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Dumas E, Grandal Rejo B, Gougis P, Houzard S, Abécassis J, Jochum F, Marande B, Ballesta A, Del Nery E, Dubois T, Alsafadi S, Asselain B, Latouche A, Espie M, Laas E, Coussy F, Bouchez C, Pierga JY, Le Bihan-Benjamin C, Bousquet PJ, Hotton J, Azencott CA, Reyal F, Hamy AS. Concomitant medication, comorbidity and survival in patients with breast cancer. Nat Commun 2024; 15:2966. [PMID: 38580683 PMCID: PMC10997660 DOI: 10.1038/s41467-024-47002-3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
Between 30% and 70% of patients with breast cancer have pre-existing chronic conditions, and more than half are on long-term non-cancer medication at the time of diagnosis. Preliminary epidemiological evidence suggests that some non-cancer medications may affect breast cancer risk, recurrence, and survival. In this nationwide cohort study, we assessed the association between medication use at breast cancer diagnosis and survival. We included 235,368 French women with newly diagnosed non-metastatic breast cancer. In analyzes of 288 medications, we identified eight medications positively associated with either overall survival or disease-free survival: rabeprazole, alverine, atenolol, simvastatin, rosuvastatin, estriol (vaginal or transmucosal), nomegestrol, and hypromellose; and eight medications negatively associated with overall survival or disease-free survival: ferrous fumarate, prednisolone, carbimazole, pristinamycin, oxazepam, alprazolam, hydroxyzine, and mianserin. Full results are available online from an interactive platform ( https://adrenaline.curie.fr ). This resource provides hypotheses for drugs that may naturally influence breast cancer evolution.
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Affiliation(s)
- Elise Dumas
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, Université Paris Cité, F-75005, Paris, France
- INSERM, U900, 75005, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006, Paris, France
| | - Beatriz Grandal Rejo
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, Université Paris Cité, F-75005, Paris, France
| | - Paul Gougis
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, Université Paris Cité, F-75005, Paris, France
| | - Sophie Houzard
- Health Data and Assessment, Health Survey Data Science and Assessment Division, French National Cancer Institute (Institut National du Cancer INCa), 92100, Boulogne-Billancourt, France
| | - Judith Abécassis
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, Université Paris Cité, F-75005, Paris, France
- INRIA, Paris-Saclay University, CEA, Palaiseau, 91120, France
| | - Floriane Jochum
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, Université Paris Cité, F-75005, Paris, France
- Department of Gynecology, Strasbourg University Hospital, Strasbourg, France
| | - Benjamin Marande
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, Université Paris Cité, F-75005, Paris, France
| | - Annabelle Ballesta
- INSERM UMR-S 900, Institut Curie, MINES ParisTech CBIO, PSL Research University, 92210, Saint-Cloud, France
| | - Elaine Del Nery
- Département de Recherche Translationnelle - Plateforme Biophenics, PICT-IBISA, PSL Research University, Paris, France
| | - Thierry Dubois
- Institut Curie - PSL Research University Translational Research Department Breast Cancer Biology Group 26 rue d'Ulm, 75005, Paris, France
| | - Samar Alsafadi
- Institut Curie, PSL Research University, Uveal Melanoma Group, Translational Research Department, Paris, France
| | | | - Aurélien Latouche
- INSERM, U900, 75005, Paris, France
- INSERM UMR-S 900, Institut Curie, MINES ParisTech CBIO, PSL Research University, 92210, Saint-Cloud, France
- Conservatoire National des Arts et Métiers, Paris, France
| | - Marc Espie
- Breast diseases Center Hôpital saint Louis APHP, Université Paris Cité, Paris, France
| | - Enora Laas
- Department of Surgical Oncology, Université Paris Cité, Institut Curie, 75005, Paris, France
| | - Florence Coussy
- Department of Medical Oncology, Université Paris Cité, Institut Curie, 75005, Paris, France
| | - Clémentine Bouchez
- Breast diseases Center Hôpital saint Louis APHP, Université Paris Cité, Paris, France
| | - Jean-Yves Pierga
- Department of Medical Oncology, Université Paris Cité, Institut Curie, 75005, Paris, France
| | - Christine Le Bihan-Benjamin
- Health Data and Assessment, Health Survey Data Science and Assessment Division, French National Cancer Institute (Institut National du Cancer INCa), 92100, Boulogne-Billancourt, France
| | - Philippe-Jean Bousquet
- Aix Marseille Univ, Inserm, IRD, SESSTIM, Équipe Labellisée Ligue Contre le Cancer, 13005, Marseille, France
- Health Survey Data Science and Assessment Division, French National Cancer Institute (Institut National du Cancer INCa), 92100, Boulogne-Billancourt, France
| | | | - Chloé-Agathe Azencott
- INSERM, U900, 75005, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006, Paris, France
- Institut Curie, PSL Research University, Paris, France
| | - Fabien Reyal
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, Université Paris Cité, F-75005, Paris, France.
- Department of Surgical Oncology, Université Paris Cité, Institut Curie, 75005, Paris, France.
- Department of Surgery, Institut Jean Godinot, Reims, France.
| | - Anne-Sophie Hamy
- Residual Tumor & Response to Treatment Laboratory, RT2Lab, Translational Research Department, INSERM, U932 Immunity and Cancer, Université Paris Cité, F-75005, Paris, France
- Department of Medical Oncology, Université Paris Cité, Institut Curie, 75005, Paris, France
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2
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Verrelle P, Gestraud P, Poyer F, Soria A, Tessier S, Lescure A, Anthony E, Corbé M, Heinrich S, Beauvineau C, Chaput L, Granzhan A, Piguel S, Perez F, Teulade-Fichou MP, Megnin-Chanet F, Del Nery E. Integrated High-Throughput Screening and Large-Scale Isobolographic Analysis to Accelerate the Discovery of Radiosensitizers With Greater Selectivity for Cancer Cells. Int J Radiat Oncol Biol Phys 2024; 118:1294-1307. [PMID: 37778425 DOI: 10.1016/j.ijrobp.2023.09.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
PURPOSE High-throughput screening (HTS) platforms have been widely used to identify candidate anticancer drugs and drug-drug combinations; however, HTS-based identification of new drug-ionizing radiation (IR) combinations has rarely been reported. Herein, we developed an integrated approach including cell-based HTS and computational large-scale isobolographic analysis to accelerate the identification of radiosensitizing compounds acting strongly and more specifically on cancer cells. METHODS AND MATERIALS In a 384-well plate format, 160 compounds likely to interfere with the cell response to radiation were screened on human glioblastoma (U251-MG) and cervix carcinoma (ME-180) cell lines, as well as on normal fibroblasts (CCD-19Lu). After drug exposure, cells were irradiated or not and short-term cell survival was assessed by high-throughput cell microscopy. Computational large-scale dose-response and isobolographic approach were used to identify promising synergistic drugs radiosensitizing cancer cells rather than normal cells. Synergy of a promising compound was confirmed on ME-180 cells by an independent 96-well assay protocol, and finally, by the gold-standard colony forming assay. RESULTS We retained 4 compounds synergistic at 2 isoeffects in U251-MG and ME-180 cell lines and 11 compounds synergistically effective in only one cancer cell line. Among these 15 promising radiosensitizers, 5 compounds showed limited toxicity combined or not with IR on normal fibroblasts. CONCLUSIONS Overall, this study demonstrated that HTS chemoradiation screening together with large-scale computational analysis is an efficient tool to identify synergistic drug-IR combinations, with concomitant assessment of unwanted toxicity on normal fibroblasts. It sparks expectations to accelerate the discovery of highly desired agents improving the therapeutic index of radiation therapy.
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Affiliation(s)
- Pierre Verrelle
- Radiation Oncology Department, Institut Curie Hospital, Paris, France; Chemistry and Modelisation for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405 Orsay, France.
| | - Pierre Gestraud
- Chemistry and Modelisation for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405 Orsay, France
| | - Florent Poyer
- Chemistry and Modelisation for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405 Orsay, France
| | - Adèle Soria
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France
| | - Sarah Tessier
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France
| | - Aurianne Lescure
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France
| | - Elodie Anthony
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France
| | - Maxime Corbé
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France
| | - Sophie Heinrich
- Experimental Radiotherapy Platform (RadeXp), Translational Research Department, Institut Curie, Orsay, France; Inserm U1021-CNRS UMR 3347, Institut Curie, Paris Saclay University
| | - Claire Beauvineau
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Ludovic Chaput
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Anton Granzhan
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Sandrine Piguel
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France; BioCIS UMR8076, Université Paris-Saclay, Faculté de Pharmacie, Orsay, France
| | - Franck Perez
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France; Cell Biology and Cancer UMR144, Institut Curie, PSL Research University, Paris, France
| | - Marie-Paule Teulade-Fichou
- Chemistry and Modelisation for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405 Orsay, France
| | - Frédérique Megnin-Chanet
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Elaine Del Nery
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France.
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Gelot C, Kovacs MT, Miron S, Mylne E, Haan A, Boeffard-Dosierre L, Ghouil R, Popova T, Dingli F, Loew D, Guirouilh-Barbat J, Del Nery E, Zinn-Justin S, Ceccaldi R. Publisher Correction: Polθ is phosphorylated by PLK1 to repair double-strand breaks in mitosis. Nature 2024; 626:E13. [PMID: 38273133 PMCID: PMC10866694 DOI: 10.1038/s41586-024-07025-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Affiliation(s)
- Camille Gelot
- INSERM U830, PSL Research University, Institut Curie, Paris, France
| | | | - Simona Miron
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Emilie Mylne
- INSERM U830, PSL Research University, Institut Curie, Paris, France
| | - Alexis Haan
- INSERM U830, PSL Research University, Institut Curie, Paris, France
| | - Liza Boeffard-Dosierre
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Rania Ghouil
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Tatiana Popova
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL Research University, Institut Curie, Paris, France
| | - Florent Dingli
- CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Damarys Loew
- CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Josée Guirouilh-Barbat
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Cochin, Paris, France
| | - Elaine Del Nery
- Department of Translational Research-Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), PSL Research University, Institut Curie, Paris, France
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Raphael Ceccaldi
- INSERM U830, PSL Research University, Institut Curie, Paris, France.
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4
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Corbe M, Boncompain G, Perez F, Del Nery E, Genovesio A. Transfer learning for versatile and training free high content screening analyses. Sci Rep 2023; 13:22599. [PMID: 38114550 PMCID: PMC10730630 DOI: 10.1038/s41598-023-49554-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023] Open
Abstract
High content screening (HCS) is a technology that automates cell biology experiments at large scale. A High Content Screen produces a high amount of microscopy images of cells under many conditions and requires that a dedicated image and data analysis workflow be designed for each assay to select hits. This heavy data analytic step remains challenging and has been recognized as one of the burdens hindering the adoption of HCS. In this work we propose a solution to hit selection by using transfer learning without additional training. A pretrained residual network is employed to encode each image of a screen into a discriminant representation. The deep features obtained are then corrected to account for well plate bias and misalignment. We then propose two training-free pipelines dedicated to the two main categories of HCS for compound selection: with or without positive control. When a positive control is available, it is used alongside the negative control to compute a linear discriminant axis, thus building a classifier without training. Once all samples are projected onto this axis, the conditions that best reproduce the positive control can be selected. When no positive control is available, the Mahalanobis distance is computed from each sample to the negative control distribution. The latter provides a metric to identify the conditions that alter the negative control's cell phenotype. This metric is subsequently used to categorize hits through a clustering step. Given the lack of available ground truth in HCS, we provide a qualitative comparison of the results obtained using this approach with results obtained with handcrafted image analysis features for compounds and siRNA screens with or without control. Our results suggests that the fully automated and generic pipeline we propose offers a good alternative to handcrafted dedicated image analysis approaches. Furthermore, we demonstrate that this solution select conditions of interest that had not been identified using the primary dedicated analysis. Altogether, this approach provides a fully automated, reproducible, versatile and comprehensive alternative analysis solution for HCS encompassing compound-based or downregulation screens, with or without positive controls, without the need for training or cell detection, or the development of a dedicated image analysis workflow.
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Affiliation(s)
- Maxime Corbe
- Computational Bioimaging and Bioinformatics, Institut de Biologie de l'Ecole Normale Supérieure, PSL University, 46 Rue d'Ulm, 75005, Paris, France
- Biophenics Laboratory, Department of Translational Research, Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, PSL Research University, 26 Rue d'Ulm, 75005, Paris, France
| | - Gaëlle Boncompain
- Dynamics of Intra-Cellular Organization - UMR144, Institut Curie, PSL Research University, Paris, France
| | - Franck Perez
- Biophenics Laboratory, Department of Translational Research, Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, PSL Research University, 26 Rue d'Ulm, 75005, Paris, France
- Dynamics of Intra-Cellular Organization - UMR144, Institut Curie, PSL Research University, Paris, France
| | - Elaine Del Nery
- Biophenics Laboratory, Department of Translational Research, Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, PSL Research University, 26 Rue d'Ulm, 75005, Paris, France.
| | - Auguste Genovesio
- Computational Bioimaging and Bioinformatics, Institut de Biologie de l'Ecole Normale Supérieure, PSL University, 46 Rue d'Ulm, 75005, Paris, France.
