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Kumar A, Kasikci Y, Badredine A, Azzag K, Quintyn Ranty ML, Zaidi F, Aragou N, Mazerolles C, Malavaud B, Mendoza-Parra MA, Vandel L, Gronemeyer H. Patient-matched analysis identifies deregulated networks in prostate cancer to guide personalized therapeutic intervention. Am J Cancer Res 2021; 11:5299-5318. [PMID: 34873462 PMCID: PMC8640800] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023] Open
Abstract
Prostate cancer (PrCa) is the second most common malignancy in men. More than 50% of advanced prostate cancers display the TMPRSS2-ERG fusion. Despite extensive cancer genome/transcriptome data, little is known about the impact of mutations and altered transcription on regulatory networks in the PrCa of individual patients. Using patient-matched normal and tumor samples, we established somatic variations and differential transcriptome profiles of primary ERG-positive prostate cancers. Integration of protein-protein interaction and gene-regulatory network databases defined highly diverse patient-specific network alterations. Different components of a given regulatory pathway were altered by novel and known mutations and/or aberrant gene expression, including deregulated ERG targets, and were validated by using a novel in silico methodology. Consequently, different sets of pathways were altered in each individual PrCa. In a given PrCa, several deregulated pathways share common factors, predicting synergistic effects on cancer progression. Our integrated analysis provides a paradigm to identify druggable key deregulated factors within regulatory networks to guide personalized therapies.
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Affiliation(s)
- Akinchan Kumar
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics and CancerIllkirch, France
- Centre National de la Recherche Scientifique, UMR7104Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258Illkirch, France
- Université de StrasbourgIllkirch, France
- Equipe Labellisée Ligue Contre le Cancer
| | - Yasenya Kasikci
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics and CancerIllkirch, France
- Centre National de la Recherche Scientifique, UMR7104Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258Illkirch, France
- Université de StrasbourgIllkirch, France
- Equipe Labellisée Ligue Contre le Cancer
| | - Alaa Badredine
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics and CancerIllkirch, France
- Centre National de la Recherche Scientifique, UMR7104Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258Illkirch, France
- Université de StrasbourgIllkirch, France
- Equipe Labellisée Ligue Contre le Cancer
- CNRS UMR8199-EGID Building, Lille University-Faculty of Medicine Henri-WarembourgLille, France
| | - Karim Azzag
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPSFrance
- Lillehei Heart Institute, Department of Medicine, University of MinnesotaMinneapolis, MN, USA
| | - Marie L Quintyn Ranty
- Institut Universitaire du Cancer Toulouse-Oncopole (IUCT-O)Toulouse, France
- Pathology Department, CHUCaen, France
| | - Falek Zaidi
- Institut Universitaire du Cancer Toulouse-Oncopole (IUCT-O)Toulouse, France
| | - Nathalie Aragou
- Institut Universitaire du Cancer Toulouse-Oncopole (IUCT-O)Toulouse, France
| | | | - Bernard Malavaud
- Institut Universitaire du Cancer Toulouse-Oncopole (IUCT-O)Toulouse, France
| | - Marco A Mendoza-Parra
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics and CancerIllkirch, France
- Centre National de la Recherche Scientifique, UMR7104Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258Illkirch, France
- Université de StrasbourgIllkirch, France
- Equipe Labellisée Ligue Contre le Cancer
- UMR 8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry-val-d’Essonne, University Paris-SaclayÉvry, France
| | - Laurence Vandel
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPSFrance
- Université Clermont Auvergne, CNRS, Inserm, GReDClermont-Ferrand, France
| | - Hinrich Gronemeyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Functional Genomics and CancerIllkirch, France
- Centre National de la Recherche Scientifique, UMR7104Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258Illkirch, France
- Université de StrasbourgIllkirch, France
- Equipe Labellisée Ligue Contre le Cancer
