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Bastard P, Cozic N, Brion R, Gaspar N, Piperno-Neumann S, Cordero C, Leculée-Thébaud E, Gomez-Mascard A, Rédini F, Marchais A, Ikonomova R, Cleirec M, Laurence V, Rigaud C, Abbas R, Verrecchia F, Brugières L, Minard-Colin V. Prognostic value of hemogram parameters in osteosarcoma: The French OS2006 experience. Pediatr Blood Cancer 2024:e31029. [PMID: 38679845 DOI: 10.1002/pbc.31029] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 03/18/2024] [Accepted: 04/04/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND Previous studies have shown that neutrophil-to-lymphocyte (NLR) ratio at diagnosis and early lymphocytes recovery on doxorubicin-based chemotherapy, may impact the outcome in patients with osteosarcoma (OST). This study aimed to evaluate the prognostic value of hemogram parameters in patients with OST treated with high-dose methotrexate and etoposide/ifosfamide (M-EI) chemotherapy. MATERIALS AND METHODS We retrospectively analyzed the prognostic value of various hemogram parameters at diagnosis and during therapy in a large consecutive cohort of patients with OST included in the French OS2006 trial and treated with M-EI chemotherapy. RESULTS A total of 164 patients were analyzed. The median age was 14.7 years (interquartile range [IQR]: 11.7-17). Median follow-up was 5.6 years (IQR: 3.3-7.7 years). Three-year event-free survival (EFS) and overall survival (OS) were 71.5% (95% confidence interval [CI]: 64%-78%) and 86.4% (95% CI: 80%-91%), respectively. In univariate analysis, blood count parameters at diagnosis and early lymphocyte recovery at Day 14 were not found prognostic of survival outcomes. By contrast, an increase of NLR ratio at Day 1 of the first EI chemotherapy (NLR-W4) was associated with reduced OS in univariate (p = .0044) and multivariate analysis (hazards ratio [HR] = 1.3, 95% CI: 1.1-1.5; p = .002), although not with EFS. After adjustment on histological response and metastatic status, an increase of the ratio NLR-W4 of 1 was associated with an increased risk of death of 30%. CONCLUSIONS We identified NLR-W4 as a potential early biomarker for survival in patients with OST treated with M-EI chemotherapy. Further studies are required to confirm the prognostic value of NLR and better identify immune mechanisms involved in disease surveillance.
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Affiliation(s)
- Paul Bastard
- Department of Oncology for Child and Adolescents, University Paris-Saclay, Gustave Roussy, Villejuif, France
| | | | - Régis Brion
- Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers (CRCI2NA), INSERM UMR 1307, CNRS UMR 6075, Université de NantesCHU de Nantes, Nantes, France
| | - Nathalie Gaspar
- Department of Oncology for Child and Adolescents, University Paris-Saclay, Gustave Roussy, Villejuif, France
- INSERM U1015, University Paris-Saclay, Gustave Roussy, Villejuif, France
| | | | - Camille Cordero
- Pediatric Oncology Department, CHU-Hôpital de la Mère et de l'Enfant, Nantes, France
| | | | - Anne Gomez-Mascard
- Department of Pathology, CHU, IUCT-Oncopole, University of Toulouse, Eq19. ONCOSARC CRCT, UMR 1037 Inserm/UT3, ERL 5294 CNRS, Toulouse, France
| | - Françoise Rédini
- Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers (CRCI2NA), INSERM UMR 1307, CNRS UMR 6075, Université de NantesCHU de Nantes, Nantes, France
| | - Antonin Marchais
- Department of Oncology for Child and Adolescents, University Paris-Saclay, Gustave Roussy, Villejuif, France
- INSERM U1015, University Paris-Saclay, Gustave Roussy, Villejuif, France
| | | | - Morgane Cleirec
- Pediatric Oncology Department, CHU-Hôpital de la Mère et de l'Enfant, Nantes, France
| | | | - Charlotte Rigaud
- Department of Oncology for Child and Adolescents, University Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Rachid Abbas
- Biostatistics Unit, Gustave Roussy, Villejuif, France
| | - Franck Verrecchia
- Centre de Recherche en Cancérologie et Immunologie Intégrée Nantes Angers (CRCI2NA), INSERM UMR 1307, CNRS UMR 6075, Université de NantesCHU de Nantes, Nantes, France
| | - Laurence Brugières
- Department of Oncology for Child and Adolescents, University Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Véronique Minard-Colin
- Department of Oncology for Child and Adolescents, University Paris-Saclay, Gustave Roussy, Villejuif, France
- INSERM U1015, University Paris-Saclay, Gustave Roussy, Villejuif, France
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2
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Mohr A, Marques Da Costa ME, Fromigue O, Audinot B, Balde T, Droit R, Abbou S, Khneisser P, Berlanga P, Perez E, Marchais A, Gaspar N. From biology to personalized medicine: recent knowledge in Osteosarcoma. Eur J Med Genet 2024:104941. [PMID: 38677541 DOI: 10.1016/j.ejmg.2024.104941] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
High-grade osteosarcoma is the most common paediatric bone cancer. More than one third of patients relapse and die of osteosarcoma using current chemotherapeutic and surgical strategies. To improve outcomes in osteosarcoma, two crucial challenges need to be tackled: 1-the identification of hard-to-treat disease, ideally from diagnosis; 2- choosing the best combined or novel therapies to eradicate tumor cells which are resistant to current therapies leading to disease dissemination and metastasize as well as their favorable microenvironment. Genetic chaos, tumor complexity and heterogeneity render this task difficult. The development of new technologies like next generation sequencing has led to an improvement in osteosarcoma oncogenesis. This review summarizes recent biological and therapeutical advances in osteosarcoma, as well as the challenges that must be overcome in order to develop personalized medicine and new therapeutic strategies and ultimately improve patient survival.
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Affiliation(s)
- Audrey Mohr
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France
| | | | - Olivia Fromigue
- National Institute for Health and Medical Research (INSERM) U981, Gustave Roussy Institute, Villejuif, France
| | - Baptiste Audinot
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France
| | - Thierno Balde
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France
| | - Robin Droit
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France
| | - Samuel Abbou
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France; Department of Oncology for Children and Adolescents, Gustave Roussy Institute, Villejuif, France
| | - Pierre Khneisser
- Department of medical Biology and pathology, Gustave Roussy Institute, Villejuif, France
| | - Pablo Berlanga
- Department of Oncology for Children and Adolescents, Gustave Roussy Institute, Villejuif, France
| | - Esperanza Perez
- Department of Oncology for Children and Adolescents, Gustave Roussy Institute, Villejuif, France
| | - Antonin Marchais
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France
| | - Nathalie Gaspar
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy Institute, Villejuif, France; Department of Oncology for Children and Adolescents, Gustave Roussy Institute, Villejuif, France.
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3
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Lim WC, Marques Da Costa ME, Godefroy K, Jacquet E, Gragert L, Rondof W, Marchais A, Nhiri N, Dalfovo D, Viard M, Labaied N, Khan AM, Dessen P, Romanel A, Pasqualini C, Schleiermacher G, Carrington M, Zitvogel L, Scoazec JY, Geoerger B, Salmon J. Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common HLA-B and TAP transcriptional silencing across advanced pediatric solid cancers. Front Immunol 2024; 14:1265469. [PMID: 38318504 PMCID: PMC10839790 DOI: 10.3389/fimmu.2023.1265469] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/06/2023] [Indexed: 02/07/2024] Open
Abstract
The human leukocyte antigen (HLA) system is a major factor controlling cancer immunosurveillance and response to immunotherapy, yet its status in pediatric cancers remains fragmentary. We determined high-confidence HLA genotypes in 576 children, adolescents and young adults with recurrent/refractory solid tumors from the MOSCATO-01 and MAPPYACTS trials, using normal and tumor whole exome and RNA sequencing data and benchmarked algorithms. There was no evidence for narrowed HLA allelic diversity but discordant homozygosity and allele frequencies across tumor types and subtypes, such as in embryonal and alveolar rhabdomyosarcoma, neuroblastoma MYCN and 11q subtypes, and high-grade glioma, and several alleles may represent protective or susceptibility factors to specific pediatric solid cancers. There was a paucity of somatic mutations in HLA and antigen processing and presentation (APP) genes in most tumors, except in cases with mismatch repair deficiency or genetic instability. The prevalence of loss-of-heterozygosity (LOH) ranged from 5.9 to 7.7% in HLA class I and 8.0 to 16.7% in HLA class II genes, but was widely increased in osteosarcoma and glioblastoma (~15-25%), and for DRB1-DQA1-DQB1 in Ewing sarcoma (~23-28%) and low-grade glioma (~33-50%). HLA class I and HLA-DR antigen expression was assessed in 194 tumors and 44 patient-derived xenografts (PDXs) by immunochemistry, and class I and APP transcript levels quantified in PDXs by RT-qPCR. We confirmed that HLA class I antigen expression is heterogeneous in advanced pediatric solid tumors, with class I loss commonly associated with the transcriptional downregulation of HLA-B and transporter associated with antigen processing (TAP) genes, whereas class II antigen expression is scarce on tumor cells and occurs on immune infiltrating cells. Patients with tumors expressing sufficient HLA class I and TAP levels such as some glioma, osteosarcoma, Ewing sarcoma and non-rhabdomyosarcoma soft-tissue sarcoma cases may more likely benefit from T cell-based approaches, whereas strategies to upregulate HLA expression, to expand the immunopeptidome, and to target TAP-independent epitopes or possibly LOH might provide novel therapeutic opportunities in others. The consequences of HLA class II expression by immune cells remain to be established. Immunogenetic profiling should be implemented in routine to inform immunotherapy trials for precision medicine of pediatric cancers.