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5
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Lamiable A, Champetier T, Leonardi F, Cohen E, Sommer P, Hardy D, Argy N, Massougbodji A, Del Nery E, Cottrell G, Kwon YJ, Genovesio A. Revealing invisible cell phenotypes with conditional generative modeling. Nat Commun 2023; 14:6386. [PMID: 37821450 PMCID: PMC10567685 DOI: 10.1038/s41467-023-42124-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
Biological sciences, drug discovery and medicine rely heavily on cell phenotype perturbation and microscope observation. However, most cellular phenotypic changes are subtle and thus hidden from us by natural cell variability: two cells in the same condition already look different. In this study, we show that conditional generative models can be used to transform an image of cells from any one condition to another, thus canceling cell variability. We visually and quantitatively validate that the principle of synthetic cell perturbation works on discernible cases. We then illustrate its effectiveness in displaying otherwise invisible cell phenotypes triggered by blood cells under parasite infection, or by the presence of a disease-causing pathological mutation in differentiated neurons derived from iPSCs, or by low concentration drug treatments. The proposed approach, easy to use and robust, opens the door to more accessible discovery of biological and disease biomarkers.
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Affiliation(s)
- Alexis Lamiable
- Computational Bioimaging and Bioinformatics, Institut de Biologie de l'Ecole Normale Supérieure, PSL University, 46, rue d'Ulm, 75005, Paris, France
| | - Tiphaine Champetier
- Computational Bioimaging and Bioinformatics, Institut de Biologie de l'Ecole Normale Supérieure, PSL University, 46, rue d'Ulm, 75005, Paris, France
- Ksilink, 16 rue d'Ankara, 67000, Strasbourg, France
| | - Francesco Leonardi
- Computational Bioimaging and Bioinformatics, Institut de Biologie de l'Ecole Normale Supérieure, PSL University, 46, rue d'Ulm, 75005, Paris, France
- Université Paris-Cité, MERIT, IRD, F-75006, Paris, France
| | - Ethan Cohen
- Computational Bioimaging and Bioinformatics, Institut de Biologie de l'Ecole Normale Supérieure, PSL University, 46, rue d'Ulm, 75005, Paris, France
| | - Peter Sommer
- Ksilink, 16 rue d'Ankara, 67000, Strasbourg, France
| | - David Hardy
- Histopathology Platform, Institut Pasteur, F-75015, Paris, France
| | - Nicolas Argy
- Université Paris-Cité, MERIT, IRD, F-75006, Paris, France
- Laboratoire de parasitologie-mycologie, Hôpital Bichat-Claude bernard, APHP, Paris, France
| | | | - Elaine Del Nery
- Biophenics, Institut Curie, PSL Research University, Department of Translational Research, Cell and Tissue Imaging Facility (PICT-IBiSA), 26 rue d'Ulm, 75005, Paris, France
| | | | - Yong-Jun Kwon
- Ksilink, 16 rue d'Ankara, 67000, Strasbourg, France.
- Personalized Therapy Discovery, Department of Oncology, Luxembourg Institute of Health, Dudelange, Luxembourg.
| | - Auguste Genovesio
- Computational Bioimaging and Bioinformatics, Institut de Biologie de l'Ecole Normale Supérieure, PSL University, 46, rue d'Ulm, 75005, Paris, France.
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6
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Gelot C, Kovacs MT, Miron S, Mylne E, Haan A, Boeffard-Dosierre L, Ghouil R, Popova T, Dingli F, Loew D, Guirouilh-Barbat J, Del Nery E, Zinn-Justin S, Ceccaldi R. Polθ is phosphorylated by PLK1 to repair double-strand breaks in mitosis. Nature 2023; 621:415-422. [PMID: 37674080 PMCID: PMC10499603 DOI: 10.1038/s41586-023-06506-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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: 09/28/2022] [Accepted: 08/01/2023] [Indexed: 09/08/2023]
Abstract
DNA double-strand breaks (DSBs) are deleterious lesions that challenge genome integrity. To mitigate this threat, human cells rely on the activity of multiple DNA repair machineries that are tightly regulated throughout the cell cycle1. In interphase, DSBs are mainly repaired by non-homologous end joining and homologous recombination2. However, these pathways are completely inhibited in mitosis3-5, leaving the fate of mitotic DSBs unknown. Here we show that DNA polymerase theta6 (Polθ) repairs mitotic DSBs and thereby maintains genome integrity. In contrast to other DSB repair factors, Polθ function is activated in mitosis upon phosphorylation by Polo-like kinase 1 (PLK1). Phosphorylated Polθ is recruited by a direct interaction with the BRCA1 C-terminal domains of TOPBP1 to mitotic DSBs, where it mediates joining of broken DNA ends. Loss of Polθ leads to defective repair of mitotic DSBs, resulting in a loss of genome integrity. This is further exacerbated in cells that are deficient in homologous recombination, where loss of mitotic DSB repair by Polθ results in cell death. Our results identify mitotic DSB repair as the underlying cause of synthetic lethality between Polθ and homologous recombination. Together, our findings reveal the critical importance of mitotic DSB repair in the maintenance of genome integrity.
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Affiliation(s)
- Camille Gelot
- INSERM U830, PSL Research University, Institut Curie, Paris, France
| | | | - Simona Miron
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Emilie Mylne
- INSERM U830, PSL Research University, Institut Curie, Paris, France
| | - Alexis Haan
- INSERM U830, PSL Research University, Institut Curie, Paris, France
| | - Liza Boeffard-Dosierre
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Rania Ghouil
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Tatiana Popova
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL Research University, Institut Curie, Paris, France
| | - Florent Dingli
- CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Damarys Loew
- CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Josée Guirouilh-Barbat
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Cochin, Paris, France
| | - Elaine Del Nery
- Department of Translational Research-Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), PSL Research University, Institut Curie, Paris, France
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Raphael Ceccaldi
- INSERM U830, PSL Research University, Institut Curie, Paris, France.
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7
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Fevre R, Mary G, Vertti-Quintero N, Durand A, Tomasi RFX, Del Nery E, Baroud CN. Combinatorial drug screening on 3D Ewing sarcoma spheroids using droplet-based microfluidics. iScience 2023; 26:106651. [PMID: 37168549 PMCID: PMC10165258 DOI: 10.1016/j.isci.2023.106651] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/02/2023] [Accepted: 04/05/2023] [Indexed: 05/13/2023] Open
Abstract
Culturing and screening cells in microfluidics, particularly in three-dimensional formats, has the potential to impact diverse areas from fundamental biology to cancer precision medicine. Here, we use a platform based on anchored droplets for drug screening. The response of spheroids of Ewing sarcoma (EwS) A673 cells to simultaneous or sequential combinations of etoposide and cisplatin was evaluated. This was done by culturing spheroids of EwS cells inside 500 nL droplets then merging them with secondary droplets containing fluorescent-barcoded drugs at different concentrations. Differences in EwS spheroid growth and viability were measured by microscopy. After drug exposure such measurements enabled estimation of their IC50 values, which were in agreement with values obtained in standard multiwell plates. Then, synergistic drug combination was evaluated. Sequential combination treatment of EwS with etoposide applied 24 h before cisplatin resulted in amplified synergistic effect. As such, droplet-based microfluidics offers the modularity required for evaluation of drug combinations.
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Affiliation(s)
- Romain Fevre
- Laboratoire d’ Hydrodynamique (LadHyX), CNRS, EcolePolytechnique, InstitutPolytechnique de Paris, 91128 Palaiseau, France
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Gaëtan Mary
- Okomera, iPEPS, the HealthTech Hub, Paris Brain Institute, HôpitalPitiéSalpêtrière, 75013 Paris, France
| | - Nadia Vertti-Quintero
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Aude Durand
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, 25-28 Rue du Dr. Roux, 75015 Paris, France
| | - Raphaël F.-X. Tomasi
- Laboratoire d’ Hydrodynamique (LadHyX), CNRS, EcolePolytechnique, InstitutPolytechnique de Paris, 91128 Palaiseau, France
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, 25-28 Rue du Dr. Roux, 75015 Paris, France
- Okomera, iPEPS, the HealthTech Hub, Paris Brain Institute, HôpitalPitiéSalpêtrière, 75013 Paris, France
| | - Elaine Del Nery
- Biophenics High-Content Screening Laboratory, Translational Research Department, PICT-IBiSA, Institut Curie, PSL Research University, 75005 Paris, France
- Corresponding author
| | - Charles N. Baroud
- Laboratoire d’ Hydrodynamique (LadHyX), CNRS, EcolePolytechnique, InstitutPolytechnique de Paris, 91128 Palaiseau, France
- Institut Pasteur, Université Paris Cité, Physical microfluidics and Bioengineering, 25-28 Rue du Dr. Roux, 75015 Paris, France
- Corresponding author
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8
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Cohen E, Corbe M, Franco CA, Vasconcelos FF, Perez F, Del Nery E, Bollot G, Genovesio A. Cell painting transfer increases screening hit rate. Biol Imaging 2023; 3:e4. [PMID: 38487691 PMCID: PMC10936370 DOI: 10.1017/s2633903x23000077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/15/2023] [Accepted: 02/26/2023] [Indexed: 03/17/2024]
Abstract
Drug discovery uses high throughput screening to identify compounds that interact with a molecular target or that alter a phenotype favorably. The cautious selection of molecules used for such a screening is instrumental and is tightly related to the hit rate. In this work, we wondered if cell painting, a general-purpose image-based assay, could be used as an efficient proxy for compound selection, thus increasing the success rate of a specific assay. To this end, we considered cell painting images with 30,000 molecules treatments, and selected compounds that produced a visual effect close to the positive control of an assay, by using the Frechet Inception Distance. We then compared the hit rates of such a preselection with what was actually obtained in real screening campaigns. As a result, cell painting would have permitted a significant increase in the success rate and, even for one of the assays, would have allowed to reach 80% of the hits with 10 times fewer compounds to test. We conclude that images of a cell painting assay can be directly used for compound selection prior to screening, and we provide a simple quantitative approach in order to do so.
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Affiliation(s)
- Ethan Cohen
- Computational Bioimaging and Bioinformatics, Institut de Biologie de l’Ecole Normale Supérieure, PSL University, Paris, France
- Synsight, 4 Rue Pierre Fontaine, 91000Évry-Courcouronnes, France
| | - Maxime Corbe
- Computational Bioimaging and Bioinformatics, Institut de Biologie de l’Ecole Normale Supérieure, PSL University, Paris, France
- Biophenics Laboratory, Institut Curie, PSL Research University, Department of Translational Research, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Cláudio A. Franco
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Católica Medical School, Católica Biomedical Research Centre, Universidade Católica Portuguesa, Lisbon, Portugal
| | - Francisca F. Vasconcelos
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Franck Perez
- Biophenics Laboratory, Institut Curie, PSL Research University, Department of Translational Research, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
- Dynamics of Intra-cellular Organisation – UMR144, Institut Curie, PSL Research University, Paris, France
| | - Elaine Del Nery
- Biophenics Laboratory, Institut Curie, PSL Research University, Department of Translational Research, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Guillaume Bollot
- Synsight, 4 Rue Pierre Fontaine, 91000Évry-Courcouronnes, France
| | - Auguste Genovesio
- Computational Bioimaging and Bioinformatics, Institut de Biologie de l’Ecole Normale Supérieure, PSL University, Paris, France
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9
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Dumas E, Grandal B, Gougis P, Houzard S, Latouche A, Toussaint A, Alsafadi S, Abecassis J, Delrieu L, Dubois T, Sella N, Espie M, Asselain B, Ballesta A, Marande B, Daoud E, Laas E, Kassara A, Jochum F, Nery ED, Anthony E, Le Bihan-Benjamin C, Bousquet PJ, Azencott CA, Reyal F, Hamy AS. Abstract P3-07-06: Comedications at Breast Cancer diagnosis impact overall survival: results from the ADRENALINE (Atlas for DRug and brEast caNcer survivAL INtEraction) study (n=235,368). Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p3-07-06] [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: 03/06/2023]
Abstract
Abstract
Background: More than half of Breast Cancer (BC) patients take chronically used non-cancer treatments (denoted as comedications) at BC diagnosis. Epidemiological evidence has reported that several non-cancer treatments may modify BC risk, BC recurrence, and overall survival (OS). The ADRENALINE project (Atlas for DRug and brEast caNcer survivAL INtEraction) analyses the impact of the use of each commonly prescribed non-cancer treatment at BC diagnosis on OS using the French social security system data on a comprehensive cohort of French BC patients. Methods: We identified all women diagnosed with an incident BC treated with surgery in France from 2011 to 2017 and affiliated to the general health insurance scheme. Women with concomitant cancer or metastases at diagnosis were discarded from the analyses. Comedication intake was defined as the delivery in pharmacy of at least 3 months of full treatment (e.g. 90 pills) the 6 months preceding BC diagnosis. A Cox proportional hazard model was used to estimate the hazard ratio (HR) for each molecule. The model was adjusted on more than 100 confounding variables: social factors, comorbidities and other comedications by Inverse Probability of Treatment Weighting (IPTW). We assumed that the adjustment was sufficient to control for confounding if the standardized mean difference of each confounder after adjustment did not exceed 0.1. Molecules which did not pass the adjustment quality test were discarded. Results: Overall, 235,368 patients were included in the study. Among 219 selected drugs, 91 passed the adjustment quality test. The full set of results is available on a web application (https://adrenaline.curie.fr). Several drugs or drug classes were associated with an improved survival: statins (e.g. rosuvastatin, HR=0.65, p< 0.001); proton-pump inhibitors (HR=0.93; p=0.002); or beta-blocking agents (atenolol, HR=0.78, p=0.003). Conversely, anti-anemic preparations (folic acid and ferrous sulfate) had a significant deleterious effect (HR = 1.63; p< 0.001). Drugs from the same therapeutic class, could have different effects: within benzodiazepines, bromazepam was protective (HR = 0.91; p = 0.038) while oxazepam was deleterious (HR = 1.37; p < 0.001). Conclusion: ADRENALINE reports the impact on BC survival of 219 widely prescribed drugs. It can be used to identify molecules with a potential protective or deleterious effect relative to BC. Some of them are currently under mechanistical investigation within a drug screening program. This atlas highlights candidates to drug-repurposing trials or pharmacovigilance warnings, and will be extended to cancers of other localizations in a near future.