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Colin F, Schauer K, Hamiche A, Martineau P, Borg JP, Bednar J, Bertolin G, Camoin L, Collette Y, Dimitrov S, Fournier I, Hyenne V, Mendoza-Parra MA, Morelli X, Rondé P, Sumara I, Tramier M, Schultz P, Goetz JG. The NANOTUMOR consortium - Towards the Tumor Cell Atlas. Biol Cell 2021; 113:272-280. [PMID: 33554340 DOI: 10.1111/boc.202000135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/25/2021] [Indexed: 02/06/2023]
Abstract
Cancer is a multi-step disease where an initial tumour progresses through critical steps shaping, in most cases, life-threatening secondary foci called metastases. The oncogenic cascade involves genetic, epigenetic, signalling pathways, intracellular trafficking and/or metabolic alterations within cancer cells. In addition, pre-malignant and malignant cells orchestrate complex and dynamic interactions with non-malignant cells and acellular matricial components or secreted factors within the tumour microenvironment that is instrumental in the progression of the disease. As our aptitude to effectively treat cancer mostly depends on our ability to decipher, properly diagnose and impede cancer progression and metastasis formation, full characterisation of molecular complexes and cellular processes at play along the metastasis cascade is crucial. For many years, the scientific community lacked adapted imaging and molecular technologies to accurately dissect, at the highest resolution possible, tumour and stromal cells behaviour within their natural microenvironment. In that context, the NANOTUMOR consortium is a French national multi-disciplinary workforce which aims at a providing a multi-scale characterisation of the oncogenic cascade, from the atomic level to the dynamic organisation of the cell in response to genetic mutations, environmental changes or epigenetic modifications. Ultimately, this program aims at identifying new therapeutic targets using innovative drug design.
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Affiliation(s)
- Florent Colin
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), CNRS SNC5055, Strasbourg, France
| | - Kristine Schauer
- CNRS UMR144, Molecular Mechanisms of Intracellular Transport group, Institut Curie, 75005 Paris, France, PSL Research University, Paris, France, Sorbonne Université, Paris, France, Inserm U1279, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Ali Hamiche
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch, France
| | - Pierre Martineau
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Jean-Paul Borg
- Aix Marseille Univ, CNRS UMR7258, INSERM UMR1068, Institut Paoli Calmettes, CRCM, Marseille, 13009, France.,Institut Universitaire de France (IUF), Paris, France
| | - Jan Bednar
- Institute for Advanced Biosciences (IAB), Université Grenoble Alpes, CNRS UMR5309, INSERM U1209, La Tronche, France
| | - Giulia Bertolin
- CNRS, Univ Rennes, IGDR (Genetics and Development Institute of Rennes), UMR 6290, Rennes, F-35000, France
| | - Luc Camoin
- Aix Marseille Univ, CNRS UMR7258, INSERM UMR1068, Institut Paoli Calmettes, CRCM, Marseille, 13009, France
| | - Yves Collette
- Aix Marseille Univ, CNRS UMR7258, INSERM UMR1068, Institut Paoli Calmettes, CRCM, Marseille, 13009, France
| | - Stephan Dimitrov
- Institute for Advanced Biosciences (IAB), Université Grenoble Alpes, CNRS UMR5309, INSERM U1209, La Tronche, France
| | - Isabelle Fournier
- Institut Universitaire de France (IUF), Paris, France.,Univ. Lille, INSERM, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, F-59000, France
| | - Vincent Hyenne
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), CNRS SNC5055, Strasbourg, France
| | - Marco A Mendoza-Parra
- UMR8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry-val-d'Essonne, University Paris-Saclay, Evry, France
| | - Xavier Morelli
- Aix Marseille Univ, CNRS UMR7258, INSERM UMR1068, Institut Paoli Calmettes, CRCM, Marseille, 13009, France
| | - Philippe Rondé
- Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.,CNRS UMR7021, Laboratoire de Bioimagerie et Pathologies, Illkirch, France
| | - Izabela Sumara
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch, France
| | - Marc Tramier
- CNRS, Univ Rennes, IGDR (Genetics and Development Institute of Rennes), UMR 6290, Rennes, F-35000, France
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch, France
| | - Jacky G Goetz
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), CNRS SNC5055, Strasbourg, France
