in DCs. Moreover, it also points to a novel layer of complexity in the modes of action of NF-κB.
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Affiliation(s)
- Tamara Salem
- Equipe labellisée par la Ligue Nationale contre le Cancer, Institut de Génétique Moléculaire de Montpellier UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier cedex 5, France and Université Montpellier 1, 5 Bd Henry IV, 34967 Montpellier cedex 2, France
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26
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Court F, Martin-Trujillo A, Romanelli V, Garin I, Iglesias-Platas I, Salafsky I, Guitart M, Perez de Nanclares G, Lapunzina P, Monk D. Genome-wide allelic methylation analysis reveals disease-specific susceptibility to multiple methylation defects in imprinting syndromes. Hum Mutat 2013; 34:595-602. [PMID: 23335487 DOI: 10.1002/humu.22276] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/07/2013] [Indexed: 12/12/2022]
Abstract
Genomic imprinting is the parent-of-origin-specific allelic transcriptional silencing observed in mammals, which is governed by DNA methylation established in the gametes and maintained throughout the development. The frequency and extent of epimutations associated with the nine reported imprinting syndromes varies because it is evident that aberrant preimplantation maintenance of imprinted differentially methylated regions (DMRs) may affect multiple loci. Using a custom Illumina GoldenGate array targeting 27 imprinted DMRs, we profiled allelic methylation in 65 imprinting defect patients. We identify multilocus hypomethylation in numerous Beckwith-Wiedemann syndrome, transient neonatal diabetes mellitus (TNDM), and pseudohypoparathyroidism 1B patients, and an individual with Silver-Russell syndrome. Our data reveal a broad range of epimutations exist in certain imprinting syndromes, with the exception of Prader-Willi syndrome and Angelman syndrome patients that are associated with solitary SNRPN-DMR defects. A mutation analysis identified a 1 bp deletion in the ZFP57 gene in a TNDM patient with methylation defects at multiple maternal DMRs. In addition, we observe missense variants in ZFP57, NLRP2, and NLRP7 that are not consistent with maternal effect and aberrant establishment or methylation maintenance, and are likely benign. This work illustrates that further extensive molecular characterization of these rare patients is required to fully understand the mechanism underlying the etiology of imprint establishment and maintenance.
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Affiliation(s)
- Franck Court
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
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27
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Borensztein M, Monnier P, Court F, Louault Y, Ripoche MA, Tiret L, Yao Z, Tapscott SJ, Forné T, Montarras D, Dandolo L. Myod and H19-Igf2 locus interactions are required for diaphragm formation in the mouse. Development 2013; 140:1231-9. [PMID: 23406902 DOI: 10.1242/dev.084665] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The myogenic regulatory factor Myod and insulin-like growth factor 2 (Igf2) have been shown to interact in vitro during myogenic differentiation. In order to understand how they interact in vivo, we produced double-mutant mice lacking both the Myod and Igf2 genes. Surprisingly, these mice display neonatal lethality due to severe diaphragm atrophy. Alteration of diaphragm muscle development occurs as early as 15.5 days post-coitum in the double-mutant embryos and leads to a defect in the terminal differentiation of muscle progenitor cells. A negative-feedback loop was detected between Myod and Igf2 in embryonic muscles. Igf2 belongs to the imprinted H19-Igf2 locus. Molecular analyses show binding of Myod on a mesodermal enhancer (CS9) of the H19 gene. Chromatin conformation capture experiments reveal direct interaction of CS9 with the H19 promoter, leading to increased H19 expression in the presence of Myod. In turn, the non-coding H19 RNA represses Igf2 expression in trans. In addition, Igf2 also negatively regulates Myod expression, possibly by reducing the expression of the Srf transcription factor, a known Myod activator. In conclusion, Igf2 and Myod are tightly co-regulated in skeletal muscles and act in parallel pathways in the diaphragm, where they affect the progression of myogenic differentiation. Igf2 is therefore an essential player in the formation of a functional diaphragm in the absence of Myod.
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Affiliation(s)
- Maud Borensztein
- Genetics and Development Department, Inserm U1016, CNRS UMR 8104, University of Paris Descartes, Institut Cochin, 75014 Paris, France
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28
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Iglesias-Platas I, Court F, Camprubi C, Sparago A, Guillaumet-Adkins A, Martin-Trujillo A, Riccio A, Moore GE, Monk D. Imprinting at the PLAGL1 domain is contained within a 70-kb CTCF/cohesin-mediated non-allelic chromatin loop. Nucleic Acids Res 2013; 41:2171-9. [PMID: 23295672 PMCID: PMC3575839 DOI: 10.1093/nar/gks1355] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [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: 09/18/2012] [Revised: 12/04/2012] [Accepted: 12/06/2012] [Indexed: 12/22/2022] Open
Abstract
Paternal duplications of chromosome 6q24, a region that contains the imprinted PLAGL1 and HYMAI transcripts, are associated with transient neonatal diabetes mellitus. A common feature of imprinted genes is that they tend to cluster together, presumably as a result of sharing common cis-acting regulatory elements. To determine the extent of this imprinted cluster in human and mouse, we have undertaken a systematic analysis of allelic expression and DNA methylation of the genes mapping within an ∼1.4-Mb region flanking PLAGL1/Plagl1. We confirm that all nine neighbouring genes are biallelically expressed in both species. In human we identify two novel paternally expressed PLAGL1 coding transcripts that originate from unique promoter regions. Chromatin immunoprecipitation for CTCF and the cohesin subunits RAD21 and SMC3 reveals evolutionarily conserved binding sites within unmethylated regions ∼5 kb downstream of the PLAGL1 differentially methylated region and within the PLAGL1 3' untranslated region (UTR). Higher-order chromatin looping occurs between these regions in both expressing and non-expressing tissues, forming a non-allelic chromatin loop around the PLAGL1/Plagl1 gene. In placenta and brain tissues, we identify an additional interaction between the PLAGL1 P3/P4 promoters and the unmethylated element downstream of the PLAGL1 differentially methylated region that we propose facilitates imprinted expression of these alternative isoforms.