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Affiliation(s)
- Wan Ching Lim
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | | | - Karine Godefroy
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Loren Gragert
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Windy Rondof
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Davide Dalfovo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mathias Viard
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Nizar Labaied
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Asif M. Khan
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | - Philippe Dessen
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Claudia Pasqualini
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gudrun Schleiermacher
- INSERM U830, Recherche Translationnelle en Oncologie Pédiatrique (RTOP), and SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), PSL Research University, Institut Curie, Paris, France
| | - Mary Carrington
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, United States
| | - Laurence Zitvogel
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jean-Yves Scoazec
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Birgit Geoerger
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jerome Salmon
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
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4
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Audinot B, Drubay D, Gaspar N, Mohr A, Cordero C, Marec-Bérard P, Lervat C, Piperno-Neumann S, Jimenez M, Mansuy L, Castex MP, Revon-Riviere G, Marie-Cardine A, Berger C, Piguet C, Massau K, Job B, Moquin-Beaudry G, Le Deley MC, Tabone MD, Berlanga P, Brugières L, Crompton BD, Marchais A, Abbou S. ctDNA quantification improves estimation of outcomes in patients with high-grade osteosarcoma: a translational study from the OS2006 trial. Ann Oncol 2023:S0923-7534(23)05113-X. [PMID: 38142939 DOI: 10.1016/j.annonc.2023.12.006] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Osteosarcoma stratification relies on clinical parameters and histological response. We developed a new personalized stratification using less invasive circulating tumor DNA (ctDNA) quantification. PATIENTS AND METHODS Plasma from patients homogeneously treated in the prospective protocol OS2006, at diagnosis, before surgery and end of treatment, were sequenced using low-passage whole-genome sequencing (lpWGS) for copy number alteration detection. We developed a prediction tool including ctDNA quantification and known clinical parameters to estimate patients' individual risk of event. RESULTS ctDNA quantification at diagnosis (diagCPA) was evaluated for 183 patients of the protocol OS2006. diagCPA as a continuous variable was a major prognostic factor, independent of other clinical parameters, including metastatic status [diagCPA hazard ratio (HR) = 3.5, P = 0.002 and 3.51, P = 0.012, for progression-free survival (PFS) and overall survival (OS)]. At the time of surgery and until the end of treatment, diagCPA was also a major prognostic factor independent of histological response (diagCPA HR = 9.2, P < 0.001 and 11.6, P < 0.001, for PFS and OS). Therefore, the addition of diagCPA to metastatic status at diagnosis or poor histological response after surgery improved the prognostic stratification of patients with osteosarcoma. We developed the prediction tool PRONOS to generate individual risk estimations, showing great performance ctDNA quantification at the time of surgery and the end of treatment still required improvement to overcome the low sensitivity of lpWGS and to enable the follow-up of disease progression. CONCLUSIONS The addition of ctDNA quantification to known risk factors improves the estimation of prognosis calculated by our prediction tool PRONOS. To confirm its value, an external validation in the Sarcoma 13 trial is underway.
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Affiliation(s)
- B Audinot
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif
| | - D Drubay
- Gustave Roussy, Office of Biostatistics and Epidemiology, Université Paris-Saclay, Villejuif; Inserm, Université Paris-Saclay, CESP U1018, Oncostat, labeled Ligue Contre le Cancer, Villejuif
| | - N Gaspar
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif; Gustave Roussy Cancer Campus, Children and Adolescent Oncology Department, Villejuif; French Cancer Society (SFCE), Bordeaux
| | - A Mohr
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif
| | - C Cordero
- Pediatric Department, Institut Curie, Paris; French Cancer Society (SFCE), Bordeaux
| | - P Marec-Bérard
- Department of Oncology for Child and Adolescent, Centre Léon Bérard, Pediatric Oncology and Hematology Institute (IHOPe), Lyon; French Cancer Society (SFCE), Bordeaux
| | - C Lervat
- Department of Pediatric Oncology, Adolescents and Young Adults, Centre Oscar Lambret, Lille; French Cancer Society (SFCE), Bordeaux
| | | | - M Jimenez
- Research and Development Department, Unicancer, Paris
| | - L Mansuy
- Department of Pediatric Hematology and Oncology, Nancy University Hospital, Vandœuvre-lès-Nancy; French Cancer Society (SFCE), Bordeaux
| | - M-P Castex
- Pediatric Oncology Immunology Hematology Unit, Children's University Hospital, Toulouse; French Cancer Society (SFCE), Bordeaux
| | - G Revon-Riviere
- Department of Pediatric Hematology and Oncology, La Timone Children's Hospital, Marseille; French Cancer Society (SFCE), Bordeaux
| | - A Marie-Cardine
- Department of Pediatric Hematology and Oncology, Rouen University Hospital, Rouen; French Cancer Society (SFCE), Bordeaux
| | - C Berger
- Department of Pediatric Oncology, North Hospital, University Hospital of Saint Etienne, Saint Etienne; French Cancer Society (SFCE), Bordeaux
| | - C Piguet
- Pediatric Oncology Hematology Unit, Limoges University Hospital, Limoges; French Cancer Society (SFCE), Bordeaux
| | - K Massau
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif
| | - B Job
- National Institute for Health and Medical Research (INSERM) US23, Gustave Roussy, Villejuif
| | - G Moquin-Beaudry
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif
| | - M-C Le Deley
- Gustave Roussy, Office of Biostatistics and Epidemiology, Université Paris-Saclay, Villejuif; Clinical Research Department, Centre Oscar Lambret, Lille
| | - M-D Tabone
- Pediatric Hematology Department, Trousseau Hospital, Sorbonne Université, Paris, France; French Cancer Society (SFCE), Bordeaux
| | - P Berlanga
- Gustave Roussy Cancer Campus, Children and Adolescent Oncology Department, Villejuif; French Cancer Society (SFCE), Bordeaux
| | - L Brugières
- Gustave Roussy Cancer Campus, Children and Adolescent Oncology Department, Villejuif; French Cancer Society (SFCE), Bordeaux
| | - B D Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston; Broad Institute of Harvard and MIT, Cambridge, USA
| | - A Marchais
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif
| | - S Abbou
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, Villejuif; Gustave Roussy Cancer Campus, Children and Adolescent Oncology Department, Villejuif; French Cancer Society (SFCE), Bordeaux.
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5
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van Ewijk R, Cleirec M, Herold N, le Deley MC, van Eijkelenburg N, Boudou-Rouquette P, Risbourg S, Strauss SJ, Palmerini E, Boye K, Kager L, Hecker-Nolting S, Marchais A, Gaspar N. A systematic review of recent phase-II trials in refractory or recurrent osteosarcoma: Can we inform future trial design? Cancer Treat Rev 2023; 120:102625. [PMID: 37738712 DOI: 10.1016/j.ctrv.2023.102625] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND/OBJECTIVE To analyze changes in recurrent/refractory osteosarcoma phase II trials over time to inform future trials in this population with poor prognosis. METHODS A systematic review of trials registered on trial registries between 01/01/2017-14/02/2022. Comparison of 98 trials identified between 2003 and 2016. Publication search/analysis for both periods, last update on 01/12/2022. RESULTS Between 2017 and 2022, 71 phase-II trials met our selection criteria (19 osteosarcoma-specific trials, 14 solid tumor trials with and 38 trials without an osteosarcoma-specific stratum). The trial number increased over time: 13.9 versus 7 trials/year (p = 0.06). Monotherapy remained the predominant treatment (62% vs. 62%, p = 1). Targeted therapies were increasingly evaluated (66% vs. 41%, P = 0.001). Heterogeneity persisted in the trial characteristics. The inclusion criteria were measurable disease (75%), evaluable disease (14%), and surgical remission (11%). 82% of the trials included pediatric or adolescent patients. Biomarker-driven trials accounted for 25% of the total trials. The survival endpoint use (rather than response) slightly increased (40% versus 31%), but the study H1/H0 hypotheses remained heterogeneous. Single-arm designs predominated over multiarm trials (n = 7). Available efficacy data on 1361 osteosarcoma patients in 58 trials remained disappointing, even though 21% of these trials were considered positive, predominantly those evaluating multi-targeted kinase inhibitors. CONCLUSION Despite observed changes in trial design and an increased number of trials investigating new therapies, high heterogeneity remained with respect to patient selection, study design, primary endpoints, and statistical hypotheses in recently registered phase II trials for osteosarcoma. Continued optimization of trial design informed by a deeper biological understanding should strengthen the development of new therapies.
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Affiliation(s)
- Roelof van Ewijk
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Morgane Cleirec
- Department of Pediatric Oncology, CHU Nantes, Nantes, France
| | - Nikolas Herold
- Paediatric Oncology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden, and Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Marie-Cécile le Deley
- Unité de Méthodologie et Biostatistiques, Centre Oscar Lambret, Lille, France; Université Paris-Saclay, Université Paris-Sud, UVSQ, CESP, INSERM, U1018 ONCOSTAT, F-94085 Villejuif, France
| | | | - Pascaline Boudou-Rouquette
- Department of Medical Oncology, Cochin Hospital, Cochin Institute, INSERMU1016, Paris Cancer Institute, CARPEM, AP-HP, Paris, France
| | - Séverine Risbourg
- Unité de Méthodologie et Biostatistiques, Centre Oscar Lambret, Lille, France
| | - Sandra J Strauss
- Department of Oncology, University College London Cancer Institute, London, UK
| | - Emanuela Palmerini
- Osteoncology, Bone and Soft Tissue Sarcomas and Innovative Therapies, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Kjetil Boye
- Department of Oncology, Oslo University Hospital, Norway
| | - Leo Kager
- St. Anna Children's Hospital, Department of Pediatrics, Medical University Vienna, Vienna, Austria; St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | | | - Antonin Marchais
- Department of Oncology for Child and Adolescents, Gustave Roussy Cancer Center, Paris-Saclay University, Villejuif, France; National Institute for Health and Medical Research (INSERM) U1015, BiiOSTeam, Gustave Roussy Institute, Villejuif, France
| | - Nathalie Gaspar
- Department of Oncology for Child and Adolescents, Gustave Roussy Cancer Center, Paris-Saclay University, Villejuif, France; National Institute for Health and Medical Research (INSERM) U1015, BiiOSTeam, Gustave Roussy Institute, Villejuif, France.
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6
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Marques Da Costa ME, Zaidi S, Scoazec JY, Droit R, Lim WC, Marchais A, Salmon J, Cherkaoui S, Morscher RJ, Laurent A, Malinge S, Mercher T, Tabone-Eglinger S, Goddard I, Pflumio F, Calvo J, Redini F, Entz-Werlé N, Soriano A, Villanueva A, Cairo S, Chastagner P, Moro M, Owens C, Casanova M, Hladun-Alvaro R, Berlanga P, Daudigeos-Dubus E, Dessen P, Zitvogel L, Lacroix L, Pierron G, Delattre O, Schleiermacher G, Surdez D, Geoerger B. A biobank of pediatric patient-derived-xenograft models in cancer precision medicine trial MAPPYACTS for relapsed and refractory tumors. Commun Biol 2023; 6:949. [PMID: 37723198 PMCID: PMC10507044 DOI: 10.1038/s42003-023-05320-0] [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: 02/17/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023] Open
Abstract
Pediatric patients with recurrent and refractory cancers are in most need for new treatments. This study developed patient-derived-xenograft (PDX) models within the European MAPPYACTS cancer precision medicine trial (NCT02613962). To date, 131 PDX models were established following heterotopical and/or orthotopical implantation in immunocompromised mice: 76 sarcomas, 25 other solid tumors, 12 central nervous system tumors, 15 acute leukemias, and 3 lymphomas. PDX establishment rate was 43%. Histology, whole exome and RNA sequencing revealed a high concordance with the primary patient's tumor profile, human leukocyte-antigen characteristics and specific metabolic pathway signatures. A detailed patient molecular characterization, including specific mutations prioritized in the clinical molecular tumor boards are provided. Ninety models were shared with the IMI2 ITCC Pediatric Preclinical Proof-of-concept Platform (IMI2 ITCC-P4) for further exploitation. This PDX biobank of unique recurrent childhood cancers provides an essential support for basic and translational research and treatments development in advanced pediatric malignancies.