Citation Format: Elise Dumas, Beatriz Grandal, Paul Gougis, Sophie Houzard, Aurélien Latouche, Aullène Toussaint, Samar Alsafadi, Judith Abecassis, Lidia Delrieu, Thierry Dubois, Nadir Sella, Marc Espie, Bernard Asselain, Annabelle Ballesta, Benjamin Marande, Eric Daoud, Enora Laas, Amyn Kassara, Floriane Jochum, Elaine Del Nery, Elodie Anthony, Christine Le Bihan-Benjamin, Philippe-Jean Bousquet, Chloé-Agathe Azencott, Fabien Reyal, Anne-Sophie Hamy. Comedications at Breast Cancer diagnosis impact overall survival: results from the ADRENALINE (Atlas for DRug and brEast caNcer survivAL INtEraction) study (n=235,368) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-07-06.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Marc Espie
- 12Centre des Maladies du Sein, Hôpital Saint-Louis
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10
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Tucker ER, Jiménez I, Chen L, Bellini A, Gorrini C, Calton E, Gao Q, Che H, Poon E, Jamin Y, Martins Da Costa B, Barker K, Shrestha S, Hutchinson JC, Dhariwal S, Goodman A, Del Nery E, Gestraud P, Bhalshankar J, Iddir Y, Saberi-Ansari E, Saint-Charles A, Geoerger B, Marques Da Costa ME, Pierre-Eugene C, Janoueix-Lerosey I, Decaudin D, Némati F, Carcaboso AM, Surdez D, Delattre O, George SL, Chesler L, Tweddle DA, Schleiermacher G. Combination Therapies Targeting Alk-Aberrant Neuroblastoma in Preclinical Models. Clin Cancer Res 2023; 29:1317-1331. [PMID: 36602782 PMCID: PMC10068437 DOI: 10.1158/1078-0432.ccr-22-2274] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/31/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
BACKGROUND ALK activating mutations are identified in approximately 10% of newly diagnosed neuroblastomas and ALK amplifications in a further 1-2% of cases. Lorlatinib, a third generation ALK inhibitor, will soon be given alongside induction chemotherapy for children with ALK-aberrant neuroblastoma. However, resistance to single agent treatment has been reported and therapies that improve the response duration are urgently required. We studied the preclinical combination of lorlatinib with chemotherapy, or with the MDM2 inhibitor, idasanutlin, as recent data has suggested that ALK inhibitor resistance can be overcome through activation of the p53-MDM2 pathway. AIMS To study the preclinical activity of ALK inhibitors alone and combined with chemotherapy or idasanutlin. METHODS We compared different ALK inhibitors in preclinical models prior to evaluating lorlatinib in combination with chemotherapy or idasanutlin. We developed a triple chemotherapy (CAV: cyclophosphamide, doxorubicin and vincristine) in vivo dosing schedule and applied this to both neuroblastoma genetically engineered mouse models (GEMM) and patient derived xenografts (PDX). RESULTS Lorlatinib in combination with chemotherapy was synergistic in immunocompetent neuroblastoma GEMM. Significant growth inhibition in response to lorlatinib was only observed in the ALK-amplified PDX model with high ALK expression. In this PDX lorlatinib combined with idasanutlin resulted in complete tumor regression and significantly delayed tumor regrowth. CONCLUSION In our preclinical neuroblastoma models, high ALK expression was associated with lorlatinib response alone or in combination with either chemotherapy or idasanutlin. The synergy between MDM2 and ALK inhibition warrants further evaluation of this combination as a potential clinical approach for children with neuroblastoma.
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Affiliation(s)
| | | | - Lindi Chen
- Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | | | | | - Qiong Gao
- Institute of Cancer Research, London, United Kingdom
| | - Harvey Che
- Institute of Cancer Research, London, United Kingdom
| | - Evon Poon
- Institute of Cancer Research, London, United Kingdom
| | - Yann Jamin
- The Institute of Cancer Research, London, London, Surrey, United Kingdom
| | | | - Karen Barker
- The Institute of Cancer Research, London, Sutton, Surrey, United Kingdom
| | | | - J Ciaran Hutchinson
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | | | - Angharad Goodman
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | | | | | | | | | | | - Birgit Geoerger
- Gustave Roussy Cancer Institute, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | | | | | | | | | | | - Angel M Carcaboso
- Institut de Recerca Sant Joan de Deu, Esplugues de Llobregat, Barcelona, Spain
| | | | | | - Sally L George
- The Institute of Cancer Research and Marsden NHS Foundation Trust, Sutton, Surrey, United Kingdom
| | - Louis Chesler
- The Institute of Cancer Research, London, London, Greater London, United Kingdom
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11
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Grisard E, Nevo N, Lescure A, Doll S, Corbé M, Jouve M, Lavieu G, Joliot A, Nery ED, Martin-Jaular L, Théry C. Homosalate boosts the release of tumour-derived extracellular vesicles with protection against anchorage-loss property. J Extracell Vesicles 2022; 11:e12242. [PMID: 35790086 PMCID: PMC9253888 DOI: 10.1002/jev2.12242] [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: 10/07/2021] [Revised: 05/16/2022] [Accepted: 06/15/2022] [Indexed: 11/07/2022] Open
Abstract
Eukaryotic cells, including cancer cells, secrete highly heterogeneous populations of extracellular vesicles (EVs). EVs could have different subcellular origin, composition and functional properties, but tools to distinguish between EV subtypes are scarce. Here, we tagged CD63‐ or CD9‐positive EVs secreted by triple negative breast cancer cells with Nanoluciferase enzyme, to set‐up a miniaturized method to quantify secretion of these two EV subtypes directly in the supernatant of cells. We performed a cell‐based high‐content screening to identify clinically‐approved drugs able to affect EV secretion. One of the identified hits is Homosalate, an anti‐inflammatory drug found in sunscreens which robustly increased EVs’ release. Comparing EVs induced by Homosalate with those induced by Bafilomycin A1, we demonstrate that: (1) the two drugs act on EVs generated in distinct subcellular compartments, and (2) EVs released by Homosalate‐, but not by Bafilomycin A1‐treated cells enhance resistance to anchorage loss in another recipient epithelial tumour cell line. In conclusion, we identified a new drug modifying EV release and demonstrated that under influence of different drugs, triple negative breast cancer cells release EV subpopulations from different subcellular origins harbouring distinct functional properties.
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Affiliation(s)
- Eleonora Grisard
- Institut Curie, PSL Research University, INSERM U932, Paris, France
| | - Nathalie Nevo
- Institut Curie, PSL Research University, INSERM U932, Paris, France
| | - Aurianne Lescure
- Institut Curie, PSL Research University, Translational Research Department, BioPhenics Platform, PICT-IBISA, Paris, France
| | - Sebastian Doll
- Institute of Metabolism and Cell Death, Helmholtz Zentrum München, Neuherberg, Germany
| | - Maxime Corbé
- Institut Curie, PSL Research University, Translational Research Department, BioPhenics Platform, PICT-IBISA, Paris, France
| | - Mabel Jouve
- Institut Curie, PSL Research University, CNRS UMR3215, Paris, France
| | - Gregory Lavieu
- Institut Curie, PSL Research University, INSERM U932, Paris, France.,Université Paris Cité, INSERM U1316, CNRS UMR 7057, Paris, France
| | - Alain Joliot
- Institut Curie, PSL Research University, INSERM U932, Paris, France
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Translational Research Department, BioPhenics Platform, PICT-IBISA, Paris, France
| | | | - Clotilde Théry
- Institut Curie, PSL Research University, INSERM U932, Paris, France
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12
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Buchou C, Laud-Duval K, van der Ent W, Grossetête S, Zaidi S, Gentric G, Corbé M, Müller K, Del Nery E, Surdez D, Delattre O. Upregulation of the Mevalonate Pathway through EWSR1-FLI1/EGR2 Regulatory Axis Confers Ewing Cells Exquisite Sensitivity to Statins. Cancers (Basel) 2022; 14:cancers14092327. [PMID: 35565457 PMCID: PMC9100622 DOI: 10.3390/cancers14092327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 04/08/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The objective of this project was to search for new dependencies in Ewing sarcoma, a deadly disease for which new therapeutic approaches are urgently needed. A pharmacological screening of off-patent approved drugs (FDA agency) and the investigation of downstream targets of EGR2 were performed. The two approaches showed the MVA pathway as a major dependency in Ewing sarcoma and statin, an inhibitor of this pathway, as a potential new therapeutic agent for the treatment of Ewing sarcoma. Abstract Ewing sarcoma (EwS) is an aggressive primary bone cancer in children and young adults characterized by oncogenic fusions between genes encoding FET-RNA-binding proteins and ETS transcription factors, the most frequent fusion being EWSR1-FLI1. We show that EGR2, an Ewing-susceptibility gene and an essential direct target of EWSR1-FLI1, directly regulates the transcription of genes encoding key enzymes of the mevalonate (MVA) pathway. Consequently, Ewing sarcoma is one of the tumors that expresses the highest levels of mevalonate pathway genes. Moreover, genome-wide screens indicate that MVA pathway genes constitute major dependencies of Ewing cells. Accordingly, the statin inhibitors of HMG-CoA-reductase, a rate-limiting enzyme of the MVA pathway, demonstrate cytotoxicity in EwS. Statins induce increased ROS and lipid peroxidation levels, as well as decreased membrane localization of prenylated proteins, such as small GTP proteins. These metabolic effects lead to an alteration in the dynamics of S-phase progression and to apoptosis. Statin-induced effects can be rescued by downstream products of the MVA pathway. Finally, we further show that statins impair tumor growth in different Ewing PDX models. Altogether, the data show that statins, which are off-patent, well-tolerated, and inexpensive compounds, should be strongly considered in the therapeutic arsenal against this deadly childhood disease.
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Affiliation(s)
- Charlie Buchou
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
| | - Karine Laud-Duval
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
| | - Wietske van der Ent
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
| | - Géraldine Gentric
- INSERM U830, Équipe Labellisée LNCC, Stress and Cancer Laboratory, PSL Research University, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France;
| | - Maxime Corbé
- Department of Translational Research, The Biophenics High-Content Screening Laboratory, PSL Research University, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (M.C.); (K.M.); (E.D.N.)
| | - Kévin Müller
- Department of Translational Research, The Biophenics High-Content Screening Laboratory, PSL Research University, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (M.C.); (K.M.); (E.D.N.)
| | - Elaine Del Nery
- Department of Translational Research, The Biophenics High-Content Screening Laboratory, PSL Research University, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (M.C.); (K.M.); (E.D.N.)
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
- Balgrist University Hospital, University of Zurich, Zurich, Forchstrasse 340, 8008 Zürich, Switzerland
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity & Plasticity of Childhood Tumors Laboratory, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, 26 rue d’ULM, 75005 Paris, France; (C.B.); (K.L.-D.); (W.v.d.E.); (S.G.); (S.Z.); (D.S.)
- Correspondence:
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13
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Lesage S, Chazal M, Beauclair G, Batalie D, Cerboni S, Couderc E, Lescure A, Del Nery E, Tangy F, Martin A, Manel N, Jouvenet N. Discovery of Genes that Modulate Flavivirus Replication in an Interferon-Dependent Manner. J Mol Biol 2022; 434:167277. [PMID: 34599939 PMCID: PMC8480147 DOI: 10.1016/j.jmb.2021.167277] [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: 08/16/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/02/2022]
Abstract
Establishment of the interferon (IFN)-mediated antiviral state provides a crucial initial line of defense against viral infection. Numerous genes that contribute to this antiviral state remain to be identified. Using a loss-of-function strategy, we screened an original library of 1156 siRNAs targeting 386 individual curated human genes in stimulated microglial cells infected with Zika virus (ZIKV), an emerging RNA virus that belongs to the flavivirus genus. The screen recovered twenty-one potential host proteins that modulate ZIKV replication in an IFN-dependent manner, including the previously known IFITM3 and LY6E. Further characterization contributed to delineate the spectrum of action of these genes towards other pathogenic RNA viruses, including Hepatitis C virus and SARS-CoV-2. Our data revealed that APOL3 acts as a proviral factor for ZIKV and several other related and unrelated RNA viruses. In addition, we showed that MTA2, a chromatin remodeling factor, possesses potent flavivirus-specific antiviral functions induced by IFN. Our work identified previously unrecognized genes that modulate the replication of RNA viruses in an IFN-dependent manner, opening new perspectives to target weakness points in the life cycle of these viruses.
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Affiliation(s)
- Sarah Lesage
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus Sensing and Signaling Unit, F-75015 Paris, France
| | - Maxime Chazal
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus Sensing and Signaling Unit, F-75015 Paris, France
| | - Guillaume Beauclair
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus Sensing and Signaling Unit, F-75015 Paris, France; Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Damien Batalie
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Molecular Genetics of RNA Viruses Unit, F-75015 Paris, France
| | - Silvia Cerboni
- Institut Curie, PSL Research University, INSERM U932, Paris, France
| | - Elodie Couderc
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus Sensing and Signaling Unit, F-75015 Paris, France; Institut Pasteur, Université de Paris, CNRS UMR 2000, Insect-Virus Interactions Unit, F-75015 Paris, France
| | - Aurianne Lescure
- Institut Curie, PSL Research University, Department of Translational Research-Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Department of Translational Research-Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Frédéric Tangy
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Viral Genomics and Vaccination Unit, F-75015 Paris, France
| | - Annette Martin
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Molecular Genetics of RNA Viruses Unit, F-75015 Paris, France
| | - Nicolas Manel
- Institut Curie, PSL Research University, INSERM U932, Paris, France. https://twitter.com/NicolasManellab
| | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus Sensing and Signaling Unit, F-75015 Paris, France.