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Affiliation(s)
- Isabel Iglesias-Platas
- Servicio de Neonatología, Hospital Sant Joan de Déu (HSJD), Fundació Sant Joan de Déu, 08950 Barcelona, Spain, Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain, Department of Environmental Science, Second University of Naples, 81100 Caserta, Italy, Institute of Genetics and Biophysics ‘Adriano. Buzzati-Traverso,’ CNR, 80131 Naples, Italy and Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, Institute of Child Health, University College London, London, WC1N 1EH UK
| | - Franck Court
- Servicio de Neonatología, Hospital Sant Joan de Déu (HSJD), Fundació Sant Joan de Déu, 08950 Barcelona, Spain, Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain, Department of Environmental Science, Second University of Naples, 81100 Caserta, Italy, Institute of Genetics and Biophysics ‘Adriano. Buzzati-Traverso,’ CNR, 80131 Naples, Italy and Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, Institute of Child Health, University College London, London, WC1N 1EH UK
| | - Cristina Camprubi
- Servicio de Neonatología, Hospital Sant Joan de Déu (HSJD), Fundació Sant Joan de Déu, 08950 Barcelona, Spain, Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain, Department of Environmental Science, Second University of Naples, 81100 Caserta, Italy, Institute of Genetics and Biophysics ‘Adriano. Buzzati-Traverso,’ CNR, 80131 Naples, Italy and Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, Institute of Child Health, University College London, London, WC1N 1EH UK
| | - Angela Sparago
- Servicio de Neonatología, Hospital Sant Joan de Déu (HSJD), Fundació Sant Joan de Déu, 08950 Barcelona, Spain, Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain, Department of Environmental Science, Second University of Naples, 81100 Caserta, Italy, Institute of Genetics and Biophysics ‘Adriano. Buzzati-Traverso,’ CNR, 80131 Naples, Italy and Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, Institute of Child Health, University College London, London, WC1N 1EH UK
| | - Amy Guillaumet-Adkins
- Servicio de Neonatología, Hospital Sant Joan de Déu (HSJD), Fundació Sant Joan de Déu, 08950 Barcelona, Spain, Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain, Department of Environmental Science, Second University of Naples, 81100 Caserta, Italy, Institute of Genetics and Biophysics ‘Adriano. Buzzati-Traverso,’ CNR, 80131 Naples, Italy and Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, Institute of Child Health, University College London, London, WC1N 1EH UK
| | - Alex Martin-Trujillo
- Servicio de Neonatología, Hospital Sant Joan de Déu (HSJD), Fundació Sant Joan de Déu, 08950 Barcelona, Spain, Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain, Department of Environmental Science, Second University of Naples, 81100 Caserta, Italy, Institute of Genetics and Biophysics ‘Adriano. Buzzati-Traverso,’ CNR, 80131 Naples, Italy and Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, Institute of Child Health, University College London, London, WC1N 1EH UK
| | - Andrea Riccio
- Servicio de Neonatología, Hospital Sant Joan de Déu (HSJD), Fundació Sant Joan de Déu, 08950 Barcelona, Spain, Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain, Department of Environmental Science, Second University of Naples, 81100 Caserta, Italy, Institute of Genetics and Biophysics ‘Adriano. Buzzati-Traverso,’ CNR, 80131 Naples, Italy and Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, Institute of Child Health, University College London, London, WC1N 1EH UK
| | - Gudrun E. Moore
- Servicio de Neonatología, Hospital Sant Joan de Déu (HSJD), Fundació Sant Joan de Déu, 08950 Barcelona, Spain, Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain, Department of Environmental Science, Second University of Naples, 81100 Caserta, Italy, Institute of Genetics and Biophysics ‘Adriano. Buzzati-Traverso,’ CNR, 80131 Naples, Italy and Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, Institute of Child Health, University College London, London, WC1N 1EH UK
| | - David Monk
- Servicio de Neonatología, Hospital Sant Joan de Déu (HSJD), Fundació Sant Joan de Déu, 08950 Barcelona, Spain, Imprinting and Cancer Group, Epigenetics and Cancer Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain, Department of Environmental Science, Second University of Naples, 81100 Caserta, Italy, Institute of Genetics and Biophysics ‘Adriano. Buzzati-Traverso,’ CNR, 80131 Naples, Italy and Fetal Growth and Development Group, Clinical and Molecular Genetics Unit, Institute of Child Health, University College London, London, WC1N 1EH UK
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29
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Iglesias-Platas I, Martin-Trujillo A, Cirillo D, Court F, Guillaumet-Adkins A, Camprubi C, Bourc’his D, Hata K, Feil R, Tartaglia G, Arnaud P, Monk D. Characterization of novel paternal ncRNAs at the Plagl1 locus, including Hymai, predicted to interact with regulators of active chromatin. PLoS One 2012; 7:e38907. [PMID: 22723905 PMCID: PMC3378578 DOI: 10.1371/journal.pone.0038907] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/14/2012] [Indexed: 11/19/2022] Open
