1
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Yabo YA, Moreno-Sanchez PM, Pires-Afonso Y, Kaoma T, Nosirov B, Scafidi A, Ermini L, Lipsa A, Oudin A, Kyriakis D, Grzyb K, Poovathingal SK, Poli A, Muller A, Toth R, Klink B, Berchem G, Berthold C, Hertel F, Mittelbronn M, Heiland DH, Skupin A, Nazarov PV, Niclou SP, Michelucci A, Golebiewska A. Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts. Genome Med 2024; 16:51. [PMID: 38566128 PMCID: PMC10988817 DOI: 10.1186/s13073-024-01321-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND A major contributing factor to glioblastoma (GBM) development and progression is its ability to evade the immune system by creating an immune-suppressive environment, where GBM-associated myeloid cells, including resident microglia and peripheral monocyte-derived macrophages, play critical pro-tumoral roles. However, it is unclear whether recruited myeloid cells are phenotypically and functionally identical in GBM patients and whether this heterogeneity is recapitulated in patient-derived orthotopic xenografts (PDOXs). A thorough understanding of the GBM ecosystem and its recapitulation in preclinical models is currently missing, leading to inaccurate results and failures of clinical trials. METHODS Here, we report systematic characterization of the tumor microenvironment (TME) in GBM PDOXs and patient tumors at the single-cell and spatial levels. We applied single-cell RNA sequencing, spatial transcriptomics, multicolor flow cytometry, immunohistochemistry, and functional studies to examine the heterogeneous TME instructed by GBM cells. GBM PDOXs representing different tumor phenotypes were compared to glioma mouse GL261 syngeneic model and patient tumors. RESULTS We show that GBM tumor cells reciprocally interact with host cells to create a GBM patient-specific TME in PDOXs. We detected the most prominent transcriptomic adaptations in myeloid cells, with brain-resident microglia representing the main population in the cellular tumor, while peripheral-derived myeloid cells infiltrated the brain at sites of blood-brain barrier disruption. More specifically, we show that GBM-educated microglia undergo transition to diverse phenotypic states across distinct GBM landscapes and tumor niches. GBM-educated microglia subsets display phagocytic and dendritic cell-like gene expression programs. Additionally, we found novel microglial states expressing cell cycle programs, astrocytic or endothelial markers. Lastly, we show that temozolomide treatment leads to transcriptomic plasticity and altered crosstalk between GBM tumor cells and adjacent TME components. CONCLUSIONS Our data provide novel insights into the phenotypic adaptation of the heterogeneous TME instructed by GBM tumors. We show the key role of microglial phenotypic states in supporting GBM tumor growth and response to treatment. Our data place PDOXs as relevant models to assess the functionality of the TME and changes in the GBM ecosystem upon treatment.
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Affiliation(s)
- Yahaya A Yabo
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Pilar M Moreno-Sanchez
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Yolanda Pires-Afonso
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Bakhtiyor Nosirov
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Andrea Scafidi
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
| | - Luca Ermini
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
| | - Anuja Lipsa
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
| | - Anaïs Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
| | - Dimitrios Kyriakis
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Suresh K Poovathingal
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
- Single Cell Analytics & Microfluidics Core, Vlaams Instituut Voor Biotechnologie-KU Leuven, 3000, Louvain, Belgium
| | - Aurélie Poli
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
| | - Arnaud Muller
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Reka Toth
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Barbara Klink
- National Center of Genetics, Laboratoire National de Santé, L-3555, Dudelange, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
- German Cancer Consortium (DKTK): Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC), Cancer Consortium (DKTK) Partner Site Dresden, and German Cancer Research Center (DKFZ), Dresden, Heidelberg, 01307, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Guy Berchem
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
- Centre Hospitalier Luxembourg, L-1210, Luxembourg, Luxembourg
| | | | - Frank Hertel
- Centre Hospitalier Luxembourg, L-1210, Luxembourg, Luxembourg
| | - Michel Mittelbronn
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), L-3555, Dudelange, Luxembourg
- National Center of Pathology (NCP), Laboratoire National de Santé, L-3555, Dudelange, Luxembourg
| | - Dieter H Heiland
- Translational Neurosurgery, Friedrich-Alexander University Erlangen Nuremberg, 91054, Erlangen, Germany
- Department of Neurosurgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen Nuremberg, 91054, Erlangen, Germany
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Department of Neurosurgery, Medical Center, University of Freiburg, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, 79106, Freiburg, Germany
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
- Department of Physics and Material Science, University Luxembourg, L-4367, Belvaux, Luxembourg
- Department of Neuroscience, University of California San Diego, La Jolla, CA, 92093, USA
| | - Petr V Nazarov
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Alessandro Michelucci
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg.
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg.
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg.
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg.