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Grants
- This work was supported by grants from Fondation Gustave Roussy; Fédération Enfants Cancers et Santé, Société Française de lutte contre les Cancers et les leucémies de l’Enfant et l’adolescent (SFCE), Association AREMIG and Thibault BRIET; Parrainage médecin-chercheur of Gustave Roussy; INSERM; Canceropôle Ile-de-France; Ligue Nationale Contre le Cancer (Equipe labellisée); Fondation ARC for the European projects ERA-NET on Translational Cancer Research (TRANSCAN 2) Joint Transnational Call 2014 (JTC 2014) ‘Targeting Of Resistance in PEDiatric Oncology (TORPEDO)’, ERA-NET TRANSCAN JTC 2014 (TRAN201501238), and TRANSCAN JTC 2017 (TRANS201801292); Agence Nationale de la Recherche (ANR-10-EQPX-03, Institut Curie Génomique d’Excellence (ICGex); IMI ITCC-P4 ; The Child Cancer Research Foundation (CCRF), Cancer Council Western Australia (CCWA); PAIR-Pédiatrie/CONECT-AML (INCa-ARC-LIGUE_11905 and Association Laurette Fugain), Ligue contre le cancer (Equipe labellisée, since 2016), OPALE Carnot institute; Dell; Fondation Bristol-Myers Squibb; Association Imagine for Margo; Association Manon Hope; L’Etoile de Martin; La Course de l’Espoir; M la vie avec Lisa; ADAM; Couleur Jade; Dans les pas du Géant; Courir pour Mathieu; Marabout de Ficelle; Olivier Chape; Les Bagouz à Manon; Association Hubert Gouin Enfance et Cancer; Les Amis de Claire; Kurt-und Senta Hermann Stiftung; Holcim Stiftung Wissen; Gertrud-Hagmann-Stiftung für Malignom-Forschung; Heidi Ras Grant Forschungszentrum fürs Kind; Children’s Liver Tumour European Research Network (ChiLTERN) EU H2020 projet (668596); Fundación FERO and the Rotary Clubs Barcelona Eixample, Barcelona Diagonal, Santa Coloma de Gramanet, München-Blutenburg, Sassella-Stiftung, Berger-Janser Stiftung and Krebsliga Zürich, Deutschland Gemeindienst e.V. and others from Barcelona and province, and No Limits Contra el Cáncer Infantil Association.
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Affiliation(s)
- Maria Eugénia Marques Da Costa
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Sakina Zaidi
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
| | - Jean-Yves Scoazec
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Robin Droit
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Gustave Roussy Cancer Campus, Bioinformatics Platform, AMMICA, INSERM US23/CNRS, UAR3655, Villejuif, France
| | - Wan Ching Lim
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jerome Salmon
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Sarah Cherkaoui
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Raphael J Morscher
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anouchka Laurent
- Gustave Roussy Cancer Campus, INSERM U1170, Université Paris-Saclay, Equipe labellisée Ligue Nationale Contre le Cancer, PEDIAC program, Villejuif, France
| | - Sébastien Malinge
- Gustave Roussy Cancer Campus, INSERM U1170, Université Paris-Saclay, Equipe labellisée Ligue Nationale Contre le Cancer, PEDIAC program, Villejuif, France
- Telethon Kids Institute - Cancer Centre, Perth Children's Hospital, Nedlands, WA, Australia
| | - Thomas Mercher
- Gustave Roussy Cancer Campus, INSERM U1170, Université Paris-Saclay, Equipe labellisée Ligue Nationale Contre le Cancer, PEDIAC program, Villejuif, France
| | | | - Isabelle Goddard
- Small Animal Platform, Cancer Research Center of Lyon, INSERM U1052, CNRS UMR 5286, Centre Léon Bérard, Claude Bernard Université Lyon 1, Lyon, France
| | - Francoise Pflumio
- UMR-E008 Stabilité Génétique, Cellules Souches et Radiations, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université de Paris-Université Paris-Saclay, 92260, Fontenay-aux-Roses, France
| | - Julien Calvo
- UMR-E008 Stabilité Génétique, Cellules Souches et Radiations, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université de Paris-Université Paris-Saclay, 92260, Fontenay-aux-Roses, France
| | | | - Natacha Entz-Werlé
- Pediatric Onco-Hematology Unit, University Hospital of Strasbourg, Strasbourg, UMR CNRS 7021, team tumoral signaling and therapeutic targets, University of Strasbourg, Faculty of Pharmacy, Illkirch, France
| | - Aroa Soriano
- Vall d'Hebron Research Institute (VHIR), Childhood Cancer and Blood Disorders Research Group, Division of Pediatric Hematology and Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Alberto Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Xenopat SL, Parc Cientific de Barcelona (PCB), Barcelona, Spain
| | | | - Pascal Chastagner
- Children University Hospital, Vandoeuvre‑lès‑Nancy, University of Nancy, Nancy, France
| | - Massimo Moro
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Cormac Owens
- Paediatric Haematology/Oncology, Children's Health Ireland, Crumlin, Dublin, Republic of Ireland
| | | | - Raquel Hladun-Alvaro
- Vall d'Hebron Research Institute (VHIR), Childhood Cancer and Blood Disorders Research Group, Division of Pediatric Hematology and Oncology, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Pablo Berlanga
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | | | - Philippe Dessen
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Gustave Roussy Cancer Campus, Bioinformatics Platform, AMMICA, INSERM US23/CNRS, UAR3655, Villejuif, France
| | - Laurence Zitvogel
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Ludovic Lacroix
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Paris, France
| | - Olivier Delattre
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Paris, France
- SiRIC RTOP (Recherche Translationnelle en Oncologie Pédiatrique); Translational Research Department, Institut Curie Research Center, PSL Research University, Institut Curie, Paris, France
| | - Gudrun Schleiermacher
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- SiRIC RTOP (Recherche Translationnelle en Oncologie Pédiatrique); Translational Research Department, Institut Curie Research Center, PSL Research University, Institut Curie, Paris, France
| | - Didier Surdez
- INSERM U830, Equipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Centre, Institut Curie Research Centre, Paris, France
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland
| | - Birgit Geoerger
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France.
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da Costa MEM, Droit R, Khneisser P, Gomez-Brouchet A, Adam-de-Beaumais T, Nolla M, Signolles N, Torrejon J, Lombard B, Loew D, Ayrault O, Scoazec JY, Geoerger B, Vassal G, Marchais A, Gaspar N. Longitudinal characterization of primary osteosarcoma and derived subcutaneous and orthotopic relapsed patient-derived xenograft models. Front Oncol 2023; 13:1166063. [PMID: 37377921 PMCID: PMC10291137 DOI: 10.3389/fonc.2023.1166063] [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: 02/14/2023] [Accepted: 04/25/2023] [Indexed: 06/29/2023] Open
Abstract
Osteosarcoma is a rare bone cancer in adolescents and young adults with a dismal prognosis because of metastatic disease and chemoresistance. Despite multiple clinical trials, no improvement in outcome has occurred in decades. There is an urgent need to better understand resistant and metastatic disease and to generate in vivo models from relapsed tumors. We developed eight new patient-derived xenograft (PDX) subcutaneous and orthotopic/paratibial models derived from patients with recurrent osteosarcoma and compared the genetic and transcriptomic landscapes of the disease progression at diagnosis and relapse with the matching PDX. Whole exome sequencing showed that driver and copy-number alterations are conserved from diagnosis to relapse, with the emergence of somatic alterations of genes mostly involved in DNA repair, cell cycle checkpoints, and chromosome organization. All PDX patients conserve most of the genetic alterations identified at relapse. At the transcriptomic level, tumor cells maintain their ossification, chondrocytic, and trans-differentiation programs during progression and implantation in PDX models, as identified at the radiological and histological levels. A more complex phenotype, like the interaction with immune cells and osteoclasts or cancer testis antigen expression, seemed conserved and was hardly identifiable by histology. Despite NSG mouse immunodeficiency, four of the PDX models partially reconstructed the vascular and immune-microenvironment observed in patients, among which the macrophagic TREM2/TYROBP axis expression, recently linked to immunosuppression. Our multimodal analysis of osteosarcoma progression and PDX models is a valuable resource to understand resistance and metastatic spread mechanisms, as well as for the exploration of novel therapeutic strategies for advanced osteosarcoma.
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Affiliation(s)
- Maria Eugenia Marques da Costa
- INSERM U1015, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Robin Droit
- INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Pierre Khneisser
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Anne Gomez-Brouchet
- Department of Pathology, IUCT-Oncopole, CHU Toulouse and University Toulouse, Pharmacology and Structural Biology Institute, CNRS UMR5089, Toulouse, France
| | - Tiphaine Adam-de-Beaumais
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Marie Nolla
- Department of Pediatric Hemato-oncology, CHU Toulouse, Toulouse, France
| | - Nicolas Signolles
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Jacob Torrejon
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM, Orsay, France
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France
- Université Paris Sud, Université Paris-Saclay, CNRS UMR, INSERM, Orsay, France
| | - Jean-Yves Scoazec
- Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Birgit Geoerger
- INSERM U1015, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gilles Vassal
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Nathalie Gaspar
- INSERM U1015, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
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Moquin-Beaudry G, da Costa MEM, Gaspar N, Marchais A. Unlocking the potential of molecular-driven stratification for osteosarcoma treatment and prognosis. Oncotarget 2023; 14:132. [PMID: 36780321 PMCID: PMC9924824 DOI: 10.18632/oncotarget.28364] [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: 02/13/2023] Open
Affiliation(s)
| | | | | | - Antonin Marchais
- Correspondence to:Antonin Marchais, INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif 94805, France; Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif 94805, France email
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9
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Lai HT, Naumova N, Marchais A, Gaspar N, Geoerger B, Brenner C. Insight into the interplay between mitochondria-regulated cell death and energetic metabolism in osteosarcoma. Front Cell Dev Biol 2022; 10:948097. [PMID: 36072341 PMCID: PMC9441498 DOI: 10.3389/fcell.2022.948097] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 05/19/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Osteosarcoma (OS) is a pediatric malignant bone tumor that predominantly affects adolescent and young adults. It has high risk for relapse and over the last four decades no improvement of prognosis was achieved. It is therefore crucial to identify new drug candidates for OS treatment to combat drug resistance, limit relapse, and stop metastatic spread. Two acquired hallmarks of cancer cells, mitochondria-related regulated cell death (RCD) and metabolism are intimately connected. Both have been shown to be dysregulated in OS, making them attractive targets for novel treatment. Promising OS treatment strategies focus on promoting RCD by targeting key molecular actors in metabolic reprogramming. The exact interplay in OS, however, has not been systematically analyzed. We therefore review these aspects by synthesizing current knowledge in apoptosis, ferroptosis, necroptosis, pyroptosis, and autophagy in OS. Additionally, we outline an overview of mitochondrial function and metabolic profiles in different preclinical OS models. Finally, we discuss the mechanism of action of two novel molecule combinations currently investigated in active clinical trials: metformin and the combination of ADI-PEG20, Docetaxel and Gemcitabine.