Abstract
Genomic imprinting is a complex epigenetic mechanism of transcriptional control that utilizes DNA methylation and histone modifications to bring about parent-of-origin specific monoallelic expression in mammals. Genes subject to imprinting are often organised in clusters associated with large non-coding RNAs (ncRNAs), some of which have cis-regulatory functions. Here we have undertaken a detailed allelic expression analysis of an imprinted domain on mouse proximal chromosome 10 comprising the paternally expressed Plagl1 gene. We identified three novel Plagl1 transcripts, only one of which contains protein-coding exons. In addition, we characterised two unspliced ncRNAs, Hymai, the mouse orthologue of HYMAI, and Plagl1it (Plagl1 intronic transcript), a transcript located in intron 5 of Plagl1. Imprinted expression of these novel ncRNAs requires DNMT3L-mediated maternal DNA methylation, which is also indispensable for establishing the correct chromatin profile at the Plagl1 DMR. Significantly, the two ncRNAs are retained in the nucleus, consistent with a potential regulatory function at the imprinted domain. Analysis with catRAPID, a protein-ncRNA association prediction algorithm, suggests that Hymai and Plagl1it RNAs both have potentially high affinity for Trithorax chromatin regulators. The two ncRNAs could therefore help to protect the paternal allele from DNA methylation by attracting Trithorax proteins that mediate H3 lysine-4 methylation. Submitted GenBank nucleotides sequences: Plagl1it: JN595789 Hymai: JN595790
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Affiliation(s)
- Isabel Iglesias-Platas
- Servicio de Neonatología, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Barcelona, Spain
| | - Alex Martin-Trujillo
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program, Bellvitge Institute for Biomedical Research, L’Hospitalet de Llobregat, Catalonia, Spain
| | - Davide Cirillo
- Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Spain
| | - Franck Court
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program, Bellvitge Institute for Biomedical Research, L’Hospitalet de Llobregat, Catalonia, Spain
| | - Amy Guillaumet-Adkins
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program, Bellvitge Institute for Biomedical Research, L’Hospitalet de Llobregat, Catalonia, Spain
| | - Cristina Camprubi
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program, Bellvitge Institute for Biomedical Research, L’Hospitalet de Llobregat, Catalonia, Spain
| | - Deborah Bourc’his
- Institut National de la Santé et de la Recherche Médicale, Unité de Génétique et Biologie du Développement, Institut Curie, Paris, France
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology and Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Robert Feil
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique and University of Montpellier, Montpellier, France
| | - Gian Tartaglia
- Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Spain
| | - Philippe Arnaud
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique and University of Montpellier, Montpellier, France
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program, Bellvitge Institute for Biomedical Research, L’Hospitalet de Llobregat, Catalonia, Spain
- * E-mail:
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30
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Tran VG, Court F, Duputié A, Antoine E, Aptel N, Milligan L, Carbonell F, Lelay-Taha MN, Piette J, Weber M, Montarras D, Pinset C, Dandolo L, Forné T, Cathala G. H19 antisense RNA can up-regulate Igf2 transcription by activation of a novel promoter in mouse myoblasts. PLoS One 2012; 7:e37923. [PMID: 22662250 PMCID: PMC3360672 DOI: 10.1371/journal.pone.0037923] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 04/26/2012] [Indexed: 12/22/2022] Open
Abstract
It was recently shown that a long non-coding RNA (lncRNA), that we named the 91H RNA (i.e. antisense H19 transcript), is overexpressed in human breast tumours and contributes in trans to the expression of the Insulin-like Growth Factor 2 (IGF2) gene on the paternal chromosome. Our preliminary experiments suggested that an H19 antisense transcript having a similar function may also be conserved in the mouse. In the present work, we further characterise the mouse 91H RNA and, using a genetic complementation approach in H19 KO myoblast cells, we show that ectopic expression of the mouse 91H RNA can up-regulate Igf2 expression in trans despite almost complete unmethylation of the Imprinting-Control Region (ICR). We then demonstrate that this activation occurs at the transcriptional level by activation of a previously unknown Igf2 promoter which displays, in mouse tissues, a preferential mesodermic expression (Pm promoter). Finally, our experiments indicate that a large excess of the H19 transcript can counteract 91H-mediated Igf2 activation. Our work contributes, in conjunction with other recent findings, to open new horizons to our understanding of Igf2 gene regulation and functions of the 91H/H19 RNAs in normal and pathological conditions.