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Siouda M, Dujardin AD, Barbollat-Boutrand L, Mendoza-Parra MA, Gibert B, Ouzounova M, Bouaoud J, Tonon L, Robert M, Foy JP, Lavergne V, Manie SN, Viari A, Puisieux A, Ichim G, Gronemeyer H, Saintigny P, Mulligan P. CDYL2 Epigenetically Regulates MIR124 to Control NF-κB/STAT3-Dependent Breast Cancer Cell Plasticity. iScience 2020; 23:101141. [PMID: 32450513 PMCID: PMC7251929 DOI: 10.1016/j.isci.2020.101141] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 12/20/2019] [Revised: 03/31/2020] [Accepted: 05/04/2020] [Indexed: 12/19/2022] Open
Abstract
Epigenetic deregulation of gene transcription is central to cancer cell plasticity and malignant progression but remains poorly understood. We found that the uncharacterized epigenetic factor chromodomain on Y-like 2 (CDYL2) is commonly over-expressed in breast cancer, and that high CDYL2 levels correlate with poor prognosis. Supporting a functional role for CDYL2 in malignancy, it positively regulated breast cancer cell migration, invasion, stem-like phenotypes, and epithelial-to-mesenchymal transition. CDYL2 regulation of these plasticity-associated processes depended on signaling via p65/NF-κB and STAT3. This, in turn, was downstream of CDYL2 regulation of MIR124 gene transcription. CDYL2 co-immunoprecipitated with G9a/EHMT2 and GLP/EHMT1 and regulated the chromatin enrichment of G9a and EZH2 at MIR124 genes. We propose that CDYL2 contributes to poor prognosis in breast cancer by recruiting G9a and EZH2 to epigenetically repress MIR124 genes, thereby promoting NF-κB and STAT3 signaling, as well as downstream cancer cell plasticity and malignant progression. Up-regulation of CDYL2 is common in breast cancer and correlates with poor prognosis CDYL2 regulates enrichment of methyltransferases G9a and EZH2 at MIR124 genes microRNA-124 regulation by CDYL2 impacts STAT3 and NF-κB signaling CDYL2 regulation of EMT, migration, invasion, and stemness is STAT3/NF-κB dependent
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Affiliation(s)
- Maha Siouda
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | - Audrey D Dujardin
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | - Laetitia Barbollat-Boutrand
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | - Marco A Mendoza-Parra
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, University of Strasbourg, Illkirch, France
| | - Benjamin Gibert
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | - Maria Ouzounova
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France; Equipe Labellisée Ligue Contre le Cancer, LabEx DEVweCAN
| | - Jebrane Bouaoud
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France; Department of Maxillo-facial Surgery and Stomatology, Pitié-Salpétrière Hospital, Pierre et Marie Curie University Paris 6, Sorbonne Paris Cite University, AP-HP, Paris 75013, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Plateforme de Bioinformatique "Gilles Thomas", Centre Léon Bérard, 28 rue Lannec, Lyon 69008, France; INRIA Grenoble-Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot-Saint-Martin 38330, France
| | - Marie Robert
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France; Equipe Labellisée Ligue Contre le Cancer, LabEx DEVweCAN
| | - Jean-Philippe Foy
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France; Equipe Labellisée Ligue Contre le Cancer, LabEx DEVweCAN
| | - Vincent Lavergne
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France; Equipe Labellisée Ligue Contre le Cancer, LabEx DEVweCAN
| | - Serge N Manie
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | - Alain Viari
- Synergie Lyon Cancer, Plateforme de Bioinformatique "Gilles Thomas", Centre Léon Bérard, 28 rue Lannec, Lyon 69008, France; INRIA Grenoble-Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot-Saint-Martin 38330, France
| | - Alain Puisieux
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France; Equipe Labellisée Ligue Contre le Cancer, LabEx DEVweCAN
| | - Gabriel Ichim
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France
| | - Hinrich Gronemeyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, University of Strasbourg, Illkirch, France
| | - Pierre Saintigny
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France; Equipe Labellisée Ligue Contre le Cancer, LabEx DEVweCAN
| | - Peter Mulligan
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, France; Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, Epigenetics and Cancer Team, Cheney A, 5e étage, 28 rue Laennec, Lyon Cedex 08 69373, France.