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Affiliation(s)
- Hong Toan Lai
- CNRS, Institut Gustave Roussy, Aspects métaboliques et systémiques de l’oncogénèse pour de nouvelles approches thérapeutiques, Université Paris-Saclay, Villejuif, France
| | - Nataliia Naumova
- CNRS, Institut Gustave Roussy, Aspects métaboliques et systémiques de l’oncogénèse pour de nouvelles approches thérapeutiques, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Nathalie Gaspar
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Birgit Geoerger
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Catherine Brenner
- CNRS, Institut Gustave Roussy, Aspects métaboliques et systémiques de l’oncogénèse pour de nouvelles approches thérapeutiques, Université Paris-Saclay, Villejuif, France
- *Correspondence: Catherine Brenner,
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Berlanga P, Pierron G, Lacroix L, Chicard M, Adam de Beaumais T, Marchais A, Harttrampf AC, Iddir Y, Larive A, Soriano Fernandez A, Hezam I, Chevassus C, Bernard V, Cotteret S, Scoazec JY, Gauthier A, Abbou S, Corradini N, André N, Aerts I, Thebaud E, Casanova M, Owens C, Hladun-Alvaro R, Michiels S, Delattre O, Vassal G, Schleiermacher G, Geoerger B. The European MAPPYACTS Trial: Precision Medicine Program in Pediatric and Adolescent Patients with Recurrent Malignancies. Cancer Discov 2022; 12:1266-1281. [PMID: 35292802 PMCID: PMC9394403 DOI: 10.1158/2159-8290.cd-21-1136] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [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: 08/20/2021] [Revised: 11/03/2021] [Accepted: 02/07/2022] [Indexed: 01/07/2023]
Abstract
ABSTRACT MAPPYACTS (NCT02613962) is an international prospective precision medicine trial aiming to define tumor molecular profiles in pediatric patients with recurrent/refractory malignancies in order to suggest the most adapted salvage treatment. From February 2016 to July 2020, 787 patients were included in France, Italy, Ireland, and Spain. At least one genetic alteration leading to a targeted treatment suggestion was identified in 436 patients (69%) with successful sequencing; 10% of these alterations were considered "ready for routine use." Of 356 patients with follow-up beyond 12 months, 107 (30%) received one or more matched targeted therapies-56% of them within early clinical trials-mainly in the AcSé-ESMART platform trial (NCT02813135). Overall, matched treatment resulted in a 17% objective response rate, and of those patients with ready for routine use alterations, it was 38%. In patients with extracerebral tumors, 76% of actionable alterations detected in tumor tissue were also identified in circulating cell-free DNA (cfDNA). SIGNIFICANCE MAPPYACTS underlines the feasibility of molecular profiling at cancer recurrence in children on a multicenter, international level and demonstrates benefit for patients with selected key drivers. The use of cfDNA deserves validation in prospective studies. Our study highlights the need for innovative therapeutic proof-of-concept trials that address the underlying cancer complexity. This article is highlighted in the In This Issue feature, p. 1171.
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Affiliation(s)
- Pablo Berlanga
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Service de Génétique, Hospital Group, Institut Curie, Paris, France
| | - Ludovic Lacroix
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Mathieu Chicard
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Research Center, PSL Research University, Institut Curie, Paris, France
| | - Tiphaine Adam de Beaumais
- Clinical Research Direction, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Anne C. Harttrampf
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Yasmine Iddir
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Research Center, PSL Research University, Institut Curie, Paris, France.,Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France
| | - Alicia Larive
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Campus, INSERM U1018, CESP, Université Paris-Saclay, Villejuif, France
| | - Aroa Soriano Fernandez
- Laboratory of Translational Research in Child and Adolescent Cancer, Vall d'Hebron Research Institute (VHIR)-UAB, Barcelona, Spain
| | - Imene Hezam
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Cecile Chevassus
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Campus, INSERM U1018, CESP, Université Paris-Saclay, Villejuif, France
| | - Virginie Bernard
- Institut Curie Genomics of Excellence (ICGex) Platform, Research Center, Institut Curie, Paris, France
| | - Sophie Cotteret
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jean-Yves Scoazec
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Arnaud Gauthier
- Department of Pathology, PSL Research University, Institut Curie, Paris, France
| | - Samuel Abbou
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Nadege Corradini
- Department of Pediatric Oncology, Institut d'Hematologie et d'Oncologie Pédiatrique/Centre Léon Bérard, Lyon, France
| | - Nicolas André
- Department of Pediatric Hematology and Oncology, Hôpital de La Timone, AP-HM, Marseille, France.,UMR Inserm 1068, CNRS UMR 7258, Aix Marseille Université U105, Marseille Cancer Research Center (CRCM), Marseille, France
| | - Isabelle Aerts
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France
| | - Estelle Thebaud
- Department of Pediatric Oncology, Centre Hospitalier Universitaire, Nantes, France
| | - Michela Casanova
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Cormac Owens
- Paediatric Haematology/Oncology, Children's Health Ireland, Crumlin, Dublin, Republic of Ireland
| | - Raquel Hladun-Alvaro
- Division of Paediatric Haematology and Oncology, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Stefan Michiels
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Campus, INSERM U1018, CESP, Université Paris-Saclay, Villejuif, France
| | - Olivier Delattre
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Research Center, PSL Research University, Institut Curie, Paris, France.,Institut Curie Genomics of Excellence (ICGex) Platform, Research Center, Institut Curie, Paris, France.,SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France
| | - Gilles Vassal
- Clinical Research Direction, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gudrun Schleiermacher
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Research Center, PSL Research University, Institut Curie, Paris, France.,SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,Corresponding Author: Birgit Geoerger, Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, 114 Rue Eduard Vaillant, 94805 Villejuif, France. Phone: 33-1-42-11-46-61; Fax: 33-1-42-11-52-75; E-mail:
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Carpentier H, Caty O, Le Petitcorps Y, Maire E, Marchais A, Eberling-Fux N, Couégnat G. In situ observation of the capillary infiltration of molten silicon in a SiC/SiC composite by X-ray radiography. Ann Ital Chir 2022. [DOI: 10.1016/j.jeurceramsoc.2021.12.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Marchais A, Marques Da Costa ME, Job B, Abbas R, Drubay D, Piperno-Neumann S, Fromigué O, Gomez-Brouchet A, Françoise R, Droit R, Lervat C, ENTZ-WERLE N, Pacquement H, Devoldere C, Cupissol D, Bodet D, GANDEMER V, Berger MG, Bérard PM, Jimenez M, Vassal G, Geoerger B, Brugieres L, Gaspar N. Immune infiltrate and tumor microenvironment transcriptional programs stratify pediatric osteosarcoma into prognostic groups at diagnosis. Cancer Res 2022; 82:974-985. [DOI: 10.1158/0008-5472.can-20-4189] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 07/26/2021] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
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Pfaff E, Adam de Beaumais T, Marchais A, van Tilburg CM, Blattner-Johnson M, Dirksen U, Øra I, Geoerger B, Schleiermacher G, Pfister SM, Witt O, Jones DTW, Vassal G. NTRK Alterations in Pediatric High-Risk Malignancies Identified Through European Clinical Sequencing Programs Constitute Promising Drug Targets. JCO Precis Oncol 2021; 5:450-454. [DOI: 10.1200/po.20.00417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Elke Pfaff
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - Tiphaine Adam de Beaumais
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - Antonin Marchais
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - Cornelis M. van Tilburg
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - Mirjam Blattner-Johnson
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - Uta Dirksen
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - Ingrid Øra
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - Birgit Geoerger
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - Gudrun Schleiermacher
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - Stefan M. Pfister
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - Olaf Witt
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - David T. W. Jones
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
| | - Gilles Vassal
- Elke Pfaff, MD, Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany; Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany; Tiphaine Adam de Beaumais, MD, Clinical Research Department, Gustave Roussy Cancer Center, Villejuif, France; Antonin Marchais, PhD, Bioinformatics and INSERM U1015, Gustave Roussy Cancer Center, University Paris
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Pasqualini C, Rubino J, Brard C, Cassard L, André N, Rondof W, Scoazec JY, Marchais A, Nebchi S, Boselli L, Grivel J, Aerts I, Thebaud E, Paoletti X, Minard-Colin V, Vassal G, Geoerger B. Phase II and biomarker study of programmed cell death protein 1 inhibitor nivolumab and metronomic cyclophosphamide in paediatric relapsed/refractory solid tumours: Arm G of AcSé-ESMART, a trial of the European Innovative Therapies for Children With Cancer Consortium. Eur J Cancer 2021; 150:53-62. [PMID: 33892407 DOI: 10.1016/j.ejca.2021.03.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 12/24/2020] [Revised: 02/19/2021] [Accepted: 03/15/2021] [Indexed: 11/15/2022]
Abstract
PURPOSE AcSé-ESMART is a European multicentre, proof-of-concept multiarm phase I/II platform trial in paediatric patients with relapsed/refractory cancer. Arm G assessed the activity and safety of nivolumab in combination with metronomic cyclophosphamide +/- irradiation. EXPERIMENTAL DESIGN Following a Phase II Simon two-stage design, nivolumab was administered intravenously at 3 mg/kg every 2 weeks of a 28-day cycle, oral cyclophosphamide at 25 mg/m2 twice a day, 1 week on/1 week off. The primary endpoint was objective response rate. Irradiation/radioablation of primary tumour or metastasis could be administered as per physician's choice. Biomarker evaluation was performed by tumour immunohistochemistry, whole exome and RNA sequencing, and immunophenotyping of peripheral blood by flow cytometry. RESULTS Thirteen patients were treated with a median age of 15 years (range: 5.5-19.4). The main histologies were high-grade glioma, neuroblastoma, and desmoplastic small round cell tumour (DSRCT). The safety profile was similar to those of single-agent nivolumab, albeit haematologic toxicity, mainly lymphocytopenia, was commonly reported with the addition of cyclophosphamide +/- irradiation. Two patients with DSRCT and ependymoma presented unconfirmed partial response and prolonged disease stabilisation. Low mutational load with modest intratumour CD3+ T-cell infiltration and immunosuppressive tumour microenvironment were observed in the tumour samples. Under combined treatment, no positive modulation of circulating T cells was displayed, while derived neutrophil-to-lymphocyte ratio increased. CONCLUSIONS Nivolumab in combination with cyclophosphamide was well tolerated but had limited activity in this paediatric setting. Metronomic cyclophosphamide did not modulate systemic immune response that could compensate limited T-cell infiltration and the immunosuppressive tumour microenvironment. CLINICALTRIALS. GOV IDENTIFIER NCT2813135.