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14
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Nelson G, Boehm U, Bagley S, Bajcsy P, Bischof J, Brown CM, Dauphin A, Dobbie IM, Eriksson JE, Faklaris O, Fernandez-Rodriguez J, Ferrand A, Gelman L, Gheisari A, Hartmann H, Kukat C, Laude A, Mitkovski M, Munck S, North AJ, Rasse TM, Resch-Genger U, Schuetz LC, Seitz A, Strambio-De-Castillia C, Swedlow JR, Alexopoulos I, Aumayr K, Avilov S, Bakker GJ, Bammann RR, Bassi A, Beckert H, Beer S, Belyaev Y, Bierwagen J, Birngruber KA, Bosch M, Breitlow J, Cameron LA, Chalfoun J, Chambers JJ, Chen CL, Conde-Sousa E, Corbett AD, Cordelieres FP, Nery ED, Dietzel R, Eismann F, Fazeli E, Felscher A, Fried H, Gaudreault N, Goh WI, Guilbert T, Hadleigh R, Hemmerich P, Holst GA, Itano MS, Jaffe CB, Jambor HK, Jarvis SC, Keppler A, Kirchenbuechler D, Kirchner M, Kobayashi N, Krens G, Kunis S, Lacoste J, Marcello M, Martins GG, Metcalf DJ, Mitchell CA, Moore J, Mueller T, Nelson MS, Ogg S, Onami S, Palmer AL, Paul-Gilloteaux P, Pimentel JA, Plantard L, Podder S, Rexhepaj E, Royon A, Saari MA, Schapman D, Schoonderwoert V, Schroth-Diez B, Schwartz S, Shaw M, Spitaler M, Stoeckl MT, Sudar D, Teillon J, Terjung S, Thuenauer R, Wilms CD, Wright GD, Nitschke R. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. J Microsc 2021; 284:56-73. [PMID: 34214188 PMCID: PMC10388377 DOI: 10.1111/jmi.13041] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/16/2021] [Indexed: 11/27/2022]
Abstract
A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
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Affiliation(s)
- Glyn Nelson
- Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Ulrike Boehm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Steve Bagley
- Visualisation, Irradiation & Analysis, Cancer Research UK Manchester Institute, Alderley Park, Macclesfield, UK
| | - Peter Bajcsy
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | | | - Claire M Brown
- Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada
| | - Aurélien Dauphin
- Unité Génétique et Biologie du Développement U934, PICT-IBiSA, Institut Curie/Inserm/CNRS/PSL Research University, Paris, France
| | - Ian M Dobbie
- Department of Biochemistry, University of Oxford, Oxford, Oxon, UK
| | - John E Eriksson
- Turku Bioscience Centre, Euro-Bioimaging ERIC, Turku, Finland
| | | | | | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ali Gheisari
- Light Microscopy Facility, CMCB Technology Platform, TU Dresden, Dresden, Germany
| | - Hella Hartmann
- Light Microscopy Facility, CMCB Technology Platform, TU Dresden, Dresden, Germany
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Alex Laude
- Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK
| | - Miso Mitkovski
- Light Microscopy Facility, Max Planck Institute of Experimental Medicine, Goettingen, Germany
| | - Sebastian Munck
- VIB BioImaging Core & VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department for Neuroscience, Leuven, Flanders, Belgium
| | | | - Tobias M Rasse
- Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ute Resch-Genger
- Division Biophotonics, Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Lucas C Schuetz
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
| | - Arne Seitz
- Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Vaud, Switzerland
| | | | - Jason R Swedlow
- Divisions of Computational Biology and Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ioannis Alexopoulos
- General Instrumentation - Light Microscopy Facility, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Karin Aumayr
- BioOptics Facility, IMP - Research Institute of Molecular Pathology, Vienna, Austria
| | - Sergiy Avilov
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gert-Jan Bakker
- Department of Cell Biology (route 283), Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Andrea Bassi
- Dipartimento di Fisica, Politecnico di Milano, Milan, Italy
| | - Hannes Beckert
- Microscopy Core Facility, Medizinische Fakultät, Universität Bonn, Bonn, Germany
| | | | - Yury Belyaev
- Microscopy Imaging Center, University of Bern, Bern, Switzerland
| | | | | | - Manel Bosch
- Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | | | - Lisa A Cameron
- Light Microscopy Core Facility, Department of Biology, Duke University, Durham, North Carolina, USA
| | - Joe Chalfoun
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - James J Chambers
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | | | - Eduardo Conde-Sousa
- i3S - Instituto de InvestigaÇão e InovaÇão em Saúde, Universidade do Porto, Porto, Portugal.,INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | | | | | - Elaine Del Nery
- BioPhenics High-Content Screening Laboratory (PICT-IBiSA), Translational Research Department, Institut Curie - PSL Research University, Paris, France
| | - Ralf Dietzel
- Omicron-Laserage Laserprodukte GmbH, Rodgau, Germany
| | | | | | | | - Hans Fried
- Light Microscope Facility, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Wah Ing Goh
- A*STAR Microscopy Platform, Research Support Centre, Agency for Science, Technology and Research, Singapore, Singapore
| | - Thomas Guilbert
- Institut Cochin, INSERM (U1016), CNRS (UMR 8104), Université de Paris (UMR-S1016), Paris, France
| | | | - Peter Hemmerich
- Core Facility Imaging, Leibniz Institute on Aging, Jena, Germany
| | | | - Michelle S Itano
- Neuroscience Microscopy Core, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Helena K Jambor
- Mildred-Scheel Nachwuchszentrum, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Stuart C Jarvis
- Prior Scientific Instruments Limited, Cambridge, Cambridgeshire, UK
| | - Antje Keppler
- EMBL Heidelberg, Global BioImaging, Heidelberg, Germany
| | | | - Marcel Kirchner
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Gabriel Krens
- Bioimaging Facility, Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Susanne Kunis
- University Osnabrueck, Biology/Chemistry, Osnabrueck, Germany
| | | | - Marco Marcello
- Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, Merseyside, UK
| | - Gabriel G Martins
- Instituto Gulbenkian de Ciencia & Faculdade de Ciencias, University of Lisboa, Oeiras, Portugal
| | | | - Claire A Mitchell
- Warwick Medical School, University of Warwick, Coventry, West Midlands, UK
| | - Joshua Moore
- Divisions of Computational Biology and Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tobias Mueller
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Vienna, Austria
| | | | - Stephen Ogg
- Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | | | - Perrine Paul-Gilloteaux
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, F-44000 Nantes, France
| | - Jaime A Pimentel
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Laure Plantard
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Santosh Podder
- Microscopy Facility, Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India
| | | | | | - Markku A Saari
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Damien Schapman
- UNIROUEN, INSERM, PRIMACEN, Normandie University, Rouen, France
| | | | - Britta Schroth-Diez
- Light Microscopy Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Michael Shaw
- National Physical Laboratory, Teddington, Middlesex, UK
| | - Martin Spitaler
- Imaging Facility, Max Planck Institute of Biochemistry, Martinsried, Munich, Germany
| | | | - Damir Sudar
- Quantitative Imaging Systems, Portland, Oregon, USA
| | - Jeremie Teillon
- Bordeaux Imaging Center, Université de Bordeaux, Bordeaux, Gironde, France
| | - Stefan Terjung
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
| | - Roland Thuenauer
- Technology Platform Microscopy and Image Analysis, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Graham D Wright
- A*STAR Microscopy Platform, Research Support Centre, Agency for Science, Technology and Research, Singapore, Singapore
| | - Roland Nitschke
- Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
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15
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Chabanon RM, Morel D, Eychenne T, Colmet-Daage L, Bajrami I, Dorvault N, Garrido M, Meisenberg C, Lamb A, Ngo C, Hopkins SR, Roumeliotis TI, Jouny S, Hénon C, Kawai-Kawachi A, Astier C, Konde A, Del Nery E, Massard C, Pettitt SJ, Margueron R, Choudhary JS, Almouzni G, Soria JC, Deutsch E, Downs JA, Lord CJ, Postel-Vinay S. PBRM1 Deficiency Confers Synthetic Lethality to DNA Repair Inhibitors in Cancer. Cancer Res 2021; 81:2888-2902. [PMID: 33888468 DOI: 10.1158/0008-5472.can-21-0628] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022]
Abstract
Inactivation of Polybromo 1 (PBRM1), a specific subunit of the PBAF chromatin remodeling complex, occurs frequently in cancer, including 40% of clear cell renal cell carcinomas (ccRCC). To identify novel therapeutic approaches to targeting PBRM1-defective cancers, we used a series of orthogonal functional genomic screens that identified PARP and ATR inhibitors as being synthetic lethal with PBRM1 deficiency. The PBRM1/PARP inhibitor synthetic lethality was recapitulated using several clinical PARP inhibitors in a series of in vitro model systems and in vivo in a xenograft model of ccRCC. In the absence of exogenous DNA damage, PBRM1-defective cells exhibited elevated levels of replication stress, micronuclei, and R-loops. PARP inhibitor exposure exacerbated these phenotypes. Quantitative mass spectrometry revealed that multiple R-loop processing factors were downregulated in PBRM1-defective tumor cells. Exogenous expression of the R-loop resolution enzyme RNase H1 reversed the sensitivity of PBRM1-deficient cells to PARP inhibitors, suggesting that excessive levels of R-loops could be a cause of this synthetic lethality. PARP and ATR inhibitors also induced cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) innate immune signaling in PBRM1-defective tumor cells. Overall, these findings provide the preclinical basis for using PARP inhibitors in PBRM1-defective cancers. SIGNIFICANCE: This study demonstrates that PARP and ATR inhibitors are synthetic lethal with the loss of PBRM1, a PBAF-specific subunit, thus providing the rationale for assessing these inhibitors in patients with PBRM1-defective cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/11/2888/F1.large.jpg.
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MESH Headings
- Animals
- Apoptosis
- Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Renal Cell/drug therapy
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cell Proliferation
- DNA Repair
- DNA-Binding Proteins/deficiency
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Kidney Neoplasms/drug therapy
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Synthetic Lethal Mutations
- Transcription Factors/deficiency
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Roman M Chabanon
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Daphné Morel
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
| | - Thomas Eychenne
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Léo Colmet-Daage
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nicolas Dorvault
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Marlène Garrido
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Cornelia Meisenberg
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | | | - Carine Ngo
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Suzanna R Hopkins
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | | | - Samuel Jouny
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Clémence Hénon
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | | | - Clémence Astier
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Asha Konde
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Department of Translational Research, The Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | | | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Raphaël Margueron
- Institut Curie, PSL Research University, INSERM Unit U934, CNRS UMR 3215, Paris, France
| | - Jyoti S Choudhary
- Functional Proteomics Team, The Institute of Cancer Research, London, United Kingdom
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, UMR 3664, Equipe Labellisée Ligue contre le Cancer, Paris, France
- Sorbonne Universités, UPMC Université Paris-VI, CNRS, UMR3664, Paris, France
| | - Jean-Charles Soria
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
| | - Eric Deutsch
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
- INSERM UMR1030 Molecular Radiotherapy and Therapeutic Innovations, Gustave Roussy, Villejuif, France
| | - Jessica A Downs
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, London, United Kingdom
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom.
| | - Sophie Postel-Vinay
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France.
- Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
- Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
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16
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Boyd JC, Pinheiro A, Del Nery E, Reyal F, Walter T. Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen. Bioinformatics 2020; 36:1607-1613. [PMID: 31608933 PMCID: PMC7058179 DOI: 10.1093/bioinformatics/btz774] [Citation(s) in RCA: 6] [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: 06/04/2019] [Revised: 09/13/2019] [Accepted: 10/08/2019] [Indexed: 11/30/2022] Open
Abstract
Motivation High-content screening is an important tool in drug discovery and characterization. Often, high-content drug screens are performed on one single-cell line. Yet, a single-cell line cannot be thought of as a perfect disease model. Many diseases feature an important molecular heterogeneity. Consequently, a drug may be effective against one molecular subtype of a disease, but less so against another. To characterize drugs with respect to their effect not only on one cell line but on a panel of cell lines is therefore a promising strategy to streamline the drug discovery process. Results The contribution of this article is 2-fold. First, we investigate whether we can predict drug mechanism of action (MOA) at the molecular level without optimization of the MOA classes to the screen specificities. To this end, we benchmark a set of algorithms within a conventional pipeline, and evaluate their MOA prediction performance according to a statistically rigorous framework. Second, we extend this conventional pipeline to the simultaneous analysis of multiple cell lines, each manifesting potentially different morphological baselines. For this, we propose multi-task autoencoders, including a domain-adaptive model used to construct domain-invariant feature representations across cell lines. We apply these methods to a pilot screen of two triple negative breast cancer cell lines as models for two different molecular subtypes of the disease. Availability and implementation https://github.com/jcboyd/multi-cell-line or https://zenodo.org/record/2677923. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joseph C Boyd
- CBIO - Centre de Bio-Informatique, MINES ParisTech, PSL Research University, Paris 75006, France.,Institut Curie, Paris Cedex 75248.,INSERM U900, Paris Cedex 75248
| | - Alice Pinheiro
- Institut Curie, Paris Cedex 75248.,INSERM U932, Paris Cedex 75248, France
| | - Elaine Del Nery
- Institut Curie, Paris Cedex 75248.,INSERM U932, Paris Cedex 75248, France
| | - Fabien Reyal
- Institut Curie, Paris Cedex 75248.,INSERM U932, Paris Cedex 75248, France
| | - Thomas Walter
- CBIO - Centre de Bio-Informatique, MINES ParisTech, PSL Research University, Paris 75006, France.,Institut Curie, Paris Cedex 75248.,INSERM U900, Paris Cedex 75248
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17
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Kozik P, Gros M, Itzhak DN, Joannas L, Heurtebise-Chrétien S, Krawczyk PA, Rodríguez-Silvestre P, Alloatti A, Magalhaes JG, Del Nery E, Borner GHH, Amigorena S. Small Molecule Enhancers of Endosome-to-Cytosol Import Augment Anti-tumor Immunity. Cell Rep 2020; 32:107905. [PMID: 32668257 PMCID: PMC7370168 DOI: 10.1016/j.celrep.2020.107905] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 05/15/2020] [Accepted: 06/24/2020] [Indexed: 12/18/2022] Open
Abstract
Cross-presentation of antigens by dendritic cells (DCs) is critical for initiation of anti-tumor immune responses. Yet, key steps involved in trafficking of antigens taken up by DCs remain incompletely understood. Here, we screen 700 US Food and Drug Administration (FDA)-approved drugs and identify 37 enhancers of antigen import from endolysosomes into the cytosol. To reveal their mechanism of action, we generate proteomic organellar maps of control and drug-treated DCs (focusing on two compounds, prazosin and tamoxifen). By combining organellar mapping, quantitative proteomics, and microscopy, we conclude that import enhancers undergo lysosomal trapping leading to membrane permeation and antigen release. Enhancing antigen import facilitates cross-presentation of soluble and cell-associated antigens. Systemic administration of prazosin leads to reduced growth of MC38 tumors and to a synergistic effect with checkpoint immunotherapy in a melanoma model. Thus, inefficient antigen import into the cytosol limits antigen cross-presentation, restraining the potency of anti-tumor immune responses and efficacy of checkpoint blockers.