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Affiliation(s)
- Van Giang Tran
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
| | - Franck Court
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
| | - Anne Duputié
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
| | - Etienne Antoine
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
| | - Nathalie Aptel
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
| | - Laura Milligan
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
| | - Françoise Carbonell
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
| | - Marie-Noëlle Lelay-Taha
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
| | - Jacques Piette
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
| | - Michaël Weber
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
| | - Didier Montarras
- Molecular Genetics of Development Unit, Department of Development Biology, URA CNRS 2578, Institut Pasteur, Paris, France
| | | | - Luisa Dandolo
- Genetics and Development Department, INSERM U567, CNRS UMR 8104, University Paris Descartes, Institut Cochin, Paris, France
| | - Thierry Forné
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
- * E-mail: (TF); (GC)
| | - Guy Cathala
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS-Université Montpellier II, Montpellier, France
- * E-mail: (TF); (GC)
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Hippert C, Ibanes S, Serratrice N, Court F, Malecaze F, Kremer EJ, Kalatzis V. Corneal transduction by intra-stromal injection of AAV vectors in vivo in the mouse and ex vivo in human explants. PLoS One 2012; 7:e35318. [PMID: 22523585 PMCID: PMC3327666 DOI: 10.1371/journal.pone.0035318] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [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: 07/25/2011] [Accepted: 03/14/2012] [Indexed: 12/13/2022] Open
Abstract
The cornea is a transparent, avascular tissue that acts as the major refractive surface of the eye. Corneal transparency, assured by the inner stroma, is vital for this role. Disruption in stromal transparency can occur in some inherited or acquired diseases. As a consequence, light entering the eye is blocked or distorted, leading to decreased visual acuity. Possible treatment for restoring transparency could be via viral-based gene therapy. The stroma is particularly amenable to this strategy due to its immunoprivileged nature and low turnover rate. We assayed the potential of AAV vectors to transduce keratocytes following intra-stromal injection in vivo in the mouse cornea and ex vivo in human explants. In murine and human corneas, we transduced the entire stroma using a single injection, preferentially targeted keratocytes and achieved long-term gene transfer (up to 17 months in vivo in mice). Of the serotypes tested, AAV2/8 was the most promising for gene transfer in both mouse and man. Furthermore, transgene expression could be transiently increased following aggression to the cornea.
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Affiliation(s)
- Claire Hippert
- Institut de Génétique Moléculaire de Montpellier, CNRS, Montpellier, France
- Universités Montpellier I & II, Montpellier, France
| | - Sandy Ibanes
- Institut de Génétique Moléculaire de Montpellier, CNRS, Montpellier, France
- Universités Montpellier I & II, Montpellier, France
| | - Nicolas Serratrice
- Institut de Génétique Moléculaire de Montpellier, CNRS, Montpellier, France
- Universités Montpellier I & II, Montpellier, France
| | - Franck Court
- Institut de Génétique Moléculaire de Montpellier, CNRS, Montpellier, France
- Universités Montpellier I & II, Montpellier, France
| | - François Malecaze
- Inserm U563, Toulouse, France
- Département d'Ophtalmologie, Hôpital Purpan, Toulouse, France
| | - Eric J. Kremer
- Institut de Génétique Moléculaire de Montpellier, CNRS, Montpellier, France
- Universités Montpellier I & II, Montpellier, France
| | - Vasiliki Kalatzis
- Institut de Génétique Moléculaire de Montpellier, CNRS, Montpellier, France
- Universités Montpellier I & II, Montpellier, France
- * E-mail:
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Horsnell J, Kallaway C, Chan C, Bristol J, Court F, Stone N. 420 Real Time Assessment of Axillary Nodes Based On Molecular Differences Using Raman Spectroscopy. Eur J Cancer 2012. [DOI: 10.1016/s0959-8049(12)70486-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Court F, Miro J, Braem C, Lelay-Taha MN, Brisebarre A, Atger F, Gostan T, Weber M, Cathala G, Forné T. Modulated contact frequencies at gene-rich loci support a statistical helix model for mammalian chromatin organization. Genome Biol 2011; 12:R42. [PMID: 21569291 PMCID: PMC3219965 DOI: 10.1186/gb-2011-12-5-r42] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 05/10/2011] [Indexed: 11/24/2022] Open
Abstract
Background Despite its critical role for mammalian gene regulation, the basic structural landscape of chromatin in living cells remains largely unknown within chromosomal territories below the megabase scale. Results Here, using the 3C-qPCR method, we investigate contact frequencies at high resolution within interphase chromatin at several mouse loci. We find that, at several gene-rich loci, contact frequencies undergo a periodical modulation (every 90 to 100 kb) that affects chromatin dynamics over large genomic distances (a few hundred kilobases). Interestingly, this modulation appears to be conserved in human cells, and bioinformatic analyses of locus-specific, long-range cis-interactions suggest that it may underlie the dynamics of a significant number of gene-rich domains in mammals, thus contributing to genome evolution. Finally, using an original model derived from polymer physics, we show that this modulation can be understood as a fundamental helix shape that chromatin tends to adopt in gene-rich domains when no significant locus-specific interaction takes place. Conclusions Altogether, our work unveils a fundamental aspect of chromatin dynamics in mammals and contributes to a better understanding of genome organization within chromosomal territories.