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Affiliation(s)
- Claudia Pasqualini
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jonathan Rubino
- Clinical Research Direction, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Caroline Brard
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Campus, INSERM U1018, CESP, Université Paris-Saclay, Villejuif, France
| | - Lydie Cassard
- Laboratory of Immune-Monitoring in Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Nicolas André
- Department of Pediatric Oncology, Hôpital de La Timone, AP-HM, Marseille, France; UMR Inserm 1068, CNRS UMR 7258, Aix Marseille Université U105, Marseille Cancer Research Center (CRCM), Marseille, France; Metronomics Global Health Initiative, Marseille, France
| | - Windy Rondof
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jean-Yves Scoazec
- Department of Medical Biology and Pathology of Translational Research and Biobank, AMMICA, Laboratory INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Souad Nebchi
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Campus, INSERM U1018, CESP, Université Paris-Saclay, Villejuif, France
| | - Lisa Boselli
- Laboratory of Immune-Monitoring in Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jonathan Grivel
- Laboratory of Immune-Monitoring in Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Isabelle Aerts
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), Institut Curie, PSL Research University, Paris, France
| | - Estelle Thebaud
- Department of Pediatric Oncology, Centre Hospitalier Universitaire, Nantes, France
| | - Xavier Paoletti
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Campus, INSERM U1018, CESP, Université Paris-Saclay, Villejuif, France
| | - Véronique Minard-Colin
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France; INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gilles Vassal
- Clinical Research Direction, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France; INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.
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15
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Abstract
Osteosarcoma is the most common bone cancer in adolescents and young adults, but it is a rare cancer with no improvement in patient survival in the last four decades. The main problem of this bone tumor is its evolution toward lung metastatic disease, despite the current treatment strategy (chemotherapy and surgery). To further improve survival, there is a strong need for new therapies that control osteosarcoma cells with metastatic potential and their favoring tumor microenvironment (ME) from the diagnosis. However, the complexity and heterogeneity of those tumor cell genomic/epigenetic and biology, the diversity of tumor ME where it develops, the sparsity of appropriate preclinical models, and the heterogeneity of therapeutic trials have rendered the task difficult. No tumor- or ME-targeted drugs are routinely available in front-line treatment. This article presents up-to-date information from preclinical and clinical studies that were recently published or presented in recent meetings which we hope might help change the osteosarcoma treatment landscape and patient survival in the near future.
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Affiliation(s)
- Nathalie Gaspar
- Department of Oncology for Child and adolescent, Gustave Roussy cancer campus. France
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, France
| | | | | | - Robin Droit
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, France
| | - Pablo Berlanga
- Department of Oncology for Child and adolescent, Gustave Roussy cancer campus. France
| | - Antonin Marchais
- National Institute for Health and Medical Research (INSERM) U1015, Gustave Roussy, France
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16
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Raoul F, Sanchez S, Dacunka M, Nazeyrollas P, Al Amoura A, Girodet B, Mailler B, Chapoutot L, Marchais A. [Complications of coronary invasive procedures in nonagenarians: A case-control study]. Ann Cardiol Angeiol (Paris) 2020; 69:219-226. [PMID: 32800321 DOI: 10.1016/j.ancard.2020.07.008] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/21/2020] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Coronary heart disease is the leading cause of morbidity and mortality in nonagenarians, whose numbers have doubled in twenty years. In the absence of recommendations, the place of coronary invasive strategy in this population remains a therapeutic challenge and its interest as well as its risks are poorly established. The aim of our study was to evaluate the safety of coronary invasive practice in the nonagenarian population for all indications. POPULATION AND METHODS This was a monocentric case-control study conducted from January 1, 2010 to May 30, 2019. The patients included were all nonagenarians who had undergone coronary angiography at the centre hospitalier de Troyes during this period. For each patient included, two controls matched on sex, date of procedure and procedure were drawn at random. The main judgment criterion was the occurrence of immediate per- or post-procedure complications during the stay in which the procedure was performed. The main secondary outcome measures were average length of stay, occurrence of intercurrent events during the stay (nosocomial infections, confusional syndrome), and loss of autonomy. RESULTS In all, 59 nonagenarians and 118 controls were included in our study. We identified 30.5% major complications in the nonagenarians versus 10.2% in the controls (P=0.001; OR=0.26 [0.1-0.6]), with a significant difference in the occurrence of cardiogenic shock (P=0.04), heart failure (P=0.02) and ventricular rhythm disorders (P=0.04). Post-procedure acute renal failure was greater in the nonagenarians (P=0.02; OR=0.20 [0.05-1.57]). The mean length of stay was on average twice as long in the nonagenarians. CONCLUSION Nonagenarian patients are subject to more complications when undergoing coronary invasive procedures compared to patients under 75.
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Affiliation(s)
- F Raoul
- Pôle vasculaire, service de cardiologie, centre hospitalier de Troyes, 101, avenue Anatole-France, 10000 Troyes, France.
| | - S Sanchez
- Pôle territorial santé publique et performance, centre hospitalier de Troyes, 101, avenue Anatole-France, 10000 Troyes, France.
| | - M Dacunka
- Pôle vasculaire, service de cardiologie, centre hospitalier de Troyes, 101, avenue Anatole-France, 10000 Troyes, France.
| | - P Nazeyrollas
- Pôle vasculaire, service de cardiologie, centre hospitalo-universitaire de Reims, 52, avenue Cognacq-Jay, 51100 Reims, France.
| | - A Al Amoura
- Pôle vasculaire, service de cardiologie, centre hospitalier de Troyes, 101, avenue Anatole-France, 10000 Troyes, France.
| | - B Girodet
- Pôle vasculaire, service de cardiologie, centre hospitalier de Troyes, 101, avenue Anatole-France, 10000 Troyes, France.
| | - B Mailler
- Pôle vasculaire, service de cardiologie, centre hospitalier de Troyes, 101, avenue Anatole-France, 10000 Troyes, France.
| | - L Chapoutot
- Pôle vasculaire, service de cardiologie, centre hospitalier de Troyes, 101, avenue Anatole-France, 10000 Troyes, France.
| | - A Marchais
- Pôle vasculaire, service de cardiologie, centre hospitalier de Troyes, 101, avenue Anatole-France, 10000 Troyes, France.
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Jullien PE, Grob S, Marchais A, Pumplin N, Chevalier C, Bonnet DMV, Otto C, Schott G, Voinnet O. Functional characterization of Arabidopsis ARGONAUTE 3 in reproductive tissues. Plant J 2020; 103:1796-1809. [PMID: 32506562 DOI: 10.1111/tpj.14868] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/08/2020] [Accepted: 05/20/2020] [Indexed: 05/03/2023]
Abstract
Arabidopsis encodes 10 ARGONAUTE (AGO) effectors of RNA silencing, canonically loaded with either 21-22 nucleotide (nt) long small RNAs (sRNAs) to mediate post-transcriptional gene silencing (PTGS) or 24 nt sRNAs to promote RNA-directed DNA methylation. Using full-locus constructs, we characterized the expression, biochemical properties and possible modes of action of AGO3. Although AGO3 arose from a recent duplication at the AGO2 locus, their expression patterns differ drastically, with AGO2 being expressed in both male and female gametes whereas AGO3 accumulates in aerial vascular terminations and specifically in chalazal seed integuments. Accordingly, AGO3 downregulation alters gene expression in siliques. Similar to AGO2, AGO3 binds sRNAs with a strong 5' adenosine bias, but unlike Arabidopsis AGO2, it binds 24 nt sRNAs most efficiently. AGO3 immunoprecipitation experiments in siliques revealed that these sRNAs mostly correspond to genes and intergenic regions in a manner reflecting their respective accumulation from their loci of origin. AGO3 localizes to the cytoplasm and co-fractionates with polysomes to possibly mediate PTGS via translation inhibition.
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Affiliation(s)
- Pauline E Jullien
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Stefan Grob
- Department of Plant and Microbial Biology, University of Zurich and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Antonin Marchais
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Nathan Pumplin
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Clement Chevalier
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Diane M V Bonnet
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Caroline Otto
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Gregory Schott
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Olivier Voinnet
- Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zurich (ETH Zurich), Universitätstrasse 2, Zurich, 8092, Switzerland
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18
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Dacunka M, Sanchez S, Chapoutot L, Marchais A. [Impact of a Home Return Assistance Service (PRADO-IC) on the re-hospitalisation rate for heart failure patients]. Ann Cardiol Angeiol (Paris) 2019; 68:310-315. [PMID: 31471045 DOI: 10.1016/j.ancard.2019.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 06/30/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Heart failure is a public health problem. Since 2013, the National Insurance has been offering the PRADO-IC service for the return home of patients hospitalised for cardiac decompensation. The aim of this study was to assess the impact of PRADO on the rate of re-hospitalisation of patients with heart failure at the centre hospitalier de Troyes (CHT). MATERIAL AND METHODS This was a 26-month monocentric retrospective study. Patients who were hospitalised for congestive heart failure in the cardiology department of the Troyes Hospital Centre from January 1, 2017 to August 31, 2018, and discharged home with the PRADO-IC service were included in the study. The primary outcome was the assessment of the number of readmissions for heart failure, 6 months before and 6 months after inclusion in the program. Secondary outcomes were the evaluation of the number of all-cause readmissions, the average length of stay and the time to readmission. RESULTS The average number of hospitalisations for cardiac decompensation before inclusion in the PRADO decreased from 0.34 to 0.25 (P=0.53) at 6 months. The average number of all-cause hospitalisations before inclusion increased from 0.57 to 0.58 (P=0.50) at 6 months. There was no significant difference in average length of stay and time to re-admission. CONCLUSION We did not highlight the impact of PRADO on the rate of re-hospitalisation of heart failure patients.
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Affiliation(s)
- M Dacunka
- Pôle vasculaire, service de cardiologie, centre hospitalier de Troyes, 101, avenue Anatole-France, 10000 Troyes, France.
| | - S Sanchez
- Pôle information médicale évaluation performance (IMEP), centre hospitalier de Troyes, hôpitaux Champagne Sud, 101, avenue Anatole CS 10178, 10003 Troyes cedex, France.
| | - L Chapoutot
- Pôle vasculaire, service de cardiologie, centre hospitalier de Troyes, 101, avenue Anatole-France, 10000 Troyes, France.
| | - A Marchais
- Pôle vasculaire, service de cardiologie, centre hospitalier de Troyes, 101, avenue Anatole-France, 10000 Troyes, France.