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Affiliation(s)
- Patrycja Kozik
- INSERM U932, PSL Research University, Institut Curie, 75005 Paris, France; MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
| | - Marine Gros
- INSERM U932, PSL Research University, Institut Curie, 75005 Paris, France
| | - Daniel N Itzhak
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Leonel Joannas
- INSERM U932, PSL Research University, Institut Curie, 75005 Paris, France
| | | | | | | | - Andrés Alloatti
- INSERM U932, PSL Research University, Institut Curie, 75005 Paris, France
| | | | - Elaine Del Nery
- Institut Curie, PSL Research University, Department of Translational Research-Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), 75005 Paris, France
| | - Georg H H Borner
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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18
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Boncompain G, Gareil N, Tessier S, Lescure A, Jones TR, Kepp O, Kroemer G, Del Nery E, Perez F. BML-265 and Tyrphostin AG1478 Disperse the Golgi Apparatus and Abolish Protein Transport in Human Cells. Front Cell Dev Biol 2019; 7:232. [PMID: 31681765 PMCID: PMC6797785 DOI: 10.3389/fcell.2019.00232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 07/11/2019] [Accepted: 09/27/2019] [Indexed: 11/28/2022] Open
Abstract
The steady-state localization of Golgi-resident glycosylation enzymes in the Golgi apparatus depends on a balance between anterograde and retrograde transport. Using the Retention Using Selective Hooks (RUSH) assay and high-content screening, we identified small molecules that perturb the localization of Mannosidase II (ManII) used as a model cargo for Golgi resident enzymes. In particular, we found that two compounds known as EGFR tyrosine kinase inhibitors, namely BML-265 and Tyrphostin AG1478 disrupt Golgi integrity and abolish secretory protein transport of diverse cargos, thus inducing brefeldin A-like effects. Interestingly, BML-265 and Tyrphostin AG1478 affect Golgi integrity and transport in human cells but not in rodent cells. The effects of BML-265 are reversible since Golgi integrity and protein transport are quickly restored upon washout of the compounds. BML-265 and Tyrphostin AG1478 do not lead to endosomal tubulation suggesting that, contrary to brefeldin A, they do not target the trans-Golgi ARF GEF BIG1 and BIG2. They quickly induce COPI dissociation from Golgi membranes suggesting that, in addition to EGFR kinase, the cis-Golgi ARF GEF GBF1 might also be a target of these molecules. Accordingly, overexpression of GBF1 prevents the effects of BML-265 and Tyrphostin AG1478 on Golgi integrity.
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Affiliation(s)
- Gaelle Boncompain
- Dynamics of Intracellular Organization Laboratory, Institut Curie, PSL Research University, Sorbonne Université, Centre National de la Recherche Scientifique, UMR 144, Paris, France
| | - Nelly Gareil
- Dynamics of Intracellular Organization Laboratory, Institut Curie, PSL Research University, Sorbonne Université, Centre National de la Recherche Scientifique, UMR 144, Paris, France
| | - Sarah Tessier
- BioPhenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, PSL Research University, Translational Research Department, Paris, France
| | - Aurianne Lescure
- BioPhenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, PSL Research University, Translational Research Department, Paris, France
| | - Thouis R. Jones
- BioPhenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, PSL Research University, Translational Research Department, Paris, France
| | - Oliver Kepp
- Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy, Villejuif, France
| | - Guido Kroemer
- Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy, Villejuif, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Department of Women’s and Children’s Health, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | - Elaine Del Nery
- BioPhenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, PSL Research University, Translational Research Department, Paris, France
| | - Franck Perez
- Dynamics of Intracellular Organization Laboratory, Institut Curie, PSL Research University, Sorbonne Université, Centre National de la Recherche Scientifique, UMR 144, Paris, France
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19
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Boncompain G, Herit F, Tessier S, Lescure A, Del Nery E, Gestraud P, Staropoli I, Fukata Y, Fukata M, Brelot A, Niedergang F, Perez F. Targeting CCR5 trafficking to inhibit HIV-1 infection. Sci Adv 2019; 5:eaax0821. [PMID: 31663020 PMCID: PMC6795511 DOI: 10.1126/sciadv.aax0821] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/26/2019] [Indexed: 05/22/2023]
Abstract
Using a cell-based assay monitoring differential protein transport in the secretory pathway coupled to high-content screening, we have identified three molecules that specifically reduce the delivery of the major co-receptor for HIV-1, CCR5, to the plasma membrane. They have no effect on the closely related receptors CCR1 and CXCR4. These molecules are also potent in primary macrophages as they markedly decrease HIV entry. At the molecular level, two of these molecules inhibit the critical palmitoylation of CCR5 and thereby block CCR5 in the early secretory pathway. Our results open a clear therapeutics avenue based on trafficking control and demonstrate that preventing HIV infection can be performed at the level of its receptor delivery.
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Affiliation(s)
- Gaelle Boncompain
- Institut Curie, PSL Research University, Sorbonne Université, Centre National de la Recherche Scientifique, UMR 144, Dynamics of Intracellular Organization Laboratory, F-75005 Paris, France
- Corresponding author. (G.B.); (F.P.)
| | - Floriane Herit
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France
| | - Sarah Tessier
- Institut Curie, PSL Research University, Translational Department, Biophenics High-Content Screening Laboratory, F-75005 Paris, France
| | - Aurianne Lescure
- Institut Curie, PSL Research University, Translational Department, Biophenics High-Content Screening Laboratory, F-75005 Paris, France
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Translational Department, Biophenics High-Content Screening Laboratory, F-75005 Paris, France
| | - Pierre Gestraud
- Institut Curie, PSL Research University, Bioinformatics Facility, INSERM U900, F-75005 Paris, France
| | - Isabelle Staropoli
- INSERM U1108, Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, F-75015 Paris, France
| | - Yuko Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Masaki Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Anne Brelot
- INSERM U1108, Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, F-75015 Paris, France
| | | | - Franck Perez
- Institut Curie, PSL Research University, Sorbonne Université, Centre National de la Recherche Scientifique, UMR 144, Dynamics of Intracellular Organization Laboratory, F-75005 Paris, France
- Corresponding author. (G.B.); (F.P.)
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20
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Vinet M, Suresh S, Maire V, Monchecourt C, Némati F, Lesage L, Pierre F, Ye M, Lescure A, Brisson A, Meseure D, Nicolas A, Rigaill G, Marangoni E, Del Nery E, Roman-Roman S, Dubois T. Protein arginine methyltransferase 5: A novel therapeutic target for triple-negative breast cancers. Cancer Med 2019; 8:2414-2428. [PMID: 30957988 PMCID: PMC6537044 DOI: 10.1002/cam4.2114] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 12/14/2018] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 01/15/2023] Open
Abstract
TNBC is a highly heterogeneous and aggressive breast cancer subtype associated with high relapse rates, and for which no targeted therapy yet exists. Protein arginine methyltransferase 5 (PRMT5), an enzyme which catalyzes the methylation of arginines on histone and non‐histone proteins, has recently emerged as a putative target for cancer therapy. Potent and specific PRMT5 inhibitors have been developed, but the therapeutic efficacy of PRMT5 targeting in TNBC has not yet been demonstrated. Here, we examine the expression of PRMT5 in a human breast cancer cohort obtained from the Institut Curie, and evaluate the therapeutic potential of pharmacological inhibition of PRMT5 in TNBC. We find that PRMT5 mRNA and protein are expressed at comparable levels in TNBC, luminal breast tumors, and healthy mammary tissues. However, immunohistochemistry analyses reveal that PRMT5 is differentially localized in TNBC compared to other breast cancer subtypes and to normal breast tissues. PRMT5 is heterogeneously expressed in TNBC and high PRMT5 expression correlates with poor prognosis within this breast cancer subtype. Using the small‐molecule inhibitor EPZ015666, we show that PRMT5 inhibition impairs cell proliferation in a subset of TNBC cell lines. PRMT5 inhibition triggers apoptosis, regulates cell cycle progression and decreases mammosphere formation. Furthermore, EPZ015666 administration to a patient‐derived xenograft model of TNBC significantly deters tumor progression. Finally, we reveal potentiation between EGFR and PRMT5 targeting, suggestive of a beneficial combination therapy. Our findings highlight a distinctive subcellular localization of PRMT5 in TNBC, and uphold PRMT5 targeting, alone or in combination, as a relevant treatment strategy for a subset of TNBC.
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Affiliation(s)
- Mathilde Vinet
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Breast Cancer Biology Group, Institut Curie, Paris, France
| | - Samyuktha Suresh
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Breast Cancer Biology Group, Institut Curie, Paris, France
| | - Virginie Maire
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Breast Cancer Biology Group, Institut Curie, Paris, France
| | - Clarisse Monchecourt
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Breast Cancer Biology Group, Institut Curie, Paris, France
| | - Fariba Némati
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Preclinical Investigation Laboratory, Institut Curie, Paris, France
| | - Laetitia Lesage
- Platform of Investigative Pathology, Department of Pathology, Institut Curie, Paris, France
| | - Fabienne Pierre
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Breast Cancer Biology Group, Institut Curie, Paris, France.,Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, Paris, France
| | - Mengliang Ye
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Breast Cancer Biology Group, Institut Curie, Paris, France
| | - Auriane Lescure
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, Paris, France
| | - Amélie Brisson
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Breast Cancer Biology Group, Institut Curie, Paris, France
| | - Didier Meseure
- Platform of Investigative Pathology, Department of Pathology, Institut Curie, Paris, France
| | - André Nicolas
- Platform of Investigative Pathology, Department of Pathology, Institut Curie, Paris, France
| | - Guillem Rigaill
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213, UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne, Paris-Cité, Orsay, France.,Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Evry Val d'Essonne, UMR CNRS 8071, ENSIIE, USC INRA, Evry, France
| | - Elisabetta Marangoni
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Preclinical Investigation Laboratory, Institut Curie, Paris, France
| | - Elaine Del Nery
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Institut Curie, Paris, France
| | - Sergio Roman-Roman
- Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - Thierry Dubois
- Translational Research Department, Institut Curie, PSL Research University, Paris, France.,Breast Cancer Biology Group, Institut Curie, Paris, France
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21
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Capmany A, Yoshimura A, Kerdous R, Caorsi V, Lescure A, Nery ED, Coudrier E, Goud B, Schauer K. MYO1C stabilizes actin and facilitates arrival of transport carriers at the Golgi apparatus. J Cell Sci 2019; 132:jcs.225029. [DOI: 10.1242/jcs.225029] [Citation(s) in RCA: 21] [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: 09/11/2018] [Accepted: 03/01/2019] [Indexed: 12/22/2022] Open
Abstract
We aim to identify the myosin motor proteins that control trafficking at the Golgi apparatus. In addition to the known Golgi-associated myosins MYO6, MYO18A and MYH9 (myosin IIA), we identify MYO1C as a novel player at the Golgi. We demonstrate that depletion of MYO1C induces Golgi apparatus fragmentation and decompaction. MYO1C accumulates at dynamic structures around the Golgi apparatus that colocalize with Golgi-associated actin dots. MYO1C depletion leads to loss of cellular F-actin, and Golgi apparatus decompaction is also observed after the inhibition or loss of the Arp2/3 complex. We show that the functional consequences of MYO1C depletion is a delay in the arrival of incoming transport carriers, both from the anterograde and retrograde routes. We propose that MYO1C stabilizes actin at the Golgi apparatus facilitating the arrival of incoming transport carriers at the Golgi.