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Affiliation(s)
- Franck Court
- Institut de Génétique Moléculaire de Montpellier (IGMM), UMR5535 CNRS, Universités Montpellier 1 et Montpellier 2, 1919, Route de Mende, 34293 Montpellier Cedex 5, France
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Horsnell J, Chan C, Bristol J, Court F, Stone N. Real Time Intraoperative Assessment of Axillary Lymph Nodes using Raman Spectroscopy. Eur J Surg Oncol 2011. [DOI: 10.1016/j.ejso.2011.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Court F, Baniol M, Hagege H, Petit JS, Lelay-Taha MN, Carbonell F, Weber M, Cathala G, Forne T. Long-range chromatin interactions at the mouse Igf2/H19 locus reveal a novel paternally expressed long non-coding RNA. Nucleic Acids Res 2011; 39:5893-906. [PMID: 21478171 PMCID: PMC3152352 DOI: 10.1093/nar/gkr209] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Parental genomic imprinting at the Igf2/H19 locus is controlled by a methylation-sensitive CTCF insulator that prevents the access of downstream enhancers to the Igf2 gene on the maternal chromosome. However, on the paternal chromosome, it remains unclear whether long-range interactions with the enhancers are restricted to the Igf2 promoters or whether they encompass the entire gene body. Here, using the quantitative chromosome conformation capture assay, we show that, in the mouse liver, the endodermal enhancers have low contact frequencies with the Igf2 promoters but display, on the paternal chromosome, strong interactions with the intragenic differentially methylated regions 1 and 2. Interestingly, we found that enhancers also interact with a so-far poorly characterized intergenic region of the locus that produces a novel imprinted long non-coding transcript that we named the paternally expressed Igf2/H19 intergenic transcript (PIHit) RNA. PIHit is expressed exclusively from the paternal chromosome, contains a novel discrete differentially methylated region in a highly conserved sequence and, surprisingly, does not require an intact ICR/H19 gene region for its imprinting. Altogether, our data reveal a novel imprinted domain in the Igf2/H19 locus and lead us to propose a model for chromatin folding of this locus on the paternal chromosome.
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Affiliation(s)
- Franck Court
- Institut de Génétique Moléculaire de Montpellier, UMR5535 CNRS Universités Montpellier I et Montpellier II, 1919 Route de Mende, 34293 Montpellier cedex 5, France
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Al-Allak A, Knight H, Walter C, Court F, Chan HY. Abstract P1-10-08: Breast Reconstruction Surgery Following Mastectomy: Love or Money? Cancer Res 2010. [DOI: 10.1158/0008-5472.sabcs10-p1-10-08] [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
Introduction
All women should be considered for breast reconstruction following mastectomy, providing they are medically fit. The proportion of women having a reconstruction varies significantly from centre to centre; a key reason for this is the availability of reconstruction in that centre. In countries with an insurance funded health care system, breast reconstruction may also be influenced by the ability to pay. In the UK, breast reconstruction is available for free on the National Health Service (NHS). The aim of our study was to identify any other factors that may influence a woman's decision to have a reconstruction. Methods
All women having a mastectomy under the care of one breast surgeon between 2000 and 2010 were included. Data were collected retrospectively and included: age at surgery, marital status, dependents under 18, employment status, home circumstances and Zip code. The Index of Multiple deprivation (IMD2007) was derived for each patient from their zip code using the UK National Statistics data. The patients were divided into two main groups: those who underwent reconstruction and those who opted for mastectomy only. The Mann-Whitney U test was used to determine whether there was a statistical difference between the two patient groups using the statistical package R.
Results
A total of 272 patients underwent mastectomy during the study period, of these patients 148 had mastectomy only (median age 67, range 34 — 95) and 124 had a reconstruction (median age 51, range 28-73). When the two groups were compared statistical analysis revealed that the reconstruction group were younger (P<0.002), more likely to be married or have a partner (p=0.00065), have dependents (P<0.0005) and work (P<0.0005). There was no significant difference between the two groups socioeconomic status.
Conclusion
These data suggest that social and economical inequalities do not affect the decision making process for breast cancer patients in a society where health care is free at the point of delivery. However young age and a stable family/partner do.
Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P1-10-08.