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Marchais A, Chevalier C, Voinnet O. Extensive profiling in Arabidopsis reveals abundant polysome-associated 24-nt small RNAs including AGO5-dependent pseudogene-derived siRNAs. RNA 2019; 25:1098-1117. [PMID: 31138671 PMCID: PMC6800511 DOI: 10.1261/rna.069294.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 04/07/2019] [Indexed: 05/19/2023]
Abstract
In a reductionist perspective, plant silencing small (s)RNAs are often classified as mediating nuclear transcriptional gene silencing (TGS) or cytosolic posttranscriptional gene silencing (PTGS). Among the PTGS diagnostics is the association of AGOs and their sRNA cargos with the translation apparatus. In Arabidopsis, this is observed for AGO1 loaded with micro(mi)RNAs and, accordingly, translational-repression (TR) is one layer of plant miRNA action. Using AGO1:miRNA-mediated TR as a paradigm, we explored, with two unrelated polysome-isolation methods, which, among the ten Arabidopsis AGOs and numerous sRNA classes, interact with translation. We found that representatives of all three AGO-clades associate with polysomes, including the TGS-effector AGO4 and stereotypical 24-nt sRNAs that normally mediate TGS of transposons/repeats. Strikingly, approximately half of these annotated 24-nt siRNAs displayed unique matches in coding regions/introns of genes, and in pseudogenes, but not in transposons/repeats commonly found in their vicinity. Protein-coding gene-derived 24-nt sRNAs correlate with gene-body methylation. Those derived from pseudogenes belong to two main clusters defined by their parental-gene expression patterns, and are vastly enriched in AGO5, itself found on polysomes. Based on their tight expression pattern in developing and mature siliques, their biogenesis, and genomic/epigenomic features of their loci-of-origin, we discuss potential roles for these hitherto unknown polysome-enriched, pseudogene-derived siRNAs.
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Affiliation(s)
- Antonin Marchais
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
| | - Clément Chevalier
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH), 8092 Zürich, Switzerland
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20
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Marques da Costa ME, Marchais A, Gomez-Brouchet A, Job B, Assoun N, Daudigeos-Dubus E, Fromigué O, Santos C, Geoerger B, Gaspar N. In-Vitro and In-Vivo Establishment and Characterization of Bioluminescent Orthotopic Chemotherapy-Resistant Human Osteosarcoma Models in NSG Mice. Cancers (Basel) 2019; 11:cancers11070997. [PMID: 31319571 PMCID: PMC6678535 DOI: 10.3390/cancers11070997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/21/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022] Open
Abstract
Osteosarcoma, the most common bone malignancy with a peak incidence at adolescence, had no survival improvement since decades. Persistent problems are chemo-resistance and metastatic spread. We developed in-vitro osteosarcoma models resistant to chemotherapy and in-vivo bioluminescent orthotopic cell-derived-xenografts (CDX). Continuous increasing drug concentration cultures in-vitro resulted in five methotrexate (MTX)-resistant and one doxorubicin (DOXO)-resistant cell lines. Resistance persisted after drug removal except for MG-63. Different resistance mechanisms were identified, affecting drug transport and action mechanisms specific to methotrexate (RFC/SCL19A1 decrease, DHFR up-regulation) for MTX-resistant lines, or a multi-drug phenomenon (PgP up-regulation) for HOS-R/DOXO. Differential analysis of copy number abnormalities (aCGH) and gene expression (RNAseq) revealed changes of several chromosomic regions translated at transcriptomic level depending on drug and cell line, as well as different pathways implicated in invasive and metastatic potential (e.g., Fas, Metalloproteinases) and immunity (enrichment in HLA cluster genes in 6p21.3) in HOS-R/DOXO. Resistant-CDX models (HOS-R/MTX, HOS-R/DOXO and Saos-2-B-R/MTX) injected intratibially into NSG mice behaved as their parental counterpart at primary tumor site; however, they exhibited a slower growth rate and lower metastatic spread, although they retained resistance and CGH main characteristics without drug pressure. These models represent valuable tools to explore resistance mechanisms and new therapies in osteosarcoma.
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Affiliation(s)
- Maria Eugénia Marques da Costa
- National Centre for Scientific Research (CNRS), UMR8203, Gustave Roussy, 94805 Villejuif, France
- University of Paris-Saclay, 91190 Saint-Aubin, France
- University of Paris Sud, 91400 Orsay, France
- Department of Biology, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, 3810 Aveiro, Portugal
| | - Antonin Marchais
- National Centre for Scientific Research (CNRS), UMR8203, Gustave Roussy, 94805 Villejuif, France
- University of Paris-Saclay, 91190 Saint-Aubin, France
- University of Paris Sud, 91400 Orsay, France
| | - Anne Gomez-Brouchet
- IUCT-Oncopole, CHU and University of Toulouse, Pathology department, 31100 Toulouse, France
- National Centre for Scientific Research (CNRS), UMR5089, 31077 Toulouse, France
| | - Bastien Job
- National Institute for Health and Medical Research (INSERM), US23, Gustave Roussy, 94805 Villejuif, France
| | - Noémie Assoun
- National Centre for Scientific Research (CNRS), UMR8203, Gustave Roussy, 94805 Villejuif, France
- University of Paris-Saclay, 91190 Saint-Aubin, France
- University of Paris Sud, 91400 Orsay, France
| | - Estelle Daudigeos-Dubus
- National Centre for Scientific Research (CNRS), UMR8203, Gustave Roussy, 94805 Villejuif, France
- University of Paris-Saclay, 91190 Saint-Aubin, France
- University of Paris Sud, 91400 Orsay, France
| | - Olivia Fromigué
- University of Paris Sud, 91400 Orsay, France
- National Institute for Health and Medical Research (INSERM), UMR981, Gustave Roussy, 94805 Villejuif, France
| | - Conceição Santos
- Department of Biology, Faculty of Sciences, University of Porto, 4000 Porto, Portugal
| | - Birgit Geoerger
- National Centre for Scientific Research (CNRS), UMR8203, Gustave Roussy, 94805 Villejuif, France
- University of Paris-Saclay, 91190 Saint-Aubin, France
- University of Paris Sud, 91400 Orsay, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy, 94805 Villejuif, France
| | - Nathalie Gaspar
- National Centre for Scientific Research (CNRS), UMR8203, Gustave Roussy, 94805 Villejuif, France.
- University of Paris-Saclay, 91190 Saint-Aubin, France.
- University of Paris Sud, 91400 Orsay, France.
- Department of Pediatric and Adolescent Oncology, Gustave Roussy, 94805 Villejuif, France.
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21
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Gökbuget D, Pereira JA, Opitz L, Christe D, Kessler T, Marchais A, Suter U. The miRNA biogenesis pathway prevents inappropriate expression of injury response genes in developing and adult Schwann cells. Glia 2018; 66:2632-2644. [PMID: 30295958 PMCID: PMC6585637 DOI: 10.1002/glia.23516] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 12/24/2022]
Abstract
Proper function of the nervous system depends on myelination. In peripheral nerves, Schwann cells (SCs) myelinate axons and the miRNA biogenesis pathway is required for developmental myelination and myelin maintenance. However, regulatory roles of this pathway at different stages of myelination are only partially understood. We addressed the requirement of the core miRNA biogenesis pathway components Dgcr8, Drosha, and Dicer in developing and adult SCs using mouse mutants with a comparative genetics and transcriptomics approach. We found that the microprocessor components Dgcr8 and Drosha are crucial for axonal radial sorting and to establish correct SC numbers upon myelination. Transcriptome analyses revealed a requirement of the microprocessor to prevent aberrantly increased expression of injury-response genes. Those genes are predicted targets of abundant miRNAs in sciatic nerves (SNs) during developmental myelination. In agreement, Dgcr8 and Dicer are required for proper maintenance of the myelinated SC state, where abundant miRNAs in adult SNs are predicted to target injury-response genes. We conclude that the miRNA biogenesis pathway in SCs is crucial for preventing inappropriate activity of injury-response genes in developing and adult SCs.
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Affiliation(s)
- Deniz Gökbuget
- ETH Zurich, Department of BiologyInstitute of Molecular Health SciencesZurichSwitzerland
| | - Jorge A. Pereira
- ETH Zurich, Department of BiologyInstitute of Molecular Health SciencesZurichSwitzerland
| | - Lennart Opitz
- ETH Zurich/University of ZurichFunctional Genomics Center ZurichZurichSwitzerland
| | - Dominik Christe
- ETH Zurich, Department of BiologyInstitute of Molecular Health SciencesZurichSwitzerland
| | - Tobias Kessler
- ETH Zurich, Department of BiologyInstitute of Molecular Health SciencesZurichSwitzerland
| | - Antonin Marchais
- ETH Zurich, Department of BiologyInstitute of Agricultural SciencesZurichSwitzerland
| | - Ueli Suter
- ETH Zurich, Department of BiologyInstitute of Molecular Health SciencesZurichSwitzerland
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22
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de Felippes FF, Marchais A, Sarazin A, Oberlin S, Voinnet O. A single miR390 targeting event is sufficient for triggering TAS3-tasiRNA biogenesis in Arabidopsis. Nucleic Acids Res 2017; 45:5539-5554. [PMID: 28334969 PMCID: PMC5435969 DOI: 10.1093/nar/gkx119] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [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: 11/15/2016] [Accepted: 02/16/2017] [Indexed: 01/19/2023] Open
Abstract
In plants, tasiRNAs form a class of endogenous secondary siRNAs produced through the action of RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) upon microRNA-mediated cleavage of non-coding TAS RNAs. In Arabidopsis thaliana, TAS1, TAS2 and TAS4 tasiRNA production proceeds via a single cleavage event mediated by 22nt-long or/and asymmetric miRNAs in an ARGONAUTE-1 (AGO1)-dependent manner. By contrast, tasiRNA production from TAS3 seems to follow the so-called ‘two-hit’ process, where dual targeting of TAS3, specifically mediated by the 21nt-long, symmetric miR390, initiates AGO7-dependent tasiRNA production. Interestingly, features for TAS3 tasiRNA production differ in other plant species and we show here that such features also enable TAS3 tasiRNA biogenesis in Arabidopsis, and that a single miR390 targeting event is, in fact, sufficient for this process, suggesting that the ‘one-hit’ model underpins all the necessary rudiments of secondary siRNA biogenesis from plant TAS transcripts. Further results suggest that the two-hit configuration likely enhances the fidelity of tasiRNA production and, hence, the accuracy of downstream gene regulation. Finally, we show that a ‘non-cleavable one-hit’ process allows tasiRNA production from both TAS1 and TAS3 transcripts, indicating that RDR6 recruitment does not require miRNA cleavage, nor does the recruitment, as we further show, of SUPRRESSOR-OF-GENE-SILENCING-3, indispensable for tasiRNA generation.