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Affiliation(s)
- Anahi Capmany
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
| | - Azumi Yoshimura
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
| | - Rachid Kerdous
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
| | | | - Aurianne Lescure
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Department of Translational Research, BioPhenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Department of Translational Research, BioPhenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Evelyne Coudrier
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
| | - Bruno Goud
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
| | - Kristine Schauer
- Institut Curie, PSL Research University, Molecular Mechanisms of Intracellular Transport group, 75248 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche144, 75005 Paris, France
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22
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Garrido MF, Martin NJP, Bertrand M, Gaudin C, Commo F, El Kalaany N, Al Nakouzi N, Fazli L, Del Nery E, Camonis J, Perez F, Lerondel S, Le Pape A, Compagno D, Gleave M, Loriot Y, Désaubry L, Vagner S, Fizazi K, Chauchereau A. Regulation of eIF4F Translation Initiation Complex by the Peptidyl Prolyl Isomerase FKBP7 in Taxane-resistant Prostate Cancer. Clin Cancer Res 2018; 25:710-723. [PMID: 30322877 DOI: 10.1158/1078-0432.ccr-18-0704] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/29/2018] [Accepted: 10/10/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Targeted therapies that use the signaling pathways involved in prostate cancer are required to overcome chemoresistance and improve treatment outcomes for men. Molecular chaperones play a key role in the regulation of protein homeostasis and are potential targets for overcoming chemoresistance.Experimental Design: We established 4 chemoresistant prostate cancer cell lines and used image-based high-content siRNA functional screening, based on gene-expression signature, to explore mechanisms of chemoresistance and identify new potential targets with potential roles in taxane resistance. The functional role of a new target was assessed by in vitro and in vivo silencing, and mass spectrometry analysis was used to identify its downstream effectors. RESULTS We identified FKBP7, a prolyl-peptidyl isomerase overexpressed in docetaxel-resistant and in cabazitaxel-resistant prostate cancer cells. This is the first study to characterize the function of human FKBP7 and explore its role in cancer. We discovered that FKBP7 was upregulated in human prostate cancers and its expression correlated with the recurrence observed in patients receiving docetaxel. FKBP7 silencing showed that FKBP7 is required to maintain the growth of chemoresistant cell lines and chemoresistant tumors in mice. Mass spectrometry analysis revealed that FKBP7 interacts with eIF4G, a component of the eIF4F translation initiation complex, to mediate the survival of chemoresistant cells. Using small-molecule inhibitors of eIF4A, the RNA helicase component of eIF4F, we were able to kill docetaxel- and cabazitaxel-resistant cells. CONCLUSIONS Targeting FKBP7 or the eIF4G-containing eIF4F translation initiation complex could be novel therapeutic strategies to eradicate taxane-resistant prostate cancer cells.
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Affiliation(s)
- Marine F Garrido
- Prostate Cancer Group, INSERM UMR981, Villejuif, France.,Univ Paris-Sud, UMR981, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Nicolas J-P Martin
- Prostate Cancer Group, INSERM UMR981, Villejuif, France.,Univ Paris-Sud, UMR981, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Matthieu Bertrand
- Prostate Cancer Group, INSERM UMR981, Villejuif, France.,Univ Paris-Sud, UMR981, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Catherine Gaudin
- Prostate Cancer Group, INSERM UMR981, Villejuif, France.,Univ Paris-Sud, UMR981, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Frédéric Commo
- Prostate Cancer Group, INSERM UMR981, Villejuif, France.,Univ Paris-Sud, UMR981, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Nassif El Kalaany
- Prostate Cancer Group, INSERM UMR981, Villejuif, France.,Univ Paris-Sud, UMR981, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Nader Al Nakouzi
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ladan Fazli
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Paris, France.,Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Jacques Camonis
- Institut Curie, PSL Research University, Paris, France.,Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France.,INSERM, U830, Paris, France
| | - Franck Perez
- Institut Curie, PSL Research University, Paris, France.,Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France.,CNRS, UMR144, Paris, France
| | | | | | - Daniel Compagno
- Molecular and Functional Glyco-Oncology Lab, IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales-Universidad de Buenos Aires, CABA, Argentina
| | - Martin Gleave
- Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yohann Loriot
- Prostate Cancer Group, INSERM UMR981, Villejuif, France.,Univ Paris-Sud, UMR981, Villejuif, France.,Gustave Roussy, Villejuif, France
| | | | - Stéphan Vagner
- Institut Curie, PSL Research University, Paris, France.,CNRS, UMR3348, Orsay, France
| | - Karim Fizazi
- Prostate Cancer Group, INSERM UMR981, Villejuif, France.,Univ Paris-Sud, UMR981, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Anne Chauchereau
- Prostate Cancer Group, INSERM UMR981, Villejuif, France. .,Univ Paris-Sud, UMR981, Villejuif, France.,Gustave Roussy, Villejuif, France
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23
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Gaudeau A, Lamamy V, Jaskowiak AL, Scerri X, Chanrion B, Dorval T, Nery ED, Perez F, Camonis J, Stéphan JP. Abstract 1487: Investigation of triple-negative breast cancer tumor conversion through high-content screening approaches. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1487] [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
Among Breast Cancer (BC) classification, Triple-Negative (TN) form is the most aggressive, lacking efficient and specific treatment. Our project aims at investigating the possibility to convert TNBC tumor cell lines in Estrogen Receptor (ER), Progesterone Receptor (PR) and/or Human Epidermal growth factor Receptor 2 (HER2)-positive cells using various modalities (siRNA, CRISPR-Cas9, small molecules). Our approach consists in optimizing a multi-parametric High-Content Screening (HCS) relying on phenotypic read-outs such as expression of TNBC positive and negative markers, cell behavior and viability. This poster will present our initial results, validation and future plans. This thesis project fits within a context of drug discovery, innovation, comparison of technologies and understanding of key biological processes and pathways, carried out in partnership between Servier Research Institute and Institut Curie.
Citation Format: Albane Gaudeau, Véronique Lamamy, Anne-Laure Jaskowiak, Xavier Scerri, Benjamin Chanrion, Thierry Dorval, Elaine Del Nery, Franck Perez, Jacques Camonis, Jean-Philippe Stéphan. Investigation of triple-negative breast cancer tumor conversion through high-content screening approaches [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1487.
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Affiliation(s)
| | | | | | - Xavier Scerri
- 1Servier Research Institute, Croissy-sur-Seine, France
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24
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Chauvin C, Leruste A, Tauziede-Espariat A, Andrianteranagna M, Surdez D, Lescure A, Han ZY, Anthony E, Richer W, Baulande S, Bohec M, Zaidi S, Aynaud MM, Maillot L, Masliah-Planchon J, Cairo S, Roman-Roman S, Delattre O, Del Nery E, Bourdeaut F. High-Throughput Drug Screening Identifies Pazopanib and Clofilium Tosylate as Promising Treatments for Malignant Rhabdoid Tumors. Cell Rep 2018; 21:1737-1745. [PMID: 29141209 DOI: 10.1016/j.celrep.2017.10.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 03/24/2017] [Revised: 08/08/2017] [Accepted: 10/19/2017] [Indexed: 01/25/2023] Open
Abstract
Rhabdoid tumors (RTs) are aggressive tumors of early childhood characterized by SMARCB1 inactivation. Their poor prognosis highlights an urgent need to develop new therapies. Here, we performed a high-throughput screening of approved drugs and identified broad inhibitors of tyrosine kinase receptors (RTKs), including pazopanib, and the potassium channel inhibitor clofilium tosylate (CfT), as SMARCB1-dependent candidates. Pazopanib targets were identified as PDGFRα/β and FGFR2, which were the most highly expressed RTKs in a set of primary tumors. Combined genetic inhibition of both these RTKs only partially recapitulated the effect of pazopanib, emphasizing the requirement for broad inhibition. CfT perturbed protein metabolism and endoplasmic reticulum stress and, in combination with pazopanib, induced apoptosis of RT cells in vitro. In vivo, reduction of tumor growth by pazopanib was enhanced in combination with CfT, matching the efficiency of conventional chemotherapy. These results strongly support testing pazopanib/CfT combination therapy in future clinical trials for RTs.
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Affiliation(s)
- Céline Chauvin
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, SiRIC, Laboratory of Translational Research in Pediatric Oncology, Paris 75005, France; Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France
| | - Amaury Leruste
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, SiRIC, Laboratory of Translational Research in Pediatric Oncology, Paris 75005, France; Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France
| | | | - Mamy Andrianteranagna
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, SiRIC, Laboratory of Translational Research in Pediatric Oncology, Paris 75005, France; Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France
| | - Didier Surdez
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France
| | - Aurianne Lescure
- Paris-Sciences-Lettres Research University, Institut Curie, Department of Translational Research, the Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris 75005, France
| | - Zhi-Yan Han
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, SiRIC, Laboratory of Translational Research in Pediatric Oncology, Paris 75005, France; Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France
| | - Elodie Anthony
- Paris-Sciences-Lettres Research University, Institut Curie, Department of Translational Research, the Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris 75005, France
| | - Wilfrid Richer
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, SiRIC, Laboratory of Translational Research in Pediatric Oncology, Paris 75005, France; Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France
| | - Sylvain Baulande
- Paris-Sciences-Lettres Research University, Institut Curie, Next Generation Sequencing Platform, Paris 75005, France
| | - Mylène Bohec
- Paris-Sciences-Lettres Research University, Institut Curie, Next Generation Sequencing Platform, Paris 75005, France
| | - Sakina Zaidi
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France
| | - Marie-Ming Aynaud
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France
| | - Laetitia Maillot
- Paris-Sciences-Lettres Research University, Institut Curie, Laboratory of Somatic Genetics, Paris 75005, France
| | - Julien Masliah-Planchon
- Paris-Sciences-Lettres Research University, Institut Curie, Laboratory of Somatic Genetics, Paris 75005, France
| | - Stefano Cairo
- LTTA Center, Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara 44121, Italy; XenTech, Evry 91000, France
| | - Sergio Roman-Roman
- Paris-Sciences-Lettres Research University, Institut Curie, Department of Translational Research, the Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris 75005, France
| | - Olivier Delattre
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, SiRIC, Laboratory of Translational Research in Pediatric Oncology, Paris 75005, France; Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France; Paris-Sciences-Lettres Research University, Institut Curie, Laboratory of Somatic Genetics, Paris 75005, France
| | - Elaine Del Nery
- Paris-Sciences-Lettres Research University, Institut Curie, Department of Translational Research, the Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris 75005, France
| | - Franck Bourdeaut
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, SiRIC, Laboratory of Translational Research in Pediatric Oncology, Paris 75005, France; Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France; Paris-Sciences-Lettres Research University, Institut Curie Hospital, Department of Pediatric Oncology- Adolescents and Young Adults, Paris 75005, France.
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25
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Rose F, Basu S, Rexhepaj E, Chauchereau A, Del Nery E, Genovesio A. Compound Functional Prediction Using Multiple Unrelated Morphological Profiling Assays. SLAS Technol 2017; 23:243-251. [PMID: 29100480 DOI: 10.1177/2472630317740831] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Phenotypic cell-based assays have proven to be efficient at discovering first-in-class therapeutic drugs mainly because they allow for scanning a wide spectrum of possible targets at once. However, despite compelling methodological advances, posterior identification of a compound's mechanism of action (MOA) has remained difficult and highly refractory to automated analyses. Methods such as the cell painting assay and multiplexing fluorescent dyes to reveal broadly relevant cellular components were recently suggested for MOA prediction. We demonstrated that adding fluorescent dyes to a single assay has limited impact on MOA prediction accuracy, as monitoring only the nuclei stain could reach compelling levels of accuracy. This observation suggested that multiplexed measurements are highly correlated and nuclei stain could possibly reflect the general state of the cell. We then hypothesized that combining unrelated and possibly simple cell-based assays could bring a solution that would be biologically and technically more relevant to predict a drug target than using a single assay multiplexing dyes. We show that such a combination of past screen data could rationally be reused in screening facilities to train an ensemble classifier to predict drug targets and prioritize a possibly large list of unknown compound hits at once.
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Affiliation(s)
- France Rose
- 1 Computational Bioimaging and Bioinformatics, Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Sreetama Basu
- 1 Computational Bioimaging and Bioinformatics, Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Elton Rexhepaj
- 1 Computational Bioimaging and Bioinformatics, Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, Paris, France.,2 Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France
| | - Anne Chauchereau
- 3 Prostate Cancer Group, Institut Gustave Roussy, Univ Paris-Sud, Inserm UMR981, Villejuif, France
| | - Elaine Del Nery
- 2 Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France
| | - Auguste Genovesio
- 1 Computational Bioimaging and Bioinformatics, Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, Paris, France
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26
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Horvath P, Aulner N, Bickle M, Davies AM, Nery ED, Ebner D, Montoya MC, Östling P, Pietiäinen V, Price LS, Shorte SL, Turcatti G, von Schantz C, Carragher NO. Screening out irrelevant cell-based models of disease. Nat Rev Drug Discov 2016; 15:751-769. [PMID: 27616293 DOI: 10.1038/nrd.2016.175] [Citation(s) in RCA: 313] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The common and persistent failures to translate promising preclinical drug candidates into clinical success highlight the limited effectiveness of disease models currently used in drug discovery. An apparent reluctance to explore and adopt alternative cell- and tissue-based model systems, coupled with a detachment from clinical practice during assay validation, contributes to ineffective translational research. To help address these issues and stimulate debate, here we propose a set of principles to facilitate the definition and development of disease-relevant assays, and we discuss new opportunities for exploiting the latest advances in cell-based assay technologies in drug discovery, including induced pluripotent stem cells, three-dimensional (3D) co-culture and organ-on-a-chip systems, complemented by advances in single-cell imaging and gene editing technologies. Funding to support precompetitive, multidisciplinary collaborations to develop novel preclinical models and cell-based screening technologies could have a key role in improving their clinical relevance, and ultimately increase clinical success rates.