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Affiliation(s)
- A Al-Allak
- Cheltenham General Hospital, Cheltenham, United Kingdom
| | - H Knight
- Cheltenham General Hospital, Cheltenham, United Kingdom
| | - C Walter
- Cheltenham General Hospital, Cheltenham, United Kingdom
| | - F Court
- Cheltenham General Hospital, Cheltenham, United Kingdom
| | - HY. Chan
- Cheltenham General Hospital, Cheltenham, United Kingdom
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Court F, Keeton S, Heary S, Grant B, Blyth K, Kernohan M, O'Donoghue J. Breast Specialist Nurses – Expensive Hand Holding or Cost-Effective Counselling? Cancer Res 2009. [DOI: 10.1158/0008-5472.sabcs-09-1075] [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
IntroductionCounselling breast cancer patients for reconstruction is complex and time consuming. Post-reconstruction satisfaction has been shown to be related to the quality of information provided to patients. Decisions regarding the type of breast reconstruction suitable for each patient is multi-factorial, including the autologous tissue available, general health, patient lifestyle and suitability, as well as patient preference. In our institution we offer a full range of reconstruction techniques. Initial pre-operative counselling is performed by a breast reconstruction specialist nurse at a consultation lasting at least 1 hour. During this time, all reconstructive options are discussed.Implications of surgery, photographs of post-operative results and the details of the procedures are explained and written information is provided. The option to meet a patient advocate at a later date is offered. An indication of the suitable reconstructive options available to the individual is given, however the surgeon, at a separate consultation lasting 10 minutes, performs the formal assessment of reconstructive type.MethodA comparison was made of patient satisfaction with pre-operative counselling and information giving, between those patients who were counselled by the operative surgeon alone and those counselled by the Breast Reconstruction Specialist nurse. A questionnaire to assess patient satisfaction with the reconstruction counselling was designed in conjunction with the Clinical Psychology team. This questionnaire was posted retrospectively to all patients who had undergone reconstruction counselling irrespective of whether they had subsequently undergone breast reconstruction. Patients were asked to respond to questions on a 5 point Likert scale. Patients were divided into 2 groups dependent on the person performing the counselling, ie. surgeon or nurse. All questionnaires were anonymous.ResultsQuestionnaires were allocated a random number and the data were analyzed independently by 2 separate clinical psychologists, blinded to which group the patients belonged to. Group 1 was counselled by the operative surgeon alone and Group 2 by the Breast Reconstruction Nurse. There was a very high response rate in both groups (70% in Group 1 and 71% in Group 2). Qualitative and quantitative data were analyzed separately. There was a high satisfaction rating in both groups with responses to all questions having a mean rating of above 4 out of 5. Patient satisfaction between the 2 groups was compared using the Mann-Whitney U test. There was no significant reported difference between how useful each of the groups found the contact.ConclusionEmploying a Specialist Nurse to perform the time-consuming pre-operative counselling for breast reconstruction is a cost effective measure, allowing Surgeons time to assess more patients or perform more appropriate skilled tasks instead. Patient satisfaction with the counselling service and information-giving was equal in both groups suggesting that nurse-led counselling, even for complex surgical procedures, is acceptable to patients. Having someone, other than the operative surgeon, give an independent and unbiased perspective on reconstructive options may be important in patient decision making.
Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1075.
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Affiliation(s)
- F. Court
- 1Royal Victoria Infirmary, United Kingdom
| | - S. Keeton
- 1Royal Victoria Infirmary, United Kingdom
| | - S. Heary
- 2Royal Victoria Infirmary, United Kingdom
| | - B. Grant
- 2Royal Victoria Infirmary, United Kingdom
| | - K. Blyth
- 2Royal Victoria Infirmary, United Kingdom
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Braem C, Recolin B, Rancourt RC, Angiolini C, Barthès P, Branchu P, Court F, Cathala G, Ferguson-Smith AC, Forné T. Genomic Matrix Attachment Region and Chromosome Conformation Capture Quantitative Real Time PCR Assays Identify Novel Putative Regulatory Elements at the Imprinted Dlk1/Gtl2 Locus. J Biol Chem 2008; 283:18612-20. [DOI: 10.1074/jbc.m801883200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Abstract
Insulators play important roles in controlling gene activity and maintaining regulatory independence between neighbouring genes. In this article, we show that the enhancer-blocking activity of the insulator present within the LTR retrotransposon Idefix can be abolished if two copies of the region containing the insulator—specifically, the long terminal repeat (LTR)—are fused to the retrotransposon's 5′ untranslated region (5′ UTR). The presence of this combination of two [LTR-5′ UTR] modules is a prerequisite for the loss of enhancer-blocking activity. We further show that the 5′ UTR causes flanking genomic sequences to be displaced to the nuclear periphery, which is not observed when two insulators are present by themselves. This study thus provides a functional link between insulators and independent genomic modules, which may cooperate to allow the specific regulation of defined genomic loci via nuclear repositioning. It further illustrates the complexity of genomic regulation within a chromatic environment with multiple functional elements.