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Affiliation(s)
- Felipe Fenselau de Felippes
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Antonin Marchais
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Alexis Sarazin
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Stefan Oberlin
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Olivier Voinnet
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
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23
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Fontaine F, Gasiorowski E, Gracia C, Ballouche M, Caillet J, Marchais A, Hajnsdorf E. The small RNA SraG participates in PNPase homeostasis. RNA 2016; 22:1560-1573. [PMID: 27495318 PMCID: PMC5029454 DOI: 10.1261/rna.055236.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/24/2016] [Indexed: 06/06/2023]
Abstract
The rpsO-pnp operon encodes ribosomal protein S15 and polynucleotide phosphorylase, a major 3'-5' exoribonuclease involved in mRNA decay in Escherichia coli The gene for the SraG small RNA is located between the coding regions of the rpsO and pnp genes, and it is transcribed in the opposite direction relative to the two genes. No function has been assigned to SraG. Multiple levels of post-transcriptional regulation have been demonstrated for the rpsO-pnp operon. Here we show that SraG is a new factor affecting pnp expression. SraG overexpression results in a reduction of pnp expression and a destabilization of pnp mRNA; in contrast, inhibition of SraG transcription results in a higher level of the pnp transcript. Furthermore, in vitro experiments indicate that SraG inhibits translation initiation of pnp Together, these observations demonstrate that SraG participates in the post-transcriptional control of pnp by a direct antisense interaction between SraG and PNPase RNAs. Our data reveal a new level of regulation in the expression of this major exoribonuclease.
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Affiliation(s)
- Fanette Fontaine
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Elise Gasiorowski
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Celine Gracia
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Mathieu Ballouche
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Joel Caillet
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Antonin Marchais
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, Université Paris Sud, 91405 Orsay, France
| | - Eliane Hajnsdorf
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
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24
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Woldemichael BT, Jawaid A, Kremer EA, Gaur N, Krol J, Marchais A, Mansuy IM. The microRNA cluster miR-183/96/182 contributes to long-term memory in a protein phosphatase 1-dependent manner. Nat Commun 2016; 7:12594. [PMID: 27558292 PMCID: PMC5007330 DOI: 10.1038/ncomms12594] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 02/12/2016] [Accepted: 07/13/2016] [Indexed: 12/24/2022] Open
Abstract
Memory formation is a complex cognitive function regulated by coordinated synaptic and nuclear processes in neurons. In mammals, it is controlled by multiple molecular activators and suppressors, including the key signalling regulator, protein phosphatase 1 (PP1). Here, we show that memory control by PP1 involves the miR-183/96/182 cluster and its selective regulation during memory formation. Inhibiting nuclear PP1 in the mouse brain, or training on an object recognition task similarly increases miR-183/96/182 expression in the hippocampus. Mimicking this increase by miR-183/96/182 overexpression enhances object memory, while knocking-down endogenous miR-183/96/182 impairs it. This effect involves the modulation of several plasticity-related genes, with HDAC9 identified as an important functional target. Further, PP1 controls miR-183/96/182 in a transcription-independent manner through the processing of their precursors. These findings provide novel evidence for a role of miRNAs in memory formation and suggest the implication of PP1 in miRNAs processing in the adult brain.
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Affiliation(s)
- Bisrat T Woldemichael
- Laboratory of Neuroepigenetics, University of Zurich/Swiss Federal Institute of Technology, Brain Research Institute, Neuroscience Center Zürich, Zurich CH-8057, Switzerland
| | - Ali Jawaid
- Laboratory of Neuroepigenetics, University of Zurich/Swiss Federal Institute of Technology, Brain Research Institute, Neuroscience Center Zürich, Zurich CH-8057, Switzerland
| | - Eloïse A Kremer
- Laboratory of Neuroepigenetics, University of Zurich/Swiss Federal Institute of Technology, Brain Research Institute, Neuroscience Center Zürich, Zurich CH-8057, Switzerland
| | - Niharika Gaur
- Laboratory of Neuroepigenetics, University of Zurich/Swiss Federal Institute of Technology, Brain Research Institute, Neuroscience Center Zürich, Zurich CH-8057, Switzerland
| | - Jacek Krol
- Friedrich Miescher Institute for Biomedical Research, Basel CH-4048, Switzerland
| | - Antonin Marchais
- Institute of Agricultural Sciences, Swiss Federal Institute of Technology, Zurich CH-8092, Switzerland
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, University of Zurich/Swiss Federal Institute of Technology, Brain Research Institute, Neuroscience Center Zürich, Zurich CH-8057, Switzerland
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Arribas-Hernández L, Marchais A, Poulsen C, Haase B, Hauptmann J, Benes V, Meister G, Brodersen P. The Slicer Activity of ARGONAUTE1 Is Required Specifically for the Phasing, Not Production, of Trans-Acting Short Interfering RNAs in Arabidopsis. Plant Cell 2016; 28:1563-80. [PMID: 27354557 PMCID: PMC4981131 DOI: 10.1105/tpc.16.00121] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/14/2016] [Accepted: 06/24/2016] [Indexed: 05/18/2023]
Abstract
ARGONAUTE1 (AGO1) mediates posttranscriptional silencing by microRNAs (miRNAs) and short interfering RNAS (siRNAs). AGO1-catalyzed RNA cleavage (slicing) represses miRNA targets, but current models also highlight the roles of slicing in formation of siRNAs and siRNA-AGO1 complexes. miRNA-guided slicing is required for biogenesis of phased, trans-acting siRNAs (tasiRNAs), whose cleaved precursor fragments are converted to double-stranded RNA by RNA-dependent RNA polymerase 6 (RDR6). In addition, unwinding of duplex siRNA bound to AGO1 requires passenger strand cleavage in vitro. In this study, we analyze how mutation of four metal ion-coordinating residues of Arabidopsis thaliana AGO1 affects slicer activity in vitro and siRNA function in vivo. We show that while all four residues are required for slicer activity, they do not contribute equally to catalysis. Moreover, passenger strand cleavage is required for assembly of active AGO1-siRNA complexes in vivo, and many AGO1-bound siRNAs are trimmed in the absence of slicer activity. Remarkably, seedlings defective in AGO1 slicer activity produce abundant siRNAs from tasiRNA loci in vivo. These siRNAs depend on RDR6 and SUPPRESSOR OF GENE SILENCING3, but unlike wild-type tasiRNAs, they are unphased. These results demonstrate that slicing is solely required for phase definition of tasiRNAs, and they strongly support recruitment of RDR6 by AGO1 rather than by cleavage fragments.
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Affiliation(s)
| | - Antonin Marchais
- Swiss Federal Institute of Technology (ETH), 8092 Zurich, Switzerland
| | - Christian Poulsen
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Bettina Haase
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Judith Hauptmann
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Vladimir Benes
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
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26
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Branscheid A, Marchais A, Schott G, Lange H, Gagliardi D, Andersen SU, Voinnet O, Brodersen P. SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis. Nucleic Acids Res 2015; 43:10975-88. [PMID: 26464441 PMCID: PMC4678812 DOI: 10.1093/nar/gkv1014] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/24/2015] [Indexed: 12/19/2022] Open
Abstract
Small regulatory RNAs are fundamental in eukaryotic and prokaryotic gene regulation. In plants, an important element of post-transcriptional control is effected by 20–24 nt microRNAs (miRNAs) and short interfering RNAs (siRNAs) bound to the ARGONAUTE1 (AGO1) protein in an RNA induced silencing complex (RISC). AGO1 may cleave target mRNAs with small RNA complementarity, but the fate of the resulting cleavage fragments remains incompletely understood. Here, we show that SKI2, SKI3 and SKI8, subunits of a cytoplasmic cofactor of the RNA exosome, are required for degradation of RISC 5′, but not 3′-cleavage fragments in Arabidopsis. In the absence of SKI2 activity, many miRNA targets produce siRNAs via the RNA-dependent RNA polymerase 6 (RDR6) pathway. These siRNAs are low-abundant, and map close to the cleavage site. In most cases, siRNAs were produced 5′ to the cleavage site, but several examples of 3′-spreading were also identified. These observations suggest that siRNAs do not simply derive from RDR6 action on stable 5′-cleavage fragments and hence that SKI2 has a direct role in limiting secondary siRNA production in addition to its function in mediating degradation of 5′-cleavage fragments.
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Affiliation(s)
- Anja Branscheid
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Antonin Marchais
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biology, LFW D17/D18, Universitätsstrasse 2, CH-8092 Zürich, Switzerland
| | - Gregory Schott
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biology, LFW D17/D18, Universitätsstrasse 2, CH-8092 Zürich, Switzerland
| | - Heike Lange
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, F-67084 Strasbourg Cedex, France
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes du CNRS, 12 Rue du Général Zimmer, F-67084 Strasbourg Cedex, France
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark
| | - Olivier Voinnet
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biology, LFW D17/D18, Universitätsstrasse 2, CH-8092 Zürich, Switzerland
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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27
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Abstract
In antiviral RNA interference (RNAi), the DICER enzyme processes virus-derived double-stranded RNA (dsRNA) into small interfering RNAs (siRNAs) that guide ARGONAUTE proteins to silence complementary viral RNA. As a counterdefense, viruses deploy viral suppressors of RNAi (VSRs). Well-established in plants and invertebrates, the existence of antiviral RNAi remains unknown in mammals. Here, we show that undifferentiated mouse cells infected with encephalomyocarditis virus (EMCV) or Nodamura virus (NoV) accumulate ~22-nucleotide RNAs with all the signature features of siRNAs. These derive from viral dsRNA replication intermediates, incorporate into AGO2, are eliminated in Dicer knockout cells, and decrease in abundance upon cell differentiation. Furthermore, genetically ablating a NoV-encoded VSR that antagonizes DICER during authentic infections reduces NoV accumulation, which is rescued in RNAi-deficient mouse cells. We conclude that antiviral RNAi operates in mammalian cells.
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Affiliation(s)
- P V Maillard
- Department of Biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zurich, Switzerland
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28
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Marí-Ordóñez A, Marchais A, Etcheverry M, Martin A, Colot V, Voinnet O. Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet 2013; 45:1029-39. [PMID: 23852169 DOI: 10.1038/ng.2703] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 06/20/2013] [Indexed: 11/09/2022]
Abstract
Transposable elements (TEs) contribute to genome size, organization and evolution. In plants, their activity is primarily controlled by transcriptional gene silencing (TGS), usually investigated at steady states, reflecting how long-established silent conditions are maintained, faithfully reiterated or temporarily modified. How active, invasive TEs are detected and silenced de novo in plants remains largely unknown. Using inbred lineages of hybrid Arabidopsis thaliana epigenomes combining wild-type and mutant chromosomes, we have deciphered the sequence of physiological and molecular events underlying the de novo invasion, proliferation and eventual demise of the single-copy endogenous retrotransposon Evadé (EVD). We show how this reconstructed TE burst causes widespread genome diversification and de novo epiallelism that could serve as sources for selectable and potentially adaptive traits.