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Affiliation(s)
- Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary; and at the Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,European Cell-Based Assays Interest Group
| | - Nathalie Aulner
- Imagopole-Citech, Institut Pasteur, Paris 75015, France.,European Cell-Based Assays Interest Group
| | - Marc Bickle
- Technology Development Studio, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.,European Cell-Based Assays Interest Group
| | - Anthony M Davies
- Translational Cell Imaging Queensland (TCIQ), Institute of Health Biomedical Innovation, Queensland University of Technology, Brisbane 4102 QLD, Australia; and The Irish National Centre for High Content Screening and Analysis, Trinity Translational Medicine Institute, Trinity College Dublin, Phase 3 Trinity Health Sciences 1.20, St James Hospital, Dublin D8, Republic of Ireland.,European Cell-Based Assays Interest Group
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Department of Translational Research, The Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), F-75005, Paris, France.,European Cell-Based Assays Interest Group
| | - Daniel Ebner
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.,European Cell-Based Assays Interest Group
| | - Maria C Montoya
- Cellomics Unit, Cell Biology &Physiology Program, Cell &Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain.,European Cell-Based Assays Interest Group
| | - Päivi Östling
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, Stockholm 17165, Sweden.,European Cell-Based Assays Interest Group
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,European Cell-Based Assays Interest Group
| | - Leo S Price
- Faculty of Science, Leiden Academic Centre for Drug Research, Toxicology, Universiteit Leiden, The Netherlands; and at OcellO, J.H Oortweg 21, 2333 CH, Leiden, The Netherlands.,European Cell-Based Assays Interest Group
| | - Spencer L Shorte
- Imagopole-Citech, Institut Pasteur, Paris 75015, France.,European Cell-Based Assays Interest Group
| | - Gerardo Turcatti
- Biomolecular Screening Facility, Swiss Federal Institute of Technology (EPFL), Lausanne CH-1015, Switzerland.,European Cell-Based Assays Interest Group
| | - Carina von Schantz
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,European Cell-Based Assays Interest Group
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK.,European Cell-Based Assays Interest Group
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Thouvenot P, Ben Yamin B, Fourrière L, Lescure A, Boudier T, Del Nery E, Chauchereau A, Goldgar DE, Houdayer C, Stoppa-Lyonnet D, Nicolas A, Millot GA. Functional Assessment of Genetic Variants with Outcomes Adapted to Clinical Decision-Making. PLoS Genet 2016; 12:e1006096. [PMID: 27272900 PMCID: PMC4894565 DOI: 10.1371/journal.pgen.1006096] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 03/14/2016] [Accepted: 05/10/2016] [Indexed: 11/22/2022] Open
Abstract
Understanding the medical effect of an ever-growing number of human variants detected is a long term challenge in genetic counseling. Functional assays, based on in vitro or in vivo evaluations of the variant effects, provide essential information, but they require robust statistical validation, as well as adapted outputs, to be implemented in the clinical decision-making process. Here, we assessed 25 pathogenic and 15 neutral missense variants of the BRCA1 breast/ovarian cancer susceptibility gene in four BRCA1 functional assays. Next, we developed a novel approach that refines the variant ranking in these functional assays. Lastly, we developed a computational system that provides a probabilistic classification of variants, adapted to clinical interpretation. Using this system, the best functional assay exhibits a variant classification accuracy estimated at 93%. Additional theoretical simulations highlight the benefit of this ready-to-use system in the classification of variants after functional assessment, which should facilitate the consideration of functional evidences in the decision-making process after genetic testing. Finally, we demonstrate the versatility of the system with the classification of siRNAs tested for human cell growth inhibition in high throughput screening. Human genetics has entered a new age with the advent of next generation sequencing. However, this great advance also comes with new concerns. Currently, the extensive use of multi-gene panels, whole exome and whole genome sequencing, is generating an ever-growing number of new DNA sequence variations detected in the disease-predisposing genes of human patients. The pathogenic or neutral status of these variants needs to be known before planning any medical act or follow-up. We show here that the status of the variants identified in the BRCA1 breast/ovarian cancer susceptibility gene can be estimated thanks to experimental systems using yeast cells and a novel computational model. Importantly, this model provides a probabilistic classification of variants, opening the possibility to integrate results from functional assays into clinical decision-making. Moreover, our computational model is directly compatible with all kinds of experimental system without any requirement for skills in statistics thanks to ready-to-use online tools. We believe that this work is a step forward in the clinical interpretation of human genetic variants.
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Affiliation(s)
- Pierre Thouvenot
- Institut Curie, PSL Research University, Paris, France
- CNRS UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Barbara Ben Yamin
- Institut Curie, PSL Research University, Paris, France
- CNRS UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Lou Fourrière
- Institut Curie, PSL Research University, Paris, France
- CNRS UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Aurianne Lescure
- Institut Curie, PSL Research University, Department of Translational Research, the Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | | | - Elaine Del Nery
- Institut Curie, PSL Research University, Department of Translational Research, the Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Anne Chauchereau
- INSERM U981, Villejuif, France
- Univ Paris-Sud, UMR981, Villejuif, France
- Institut Gustave Roussy, Villejuif, France
| | - David E. Goldgar
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Claude Houdayer
- Service de Génétique Oncologique, Institut Curie, Paris, France
- INSERM U830, Paris, France
- Université Paris Descartes, Paris, France
| | - Dominique Stoppa-Lyonnet
- Service de Génétique Oncologique, Institut Curie, Paris, France
- INSERM U830, Paris, France
- Université Paris Descartes, Paris, France
| | - Alain Nicolas
- Institut Curie, PSL Research University, Paris, France
- CNRS UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Gaël A. Millot
- Institut Curie, PSL Research University, Paris, France
- CNRS UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
- * E-mail:
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28
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Canal F, Anthony E, Lescure A, Del Nery E, Camonis J, Perez F, Ragazzon B, Perret C. A kinome siRNA screen identifies HGS as a potential target for liver cancers with oncogenic mutations in CTNNB1. BMC Cancer 2015; 15:1020. [PMID: 26715116 PMCID: PMC4696130 DOI: 10.1186/s12885-015-2037-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 01/05/2015] [Accepted: 12/20/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Aberrant activation of the Wnt/β-catenin pathway is a major and frequent event in liver cancer, but inhibition of oncogenic β-catenin signaling has proven challenging. The identification of genes that are synthetically lethal in β-catenin-activated cancer cells would provide new targets for therapeutic drug design. METHODS We transfected the parental HuH6 hepatoblastoma cell line with a doxycycline-inducible shRNA against CTNNB1 (gene coding for β-catenin) to obtain an isogenic cell line pair with or without aberrant β-catenin signaling. Using this hepatoblastoma isogenic cell line pair, we performed a human kinome-wide siRNA screen to identify synthetic lethal interactions with oncogenic CTNNB1. The phenotypic readouts of the screen were cell proliferation, cell cycle arrest and apoptosis, which were assessed by image-based analysis. In addition, apoptosis was assessed by flow cytometric experiments and immunoblotting. The potential synthetic lethal relationship between candidates genes identified in the screen and oncogenic CTNNB1 was also investigated in a different cellular context, a colorectal HCT116 isogenic cell line pair. RESULTS We first determined the experimental conditions that led to the efficient expression of shRNA against CTNNB1 and maximal reduction of β-catenin signaling activity in response to doxycycline treatment. Following high throughput screening in which 687 genes coding for kinases and proteins related to kinases (such as pseudokinases and phosphatases) were targeted, we identified 52 genes required for HuH6 survival. The silencing of five of these genes selectively impaired the viability of HuH6 cells with high β-catenin signaling: HGS, STRADA, FES, BRAF and PKMYT1. Among these candidates, HGS depletion had the strongest inhibitory effect on cell growth and led to apoptosis specifically in HuH6 with high β-catenin activity, while HuH6 with low β-catenin activity were spared. In addition, HGS was identified as a potential synthetic lethal partner of oncogenic CTNNB1 in the HCT116 colorectal isogenic cell line pair. CONCLUSIONS These results demonstrate the existence of crosstalk between β-catenin signaling and HGS. Importantly, HGS depletion specifically affected cells with uncontrolled β-catenin signaling activity in two different types of cancer (Hepatoblastoma HuH6 and colorectal HCT116), and thus may represent a new potential target for novel therapeutic strategies in liver and colorectal cancer.
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Affiliation(s)
- Frédéric Canal
- Department Development, Reproduction and Cancer, INSERM U1016, Institut Cochin, 24, rue du Faubourg Saint-Jacques, 75014, Paris, France. .,CNRS UMR8104, Paris, France. .,Université Paris Descartes, Sorbonne, Paris Cité, France. .,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France. .,Laboratoire de Génétique et Biologie Cellulaire, Université de Versailles St-Quentin en Yvelines, Montigny le Bretonneux, France.
| | - Elodie Anthony
- Department of Translational Research, the Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France.
| | - Aurianne Lescure
- Department of Translational Research, the Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France.
| | - Elaine Del Nery
- Department of Translational Research, the Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France.
| | - Jacques Camonis
- Department of Translational Research, the Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France.
| | - Franck Perez
- Department of Translational Research, the Biophenics High-Content Screening Laboratory, Institut Curie, PSL Research University, Paris, France.
| | - Bruno Ragazzon
- Department Development, Reproduction and Cancer, INSERM U1016, Institut Cochin, 24, rue du Faubourg Saint-Jacques, 75014, Paris, France. .,CNRS UMR8104, Paris, France. .,Université Paris Descartes, Sorbonne, Paris Cité, France.
| | - Christine Perret
- Department Development, Reproduction and Cancer, INSERM U1016, Institut Cochin, 24, rue du Faubourg Saint-Jacques, 75014, Paris, France. .,CNRS UMR8104, Paris, France. .,Université Paris Descartes, Sorbonne, Paris Cité, France. .,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.
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29
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Mahmood SF, Gruel N, Chapeaublanc E, Lescure A, Jones T, Reyal F, Vincent-Salomon A, Raynal V, Pierron G, Perez F, Camonis J, Del Nery E, Delattre O, Radvanyi F, Bernard-Pierrot I. A siRNA screen identifies RAD21, EIF3H, CHRAC1 and TANC2 as driver genes within the 8q23, 8q24.3 and 17q23 amplicons in breast cancer with effects on cell growth, survival and transformation. Carcinogenesis 2013; 35:670-82. [PMID: 24148822 DOI: 10.1093/carcin/bgt351] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
RNA interference has boosted the field of functional genomics, by making it possible to carry out 'loss-of-function' screens in cultured cells. Here, we performed a small interfering RNA screening, in three breast cancer cell lines, for 101 candidate driver genes overexpressed in amplified breast tumors and belonging to eight amplicons on chromosomes 8q and 17q, investigating their role in cell survival/proliferation. This screening identified eight driver genes that were amplified, overexpressed and critical for breast tumor cell proliferation or survival. They included the well-described oncogenic driver genes for the 17q12 amplicon, ERBB2 and GRB7. Four of six other candidate driver genes-RAD21 and EIF3H, both on chromosome 8q23, CHRAC1 on chromosome 8q24.3 and TANC2 on chromosome 17q23-were confirmed to be driver genes regulating the proliferation/survival of clonogenic breast cancer cells presenting an amplification of the corresponding region. Indeed, knockdown of the expression of these genes decreased cell viability, through both cell cycle arrest and apoptosis induction, and inhibited the formation of colonies in anchorage-independent conditions, in soft agar. Strategies for inhibiting the expression of these genes or the function of the proteins they encode are therefore of potential value for the treatment of breast cancers presenting amplifications of the corresponding genomic region.
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30
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Schauer K, Grossier JP, Duong T, Chapuis V, Degot S, Lescure A, Del Nery E, Goud B. A Novel Organelle Map Framework for High-Content Cell Morphology Analysis in High Throughput. ACTA ACUST UNITED AC 2013; 19:317-24. [DOI: 10.1177/1087057113497399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A screening procedure was developed that takes advantage of the cellular normalization by micropatterning and a novel quantitative organelle mapping approach that allows unbiased and automated cell morphology comparison using black-box statistical testing. Micropatterns of extracellular matrix proteins force cells to adopt a reproducible shape and distribution of intracellular compartments avoiding strong cell-to-cell variation that is a major limitation of classical culture conditions. To detect changes in cell morphology induced by compound treatment, fluorescently labeled intracellular structures from several tens of micropatterned cells were transformed into probabilistic density maps. Then, the similarity or difference between two given density maps was quantified using statistical testing that evaluates differences directly from the data without additional analysis or any subjective decision. The versatility of this organelle mapping approach for different magnifications and its performance for different cell shapes has been assessed. Density-based analysis detected changes in cell morphology due to compound treatment in a small-scale proof-of-principle screen demonstrating its compatibility with high-throughput screening. This novel tool for high-content and high-throughput cellular phenotyping can potentially be used for a wide range of applications from drug screening to careful characterization of cellular processes.
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Affiliation(s)
- Kristine Schauer
- Molecular Mechanisms of Intracellular Transport, Unité Mixte de Recherche144 Centre National de la Recherche Scientifique/Institut Curie, Paris, France
| | - Jean-Philippe Grossier
- Molecular Mechanisms of Intracellular Transport, Unité Mixte de Recherche144 Centre National de la Recherche Scientifique/Institut Curie, Paris, France
| | - Tarn Duong
- Molecular Mechanisms of Intracellular Transport, Unité Mixte de Recherche144 Centre National de la Recherche Scientifique/Institut Curie, Paris, France
- Current address: Theoretical and Applied Statistics Laboratory (LSTA), University of Paris, Paris, France
| | | | | | - Aurianne Lescure
- BioPhenics Platform, Institut Curie–Translational Research Department, Hôpital Saint Louis, Paris, France
| | - Elaine Del Nery
- BioPhenics Platform, Institut Curie–Translational Research Department, Hôpital Saint Louis, Paris, France
| | - Bruno Goud
- Molecular Mechanisms of Intracellular Transport, Unité Mixte de Recherche144 Centre National de la Recherche Scientifique/Institut Curie, Paris, France
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31
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Pauwels E, Surdez D, Stoll G, Lescure A, Del Nery E, Delattre O, Stoven V. A probabilistic model for cell population phenotyping using HCS data. PLoS One 2012; 7:e42715. [PMID: 22927936 PMCID: PMC3426525 DOI: 10.1371/journal.pone.0042715] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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: 03/19/2012] [Accepted: 07/11/2012] [Indexed: 11/18/2022] Open
Abstract
High Content Screening (HCS) platforms allow screening living cells under a wide range of experimental conditions and give access to a whole panel of cellular responses to a specific treatment. The outcome is a series of cell population images. Within these images, the heterogeneity of cellular response to the same treatment leads to a whole range of observed values for the recorded cellular features. Consequently, it is difficult to compare and interpret experiments. Moreover, the definition of phenotypic classes at a cell population level remains an open question, although this would ease experiments analyses. In the present work, we tackle these two questions. The input of the method is a series of cell population images for which segmentation and cellular phenotype classification has already been performed. We propose a probabilistic model to represent and later compare cell populations. The model is able to fully exploit the HCS-specific information: "dependence structure of population descriptors" and "within-population variability". The experiments we carried out illustrate how our model accounts for this specific information, as well as the fact that the model benefits from considering them. We underline that these features allow richer HCS data analysis than simpler methods based on single cellular feature values averaged over each well. We validate an HCS data analysis method based on control experiments. It accounts for HCS specificities that were not taken into account by previous methods but have a sound biological meaning. Biological validation of previously unknown outputs of the method constitutes a future line of work.