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Affiliation(s)
- E. Brasset
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
| | - F. Bantignies
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
| | - F. Court
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
| | - S. Cheresiz
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
| | - C. Conte
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
| | - C. Vaury
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
- *To whom correspondence should be addressed 33 4 73 17 81 7133 4 73 27 61 32
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Ritzenthaler S, Court F, Girard-Reydet E, Leibler L, Pascault JP. ABC Triblock Copolymers/Epoxy−Diamine Blends. 2. Parameters Controlling the Morphologies and Properties. Macromolecules 2002. [DOI: 10.1021/ma0211075] [Citation(s) in RCA: 219] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. Ritzenthaler
- Laboratoire des Matériaux Macromoléculaires UMR CNRS 5627, Institut National des Sciences AppliquéesBât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; Centre d'Etude de Recherche et Développement ATOFINA, 27470 Serquigny, France; and Laboratoire Matière Molle et Chimie, UMR ESPCI-CNRS-ATOFINA, 10 rue Vauquelin, 75231 Paris Cedex 05, France
| | - F. Court
- Laboratoire des Matériaux Macromoléculaires UMR CNRS 5627, Institut National des Sciences AppliquéesBât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; Centre d'Etude de Recherche et Développement ATOFINA, 27470 Serquigny, France; and Laboratoire Matière Molle et Chimie, UMR ESPCI-CNRS-ATOFINA, 10 rue Vauquelin, 75231 Paris Cedex 05, France
| | - E. Girard-Reydet
- Laboratoire des Matériaux Macromoléculaires UMR CNRS 5627, Institut National des Sciences AppliquéesBât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; Centre d'Etude de Recherche et Développement ATOFINA, 27470 Serquigny, France; and Laboratoire Matière Molle et Chimie, UMR ESPCI-CNRS-ATOFINA, 10 rue Vauquelin, 75231 Paris Cedex 05, France
| | - L. Leibler
- Laboratoire des Matériaux Macromoléculaires UMR CNRS 5627, Institut National des Sciences AppliquéesBât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; Centre d'Etude de Recherche et Développement ATOFINA, 27470 Serquigny, France; and Laboratoire Matière Molle et Chimie, UMR ESPCI-CNRS-ATOFINA, 10 rue Vauquelin, 75231 Paris Cedex 05, France
| | - J. P. Pascault
- Laboratoire des Matériaux Macromoléculaires UMR CNRS 5627, Institut National des Sciences AppliquéesBât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; Centre d'Etude de Recherche et Développement ATOFINA, 27470 Serquigny, France; and Laboratoire Matière Molle et Chimie, UMR ESPCI-CNRS-ATOFINA, 10 rue Vauquelin, 75231 Paris Cedex 05, France
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Ritzenthaler S, Court F, David L, Girard-Reydet E, Leibler L, Pascault JP. ABC Triblock Copolymers/Epoxy−Diamine Blends. 1. Keys To Achieve Nanostructured Thermosets. Macromolecules 2002. [DOI: 10.1021/ma0121868] [Citation(s) in RCA: 228] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. Ritzenthaler
- Laboratoire des Matériaux Macromoléculaires UMR CNRS 5627, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; Centre d'Etude de Recherche et Développement ATOFINA, 27470 Serquigny, France; GEMPPM, UMR−CNRS 5510, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; and Laboratoire Matière Molle et Chimie, UMR ESPCI−CNRS-ATOFINA, 10 rue Vauquelin, 75231 Paris Cedex 05,
| | - F. Court
- Laboratoire des Matériaux Macromoléculaires UMR CNRS 5627, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; Centre d'Etude de Recherche et Développement ATOFINA, 27470 Serquigny, France; GEMPPM, UMR−CNRS 5510, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; and Laboratoire Matière Molle et Chimie, UMR ESPCI−CNRS-ATOFINA, 10 rue Vauquelin, 75231 Paris Cedex 05,
| | - L. David
- Laboratoire des Matériaux Macromoléculaires UMR CNRS 5627, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; Centre d'Etude de Recherche et Développement ATOFINA, 27470 Serquigny, France; GEMPPM, UMR−CNRS 5510, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; and Laboratoire Matière Molle et Chimie, UMR ESPCI−CNRS-ATOFINA, 10 rue Vauquelin, 75231 Paris Cedex 05,
| | - E. Girard-Reydet
- Laboratoire des Matériaux Macromoléculaires UMR CNRS 5627, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; Centre d'Etude de Recherche et Développement ATOFINA, 27470 Serquigny, France; GEMPPM, UMR−CNRS 5510, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; and Laboratoire Matière Molle et Chimie, UMR ESPCI−CNRS-ATOFINA, 10 rue Vauquelin, 75231 Paris Cedex 05,
| | - L. Leibler
- Laboratoire des Matériaux Macromoléculaires UMR CNRS 5627, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; Centre d'Etude de Recherche et Développement ATOFINA, 27470 Serquigny, France; GEMPPM, UMR−CNRS 5510, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; and Laboratoire Matière Molle et Chimie, UMR ESPCI−CNRS-ATOFINA, 10 rue Vauquelin, 75231 Paris Cedex 05,
| | - J. P. Pascault
- Laboratoire des Matériaux Macromoléculaires UMR CNRS 5627, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; Centre d'Etude de Recherche et Développement ATOFINA, 27470 Serquigny, France; GEMPPM, UMR−CNRS 5510, Institut National des Sciences Appliquées, Bât. Jules Verne, 20 Avenue Albert Einstein, 69621 Villeurbanne Cedex, France; and Laboratoire Matière Molle et Chimie, UMR ESPCI−CNRS-ATOFINA, 10 rue Vauquelin, 75231 Paris Cedex 05,
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Mack TG, Reiner M, Beirowski B, Mi W, Emanuelli M, Wagner D, Thomson D, Gillingwater T, Court F, Conforti L, Fernando FS, Tarlton A, Andressen C, Addicks K, Magni G, Ribchester RR, Perry VH, Coleman MP. Wallerian degeneration of injured axons and synapses is delayed by a Ube4b/Nmnat chimeric gene. Nat Neurosci 2001; 4:1199-206. [PMID: 11770485 DOI: 10.1038/nn770] [Citation(s) in RCA: 469] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Axons and their synapses distal to an injury undergo rapid Wallerian degeneration, but axons in the C57BL/WldS mouse are protected. The degenerative and protective mechanisms are unknown. We identified the protective gene, which encodes an N-terminal fragment of ubiquitination factor E4B (Ube4b) fused to nicotinamide mononucleotide adenylyltransferase (Nmnat), and showed that it confers a dose-dependent block of Wallerian degeneration. Transected distal axons survived for two weeks, and neuromuscular junctions were also protected. Surprisingly, the Wld protein was located predominantly in the nucleus, indicating an indirect protective mechanism. Nmnat enzyme activity, but not NAD+ content, was increased fourfold in WldS tissues. Thus, axon protection is likely to be mediated by altered ubiquitination or pyridine nucleotide metabolism.