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Affiliation(s)
- Arturo Marí-Ordóñez
- Swiss Federal Institute of Technology (ETH-Z), Department of Biology, Zurich, Switzerland
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29
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Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, Cognat V, Colot V, Voinnet O, Heard E, Ciaudo C, Barillot E. ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics 2012; 28:3147-9. [PMID: 23044543 DOI: 10.1093/bioinformatics/bts587] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
SUMMARY Non-coding RNA (ncRNA) PROfiling in small RNA (sRNA)-seq (ncPRO-seq) is a stand-alone, comprehensive and flexible ncRNA analysis pipeline. It can interrogate and perform detailed profiling analysis on sRNAs derived from annotated non-coding regions in miRBase, Rfam and RepeatMasker, as well as specific regions defined by users. The ncPRO-seq pipeline performs both gene-based and family-based analyses of sRNAs. It also has a module to identify regions significantly enriched with short reads, which cannot be classified under known ncRNA families, thus enabling the discovery of previously unknown ncRNA- or small interfering RNA (siRNA)-producing regions. The ncPRO-seq pipeline supports input read sequences in fastq, fasta and color space format, as well as alignment results in BAM format, meaning that sRNA raw data from the three current major platforms (Roche-454, Illumina-Solexa and Life technologies-SOLiD) can be analyzed with this pipeline. The ncPRO-seq pipeline can be used to analyze read and alignment data, based on any sequenced genome, including mammals and plants. AVAILABILITY Source code, annotation files, manual and online version are available at http://ncpro.curie.fr/. CONTACT bioinfo.ncproseq@curie.fr or cciaudo@ethz.ch SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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30
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Garcia D, Garcia S, Pontier D, Marchais A, Renou JP, Lagrange T, Voinnet O. Ago hook and RNA helicase motifs underpin dual roles for SDE3 in antiviral defense and silencing of nonconserved intergenic regions. Mol Cell 2012; 48:109-20. [PMID: 22940249 DOI: 10.1016/j.molcel.2012.07.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/22/2012] [Accepted: 07/25/2012] [Indexed: 10/27/2022]
Abstract
In Arabidopsis thaliana, the putative RNA-helicase SDE3 assists posttranscriptional-gene-silencing (PTGS) amplification by RNA-dependent-RNA-polymerase-6 (RDR6). SDE3 homologs in Drosophila, worm and human contribute to silence viruses, transposons or recently duplicated genes but the underlying mechanisms remain largely unknown. Here, we demonstrate that SDE3 is present with the PTGS effectors AGO1 and AGO2 in higher-order protein complexes owing to a specialized GW-repeat-containing C-terminal domain. We uncover an essential contribution of the RNA-helicase activity and a facilitating role for AGO binding in SDE3 action, which occurs downstream of RDR6. We show that these biochemical properties underpin dual roles for SDE3 in antiviral defense and, unexpectedly, in transposon silencing via a hitherto unanticipated pathway that correlates with DNA methylation, suggesting a continuum of action between PTGS and chromatin-level silencing. We identified endogenous SDE3 targets corresponding to nonconserved intergenic regions, transposons and recently evolved pseudogenes, unraveling striking functional convergences among plant and metazoan SDE3 pathways.
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Affiliation(s)
- Damien Garcia
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Strasbourg, France
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31
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Abstract
Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and cis-regulatory RNAs, from other conserved sequences. In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to identify previously undetected RNA genes or elements. Furthermore, as NAPP clusters contain both coding and non-coding sequences with similar occurrence profiles, they can be analyzed under a functional perspective. We recently improved the NAPP pipeline and applied it to a collection of 949 bacterial and 68 archaeal species. The database and web interface available at http://napp.u-psud.fr/ enable detailed analysis of NAPP clusters enriched in non-coding RNAs, graphical display of phylogenetic profiles, visualization of predicted RNAs in their genome context and extraction of predicted RNAs for use with genome browsers or other software.
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Affiliation(s)
- Alban Ott
- Institut de Génétique et Microbiologie, UMR 8621, CNRS, Université Paris Sud, bâtiment 400, 91405 Orsay Cedex, France
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32
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Marchais A, Duperrier S, Durand S, Gautheret D, Stragier P. CsfG, a sporulation-specific, small non-coding RNA highly conserved in endospore formers. RNA Biol 2011; 8:358-64. [PMID: 21532344 DOI: 10.4161/rna.8.3.14998] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Endospore formation is a characteristic shared by some Bacilli and Clostridia that involves the creation of two cell types, the forespore and the mother cell. Hundreds of protein-encoding genes have been shown to be transcribed in a cell-specific fashion during this developmental process in Bacillus subtilis. We have used a phylogenetic profiling procedure to identify clusters of B. subtilis coding and non-coding sequences that co-occur in other endospore formers. One such cluster shows a strong bias for sporulation-related genes (42 % among 156 genes) and is enriched in potential non-coding RNAs. We have studied one RNA candidate, encoded in the ylbG-ylbH interval. In vivo analysis using a transcriptional fusion to the Escherichia coli lacZ gene demonstrates that this region of the chromosome contains a gene, csfG, encoding a 147-nucleotide RNA that is transcribed only during sporulation, specifically in the forespore. csfG is present in many endospore formers, mostly Bacilli and some Clostridia, whereas it is absent from bacteria that do not produce endospores. All CsfG RNAs contain a strongly conserved, pyrimidine-rich, central motif that overlaps a potential stem-loop structure. The remarkable conservation of this sequence in widely divergent bacteria suggests that it plays a conserved physiological role, presumably by interacting with an unidentified target in the forespore, where it contributes to the acquisition of the spore properties.
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Affiliation(s)
- Antonin Marchais
- CNRS-UMR8621, Institut de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
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Naville M, Ghuillot-Gaudeffroy A, Marchais A, Gautheret D. ARNold: a web tool for the prediction of Rho-independent transcription terminators. RNA Biol 2011; 8:11-3. [PMID: 21282983 DOI: 10.4161/rna.8.1.13346] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Rho-independent termination is a major mechanism of transcriptional arrest in bacteria that controls both normal 3' termination and a wide array of regulatory attenuation events. Detecting Rho-independent terminators is an obliged step in the annotation of bacterial operons. Yet, while several efficient algorithms are available for this purpose, there is no freely available web site enabling a rapid scanning of raw genomic sequence for the presence of terminators. Here we implemented such a web server, which combines two published prediction algorithms, Erpin and RNAmotif, and performs nearly as well as more complex procedures while being accessible to the non specialist. The ARNold Web server is available at : http://rna.igmors.u-psud.fr/toolbox/arnold/
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Affiliation(s)
- Magali Naville
- Univ. Paris-Sud 11, CNRS, UMR8621, Institut de Génétique et Microbiologie, Orsay Cedex, France
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Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, Skorski P, Borezée-Durant E, Barbet R, Jacquet E, Jacq A, Gautheret D, Felden B, Vogel J, Bouloc P. Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res 2010; 38:6620-36. [PMID: 20511587 PMCID: PMC2965222 DOI: 10.1093/nar/gkq462] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Using an experimental approach, we investigated the RNome of the pathogen Staphylococcus aureus to identify 30 small RNAs (sRNAs) including 14 that are newly confirmed. Among the latter, 10 are encoded in intergenic regions, three are generated by premature transcription termination associated with riboswitch activities, and one is expressed from the complementary strand of a transposase gene. The expression of four sRNAs increases during the transition from exponential to stationary phase. We focused our study on RsaE, an sRNA that is highly conserved in the bacillales order and is deleterious when over-expressed. We show that RsaE interacts in vitro with the 5' region of opp3A mRNA, encoding an ABC transporter component, to prevent formation of the ribosomal initiation complex. A previous report showed that RsaE targets opp3B which is co-transcribed with opp3A. Thus, our results identify an unusual case of riboregulation where the same sRNA controls an operon mRNA by targeting two of its cistrons. A combination of biocomputational and transcriptional analyses revealed a remarkably coordinated RsaE-dependent downregulation of numerous metabolic enzymes involved in the citrate cycle and the folate-dependent one-carbon metabolism. As we observed that RsaE accumulates transiently in late exponential growth, we propose that RsaE functions to ensure a coordinate downregulation of the central metabolism when carbon sources become scarce.
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Affiliation(s)
- Chantal Bohn
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, IFR115, Centre scientifique d'Orsay, Université Paris-Sud, bâtiment 400, 91405 Orsay Cedex, France
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Abstract
The expression of trans-acting small RNAs in firmicutes has been poorly documented to date. This gap is being filled quickly in the genus Staphylococcus, which is both a model firmicute and an important human pathogen. Here we analyze RsaOG, a novel small RNA family specific to Staphylococcus and highly transcribed. This well conserved element, first discovered in a computational screen, was precisely mapped in the genome by RACE mapping and the identification of a putative transcriptional promoter. The proposed secondary structure presents two highly conserved unpaired sequences, part of which can form a pseudoknot. We suggest a possible involvement of the remaining conserved single stranded region in trans regulatory interactions.
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Affiliation(s)
- Antonin Marchais
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, Université Paris Sud, Orsay, France
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Marchais A, Naville M, Bohn C, Bouloc P, Gautheret D. SINGLE‐PASS CLASSIFICATION OF ALL NON‐CODING SEQUENCES IN A BACTERIAL GENOME USING PHYLOGENETIC PROFILES. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.841.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Antonin Marchais
- Institut de genetique et de microbiologieOrsayFranceMetropolitan
| | - Magali Naville
- Institut de genetique et de microbiologieOrsayFranceMetropolitan
| | - Chantal Bohn
- Institut de genetique et de microbiologieOrsayFranceMetropolitan
| | - Philippe Bouloc
- Institut de genetique et de microbiologieOrsayFranceMetropolitan
| | - Daniel Gautheret
- Institut de genetique et de microbiologieOrsayFranceMetropolitan
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Marchais A, Naville M, Bohn C, Bouloc P, Gautheret D. Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles. Genome Res 2009; 19:1084-92. [PMID: 19237465 DOI: 10.1101/gr.089714.108] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Identification and characterization of functional elements in the noncoding regions of genomes is an elusive and time-consuming activity whose output does not keep up with the pace of genome sequencing. Hundreds of bacterial genomes lay unexploited in terms of noncoding sequence analysis, although they may conceal a wide diversity of novel RNA genes, riboswitches, or other regulatory elements. We describe a strategy that exploits the entirety of available bacterial genomes to classify all noncoding elements of a selected reference species in a single pass. This method clusters noncoding elements based on their profile of presence among species. Most noncoding RNAs (ncRNAs) display specific signatures that enable their grouping in distinct clusters, away from sequence conservation noise and other elements such as promoters. We submitted 24 ncRNA candidates from Staphylococcus aureus to experimental validation and confirmed the presence of seven novel small RNAs or riboswitches. Besides offering a powerful method for de novo ncRNA identification, the analysis of phylogenetic profiles opens a new path toward the identification of functional relationships between co-evolving coding and noncoding elements.
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Affiliation(s)
- Antonin Marchais
- Université Paris-Sud 11, CNRS, UMR8621, Institut de Génétique et Microbiologie, F-91405 Orsay Cedex, France
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