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Affiliation(s)
- Edouard Pauwels
- Mines ParisTech, Centre for Computational Biology, Fontainebleau Cedex, France.
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Cascone I, Selimoglu R, Ozdemir C, Del Nery E, Yeaman C, White M, Camonis J. Distinct roles of RalA and RalB in the progression of cytokinesis are supported by distinct RalGEFs. EMBO J 2008; 27:2375-87. [PMID: 18756269 DOI: 10.1038/emboj.2008.166] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2008] [Accepted: 07/31/2008] [Indexed: 01/03/2023] Open
Abstract
The Ras family G-proteins RalA and RalB make critical non-overlapping contributions to the generation of a tumorigenic regulatory network, supporting bypass of the normal restraints on both cell proliferation and survival. The Sec6/8 complex, or exocyst, has emerged as a principal direct effector complex for Ral GTPases. Here, we show that RalA and RalB support mitotic progression through mobilization of the exocyst for two spatially and kinetically distinct steps of cytokinesis. RalA is required to tether the exocyst to the cytokinetic furrow in early cytokinesis. RalB is then required for recruitment of the exocyst to the midbody of this bridge to drive abscission and completion of cytokinesis. The collaborative action of RalA and RalB is specified by discrete subcellular compartmentalization and unique pairs of RalGEF proteins that provide inputs from both Ras-family protein-dependent and protein-independent regulatory cues. This suggests that Ral GTPases integrate diverse upstream signals to choreograph multiple roles for the exocyst in mitotic progression.
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Abstract
The closely related Rab6 isoforms, Rab6A and Rab6A', have been shown to regulate vesicular trafficking within the Golgi and post-Golgi compartments, but studies using dominant active or negative mutant suggested conflicting models. Here, we report that reduction in the expression of Rab6 isoform using specific small interfering RNA reveals noticeable differences in the Rab6A and Rab6A' biological functions. Surprisingly, Rab6A seems to be largely dispensable in membrane trafficking events, whereas knocking down the expression of Rab6A' hampers the intracellular transport of the retrograde cargo marker, the Shiga Toxin B-subunit along the endocytic pathway, and causes defects in Golgi- associated protein recycling through the endoplasmic reticulum. We also showed that Rab6A' is required for cell cycle progression through mitosis and identify Ile(62) as a key residue for uncoupling Rab6A' functions in mitosis and retrograde trafficking. Thus, our work shows that Rab6A and Rab6A' perform different functions within the cell and suggests a novel role for Rab6A' as the major Rab6 isoform regulating previously described Rab6-dependent transport pathways.
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Affiliation(s)
- Elaine Del Nery
- Molecular Mechanisms of Intracellular Transport, UMR CNRS 144, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
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Miserey-Lenkei S, Couëdel-Courteille A, Del Nery E, Bardin S, Piel M, Racine V, Sibarita JB, Perez F, Bornens M, Goud B. A role for the Rab6A' GTPase in the inactivation of the Mad2-spindle checkpoint. EMBO J 2006; 25:278-89. [PMID: 16395330 PMCID: PMC1383512 DOI: 10.1038/sj.emboj.7600929] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 11/30/2005] [Indexed: 12/21/2022] Open
Abstract
The two isoforms of the Rab6 GTPase, Rab6A and Rab6A', regulate a retrograde transport route connecting early endosomes and the endoplasmic reticulum via the Golgi complex in interphasic cells. Here we report that when Rab6A' function is altered cells are unable to progress normally through mitosis. Such cells are blocked in metaphase, despite displaying a normal Golgi fragmentation and with the Mad2-spindle checkpoint activated. Furthermore, the Rab6 effector p150(Glued), a subunit of the dynein/dynactin complex, remains associated with some kinetochores. A similar phenotype was observed when GAPCenA, a GTPase-activating protein of Rab6, was depleted from cells. Our results suggest that Rab6A' likely regulates the dynamics of the dynein/dynactin complex at the kinetochores and consequently the inactivation of the Mad2-spindle checkpoint. Rab6A', through its interaction with p150(Glued) and GAPCenA, may thus participate in a pathway involved in the metaphase/anaphase transition.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Bruno Goud
- UMR 144 CNRS/IC, Institut Curie, Paris, France
- UMR 144 CNRS/Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France. Tel.: +33 1 4234 6398; Fax: +33 1 4234 6382; E-mail:
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35
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Hemerly JP, Oliveira V, Del Nery E, Morty RE, Andrews NW, Juliano MA, Juliano L. Subsite specificity (S3, S2, S1', S2' and S3') of oligopeptidase B from Trypanosoma cruzi and Trypanosoma brucei using fluorescent quenched peptides: comparative study and identification of specific carboxypeptidase activity. Biochem J 2003; 373:933-9. [PMID: 12737623 PMCID: PMC1223545 DOI: 10.1042/bj20030342] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2003] [Revised: 05/02/2003] [Accepted: 05/09/2003] [Indexed: 11/17/2022]
Abstract
We characterized the extended substrate binding site of recombinant oligopeptidase B enzymes from Trypanosoma cruzi (Tc-OP) and Trypanosoma brucei (Tb-OP), evaluating the specificity of their S3, S2, S1', S2' and S3' subsites. Five series of internally quenched fluorescent peptides based on the substrate Abz-AGGRGAQ-EDDnp [where Abz is o -aminobenzoic acid and EDDnp is N -(2,4-dinitrophenyl)ethylenediamine] were designed to contain amino acid residues with side chains of a minimum size, and each residue position of this substrate was modified. Synthetic peptides of different lengths derived from the human kininogen sequence were also examined, and peptides of up to 17 amino acids were found to be hydrolysed by Tc-OP and Tb-OP. These two oligopeptidases were essentially arginyl hydrolases, since for all peptides examined the only cleavage site was the Arg-Xaa bond. We also demonstrated that Tc-OP and Tb-OP have a very specific carboxypeptidase activity for basic amino acids, which depends on the presence of at least of a pair of basic amino acids at the C-terminal end of the substrate. The peptide with triple Arg residues (Abz-AGRRRAQ-EDDnp) was an efficient substrate for Tc-OP and Tb-OP: the Arg-Ala peptide bond was cleaved first and then two C-terminal Arg residues were successively removed. The S1' subsite seems to be an important determinant of the specificity of both enzymes, showing a preference for Tyr, Ser, Thr and Gln as hydrogen donors. The presence of these amino acids at P1' resulted in substrates that were hydrolysed with K (m) values in the sub-micromolar range. Taken together, this work supports the view that oligopeptidase B is a specialized protein-processing enzyme with a specific carboxypeptidase activity. Excellent substrates were obtained for Tb-OP and Tc-OP (Abz-AMRRTISQ-EDDnp and Abz-AHKRYSHQ-EDDnp respectively), which were hydrolysed with remarkably high k (cat) and low K (m) values.
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Affiliation(s)
- Jefferson P Hemerly
- Department of Biophysics, Escola Paulista de Medicina, Rua Três de Maio 100, São Paulo SP 04044-020, Brazil
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Matanis T, Akhmanova A, Wulf P, Del Nery E, Weide T, Stepanova T, Galjart N, Grosveld F, Goud B, De Zeeuw CI, Barnekow A, Hoogenraad CC. Bicaudal-D regulates COPI-independent Golgi-ER transport by recruiting the dynein-dynactin motor complex. Nat Cell Biol 2002; 4:986-92. [PMID: 12447383 DOI: 10.1038/ncb891] [Citation(s) in RCA: 374] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2002] [Revised: 09/12/2002] [Accepted: 10/28/2002] [Indexed: 11/09/2022]
Abstract
The small GTPase Rab6a is involved in the regulation of membrane traffic from the Golgi apparatus towards the endoplasmic reticulum (ER) in a coat complex coatomer protein I (COPI)-independent pathway. Here, we used a yeast two-hybrid approach to identify binding partners of Rab6a. In particular, we identified the dynein-dynactin-binding protein Bicaudal-D1 (BICD1), one of the two mammalian homologues of Drosophila Bicaudal-D. BICD1 and BICD2 colocalize with Rab6a on the trans-Golgi network (TGN) and on cytoplasmic vesicles, and associate with Golgi membranes in a Rab6-dependent manner. Overexpression of BICD1 enhances the recruitment of dynein-dynactin to Rab6a-containing vesicles. Conversely, overexpression of the carboxy-terminal domain of BICD, which can interact with Rab6a but not with cytoplasmic dynein, inhibits microtubule minus-end-directed movement of green fluorescent protein (GFP)-Rab6a vesicles and induces an accumulation of Rab6a and COPI-independent ER cargo in peripheral structures. These data suggest that coordinated action between Rab6a, BICD and the dynein-dynactin complex controls COPI-independent Golgi-ER transport.
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Affiliation(s)
- Theodoros Matanis
- Department of Experimental Tumorbiology, University of Muenster, Badestrasse 9, D-48149 Muenster, Germany
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Meldal M, Svendsen IB, Juliano L, Juliano MA, Nery ED, Scharfstein J. Inhibition of cruzipain visualized in a fluorescence quenched solid-phase inhibitor library assay. D-amino acid inhibitors for cruzipain, cathepsin B and cathepsin L. J Pept Sci 1998; 4:83-91. [PMID: 9620612 DOI: 10.1002/(sici)1099-1387(199804)4:2<83::aid-psc124>3.0.co;2-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [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
A PEGA-resin was derivatized with a 3:1 mixture of hydroxymethyl benzoic acid and Fmoc-Lys(Boc)-OH and the fluorogenic substrate Ac-Y(NO2)KLRFSKQK(Abz)-PEGA was assembled on the lysine using the active ester approach. Following esterification of the hydroxymethyl benzoic acid with Fmoc-Val-OH a library XXX-k/r-XXXV containing approximately 200,000 beads was assembled by split synthesis. The resulting 'one bead, two peptides' library was subjected to extensive hydrolysis with cruzipain. One hundred darker beads were isolated and the 14 most persistently dark beads were collected and sequenced. The putative inhibitor peptides and several analogues were synthesized and found to be competitive microM to nM inhibitors of cruzipain in solution. The inhibitory activity was found to be unspecific to cruzipain when compared with cathepsins B and L and specific when compared with kallikrein. One of the inhibitors was docked into the active site of cathepsin B and was found most probably to bind to the enzyme cavity in an unusual manner, owing to the inserted D-amino acid residue.
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Affiliation(s)
- M Meldal
- Carlsberg Laboratory, Valby, Copenhagen, Denmark
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Nery ED, Juliano MA, Meldal M, Svendsen I, Scharfstein J, Walmsley A, Juliano L. Characterization of the substrate specificity of the major cysteine protease (cruzipain) from Trypanosoma cruzi using a portion-mixing combinatorial library and fluorogenic peptides. Biochem J 1997; 323 ( Pt 2):427-33. [PMID: 9163334 PMCID: PMC1218337 DOI: 10.1042/bj3230427] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The substrate specificity of the major cysteinyl proteinase of the parasitic protozoan Trypanosoma cruzi (cruzipain) was investigated, by combinatorial replacement of amino acid residues at positions P5-P'5, using a fluorescent quenched solid-phase library assay. Positively charged residues appear to be a general preference in the P5-P3 and the P'5-P'3 positions, while a hydrophobic residue was always required at the P2 position. A broad range of amino acids could be accepted at the P'1 position. A clear difference in terms of specificity between cruzipain and human cathepsin L was observed for the accommodation of Pro at the P2 position. The P1 specificity was investigated by a more detailed enzyme kinetic analysis using peptidyl-MCA (where MCA is methylcoumarin amide) and Abz-peptidyl-EDDnp [where Abz is o-aminobenzoic acid and EDDnp is N-(2,4-dinitrophenyl)ethylenediamine] as substrates, and the results were compared with those obtained using human cathepsin L. Cruzipain showed a clear preference for benzyl-Cys or Arg at the P1 position. Human cathepsin L presented similar behaviour to that of cruzipain for the hydrolysis of the epsilon-NH2-Cap-Leu-Xaa-MCA (where Cap is epsilon-aminocaproyl) and Abz-Lys-Leu-Xaa-Phe-Ser-Lys-Gln-EDDnp series, whereas the mammalian enzyme was able to tolerate large P1 residues, such as phenylalanine, better than cruzipain in the latter series.
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Affiliation(s)
- E D Nery
- Department of Biophysics, Escola Paulista de Medicina, Rua Tres de Maio 100, 04044-020 São Paulo, Brazil
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