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Affiliation(s)
- T G Mack
- Center for Molecular Medicine (ZMMK) and Institute for Genetics, University of Cologne, Zuelpicher Strasse 47, D-50674 Cologne, Germany
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Abstract
Injured nerves of Wld(s) mice neither degenerate nor regenerate for several weeks. We have conjectured that Wld(s) axons have the ability to regenerate but its expression is impaired by the Schwann cells of the undegenerated distal stump. To test this conjecture, transcription was locally arrested with actinomycin D (ActD), nerves were crushed, and regrowth was evaluated. In normal CD1 nerves injected with ActD 3 days before the crush, the rate of elongation was not affected but the delay of regrowth was shortened. In sharp contrast, ActD normalized the elongation of Wld(s) axons. When Wld(s) nerves were crushed past the treated segment, axons did not regenerate. After 7, but not 4, days of treatment, intact CD1 and Wld(s) axons presented a local sprouting response. We conclude that Wld(s) axons can regenerate in a normal way but do not do so because the undegenerated Schwann cells of the distal stump repress the regrowth program. We present a model axon that includes a destruction program and a post-transcriptional trophic regulation of its phenotype.
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Affiliation(s)
- F Court
- Unidad de Neurobiología Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
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Abstract
Calliphora vicina larvae were fed on drug-laden muscle from three suicides involving amitriptyline, temazepam and a combination of trazodone and trimipramine; triplicate daily harvestings were analysed. The limit of detection for all four drugs was 0.01 micrograms drug/g larvae. Mean drug concentrations (microgram/g) in the initial muscle were:amitriptyline, 2.68; temazepam, 4.04; trazodone, 21.56; and trimipramine, 19.58. Larval rearings for days 4-8 (15 larval samples per drug) had mean and ranges of drug concentrations (microgram/g) of 0.10 (r, 0.02-0.24) for amitriptyline; 0.52 (r, 0.26-0.78) for temazepam; 0.13 (r, 0.05-0.32) for trazodone; and 0.28 (r, 0.10-0.59) for trimipramine. After day 8 there was a precipitous fall in larval drug concentrations associated with pupariation. At day 11 ranges of drug concentrations (microgram/g) were: amitriptyline, < 0.01-0.01; temazepam, 0.01-0.08; trazodone, < 0.01-0.01; and trimipramine, 0.04-0.04. Day 16 pupae had corresponding ranges (microgram/g) of < 0.01, 0.01-0.01, < 0.01 and < 0.01-0.02. Transfer to drug-free food at day 5 led to similar falls in drug concentrations (microgram/g) from day 5 to day 6: 0.08-0.03 for amitriptyline, 0.61-0.09 for temazepam, 0.13-0.01 for trazodone, and 0.30-0.02 for trimipramine. The results show considerable variation in larval drug concentrations, both at the same developmental stage and at different stages of the life cycle, under conditions which closely reflect case situations. In practice, the precipitous decrease in drug concentrations in non-feeding larvae and at pupariation make it desirable to sample only larvae actively feeding on a corpse.
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Affiliation(s)
- D W Sadler
- Department of Forensic Medicine, University of Dundee, Royal Infirmary, Scotland, UK
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Martínez L, Troncoso P, Court F, Dougnac A, Rodríguez L. The arteriovenous oxygen gradient as an index of renal blood flow: a study in dog kidneys and renal transplant patients. Transplant Proc 1992; 24:3076-7. [PMID: 1466062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- L Martínez
- Department of Nephro-Urology, Pontificia Universidad Católica de Chile, School of Medicine, Santiago
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Court F, Guzmán S, Rahmer A. [Pseudo-obstruction of the colon]. Rev Med Chil 1986; 114:1067-9. [PMID: 3602683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Haut J, Pinon-Pignero F, Quentel G, Court F. [Unusual aspect of vitreous posterior detachment]. Bull Soc Ophtalmol Fr 1985; 85:953, 956-7. [PMID: 3836795] [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: 01/07/2023]
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