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Mendoza-Parra MA, Sankar M, Walia M, Gronemeyer H. POLYPHEMUS: R package for comparative analysis of RNA polymerase II ChIP-seq profiles by non-linear normalization. Nucleic Acids Res 2011; 40:e30. [PMID: 22156059 PMCID: PMC3287170 DOI: 10.1093/nar/gkr1205] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [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] [Indexed: 11/23/2022] Open
Abstract
Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is increasingly used to map protein–chromatin interactions at global scale. The comparison of ChIP-seq profiles for RNA polymerase II (PolII) established in different biological contexts, such as specific developmental stages or specific time-points during cell differentiation, provides not only information about the presence/accumulation of PolII at transcription start sites (TSSs) but also about functional features of transcription, including PolII stalling, pausing and transcript elongation. However, annotation and normalization tools for comparative studies of multiple samples are currently missing. Here, we describe the R-package POLYPHEMUS, which integrates TSS annotation with PolII enrichment over TSSs and coding regions, and normalizes signal intensity profiles. Thereby POLYPHEMUS facilitates to extract information about global PolII action to reveal changes in the functional state of genes. We validated POLYPHEMUS using a kinetic study on retinoic acid-induced differentiation and a publicly available data set from a comparative PolII ChIP-seq profiling in Caenorhabditis elegans. We demonstrate that POLYPHEMUS corrects the data sets by normalizing for technical variation between samples and reveal the potential of the algorithm in comparing multiple data sets to infer features of transcription regulation from dynamic PolII binding profiles.
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Affiliation(s)
- Marco A Mendoza-Parra
- Department of Cancer Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404 Illkirch Cedex, France.
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Mendoza-Parra MA, Walia M, Sankar M, Gronemeyer H. Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics. Mol Syst Biol 2011; 7:538. [PMID: 21988834 PMCID: PMC3261707 DOI: 10.1038/msb.2011.73] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [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: 03/03/2011] [Accepted: 08/20/2011] [Indexed: 01/11/2023] Open
Abstract
Retinoic acid (RA) triggers physiological processes by activating heterodimeric transcription factors (TFs) comprising retinoic acid receptor (RARα, β, γ) and retinoid X receptor (RXRα, β, γ). How a single signal induces highly complex temporally controlled networks that ultimately orchestrate physiological processes is unclear. Using an RA-inducible differentiation model, we defined the temporal changes in the genome-wide binding patterns of RARγ and RXRα and correlated them with transcription regulation. Unexpectedly, both receptors displayed a highly dynamic binding, with different RXRα heterodimers targeting identical loci. Comparison of RARγ and RXRα co-binding at RA-regulated genes identified putative RXRα-RARγ target genes that were validated with subtype-selective agonists. Gene-regulatory decisions during differentiation were inferred from TF-target gene information and temporal gene expression. This analysis revealed six distinct co-expression paths of which RXRα-RARγ is associated with transcription activation, while Sox2 and Egr1 were predicted to regulate repression. Finally, RXRα-RARγ regulatory networks were reconstructed through integration of functional co-citations. Our analysis provides a dynamic view of RA signalling during cell differentiation, reveals RAR heterodimer dynamics and promiscuity, and predicts decisions that diversify the RA signal into distinct gene-regulatory programs.
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Affiliation(s)
- Marco A Mendoza-Parra
- Department of Cancer Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, Illkirch Cedex, France
| | - Mannu Walia
- Department of Cancer Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, Illkirch Cedex, France
| | - Martial Sankar
- Department of Cancer Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, Illkirch Cedex, France
| | - Hinrich Gronemeyer
- Department of Cancer Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, Illkirch Cedex, France
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