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Merz MP, Seal SV, Grova N, Mériaux S, Guebels P, Kanli G, Mommaerts E, Nicot N, Kaoma T, Keunen O, Nazarov PV, Turner JD. Early-life influenza A (H1N1) infection independently programs brain connectivity, HPA AXIS and tissue-specific gene expression profiles. Sci Rep 2024; 14:5898. [PMID: 38467724 PMCID: PMC10928197 DOI: 10.1038/s41598-024-56601-5] [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: 09/22/2023] [Accepted: 03/08/2024] [Indexed: 03/13/2024] Open
Abstract
Early-life adversity covers a range of physical, social and environmental stressors. Acute viral infections in early life are a major source of such adversity and have been associated with a broad spectrum of later-life effects outside the immune system or "off-target". These include an altered hypothalamus-pituitary-adrenal (HPA) axis and metabolic reactions. Here, we used a murine post-natal day 14 (PND 14) Influenza A (H1N1) infection model and applied a semi-holistic approach including phenotypic measurements, gene expression arrays and diffusion neuroimaging techniques to investigate HPA axis dysregulation, energy metabolism and brain connectivity. By PND 56 the H1N1 infection had been resolved, and there was no residual gene expression signature of immune cell infiltration into the liver, adrenal gland or brain tissues examined nor of immune-related signalling. A resolved early-life H1N1 infection had sex-specific effects. We observed retarded growth of males and altered pre-stress (baseline) blood glucose and corticosterone levels at PND42 after the infection was resolved. Cerebral MRI scans identified reduced connectivity in the cortex, midbrain and cerebellum that were accompanied by tissue-specific gene expression signatures. Gene set enrichment analysis confirmed that these were tissue-specific changes with few common pathways. Early-life infection independently affected each of the systems and this was independent of HPA axis or immune perturbations.
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Affiliation(s)
- Myriam P Merz
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de Université, L-4365, Esch-Sur-Alzette, Luxembourg
- Central Biobank Charité, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Snehaa V Seal
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de Université, L-4365, Esch-Sur-Alzette, Luxembourg
| | - Nathalie Grova
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Inserm U1256, NGERE, Nutrition-Génétique Et Exposition Aux Risques Environnementaux, Université de Lorraine, 54000, Nancy, France
| | - Sophie Mériaux
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
| | - Pauline Guebels
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
| | - Georgia Kanli
- In Vivo Imaging Platform, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Translational Radiomics, Department of Cancer Research, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Elise Mommaerts
- LuxGen Genome Center, Laboratoire National de Santé, Luxembourg Institute of Health, 3555, Dudelange, Luxembourg
| | - Nathalie Nicot
- LuxGen Genome Center, Laboratoire National de Santé, Luxembourg Institute of Health, 3555, Dudelange, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Data Integration and Analysis Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Olivier Keunen
- In Vivo Imaging Platform, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Translational Radiomics, Department of Cancer Research, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Petr V Nazarov
- Bioinformatics Platform, Data Integration and Analysis Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Multiomics Data Science Research Group, Department of Cancer Research, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Jonathan D Turner
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg.
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3
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Yabo YA, Moreno-Sanchez PM, Pires-Afonso Y, Kaoma T, Nosirov B, Scafidi A, Ermini L, Lipsa A, Oudin A, Kyriakis D, Grzyb K, Poovathingal SK, Poli A, Muller A, Toth R, Klink B, Berchem G, Berthold C, Hertel F, Mittelbronn M, Heiland DH, Skupin A, Nazarov PV, Niclou SP, Michelucci A, Golebiewska A. Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts. bioRxiv 2023:2023.03.05.531162. [PMID: 36945572 PMCID: PMC10028830 DOI: 10.1101/2023.03.05.531162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Background A major contributing factor to glioblastoma (GBM) development and progression is its ability to evade the immune system by creating an immune-suppressive environment, where GBM-associated myeloid cells, including resident microglia and peripheral monocyte-derived macrophages, play critical pro-tumoral roles. However, it is unclear whether recruited myeloid cells are phenotypically and functionally identical in GBM patients and whether this heterogeneity is recapitulated in patient-derived orthotopic xenografts (PDOXs). A thorough understanding of the GBM ecosystem and its recapitulation in preclinical models is currently missing, leading to inaccurate results and failures of clinical trials. Methods Here, we report systematic characterization of the tumor microenvironment (TME) in GBM PDOXs and patient tumors at the single-cell and spatial levels. We applied single-cell RNA-sequencing, spatial transcriptomics, multicolor flow cytometry, immunohistochemistry and functional studies to examine the heterogeneous TME instructed by GBM cells. GBM PDOXs representing different tumor phenotypes were compared to glioma mouse GL261 syngeneic model and patient tumors. Results We show that GBM tumor cells reciprocally interact with host cells to create a GBM patient-specific TME in PDOXs. We detected the most prominent transcriptomic adaptations in myeloid cells, with brain-resident microglia representing the main population in the cellular tumor, while peripheral-derived myeloid cells infiltrated the brain at sites of blood-brain barrier disruption. More specifically, we show that GBM-educated microglia undergo transition to diverse phenotypic states across distinct GBM landscapes and tumor niches. GBM-educated microglia subsets display phagocytic and dendritic cell-like gene expression programs. Additionally, we found novel microglial states expressing cell cycle programs, astrocytic or endothelial markers. Lastly, we show that temozolomide treatment leads to transcriptomic plasticity and altered crosstalk between GBM tumor cells and adjacent TME components. Conclusions Our data provide novel insights into the phenotypic adaptation of the heterogeneous TME instructed by GBM tumors. We show the key role of microglial phenotypic states in supporting GBM tumor growth and response to treatment. Our data place PDOXs as relevant models to assess the functionality of the TME and changes in the GBM ecosystem upon treatment.
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Affiliation(s)
- Yahaya A Yabo
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Pilar M Moreno-Sanchez
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Yolanda Pires-Afonso
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Tony Kaoma
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Bakhtiyor Nosirov
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Andrea Scafidi
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Luca Ermini
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
| | - Anuja Lipsa
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
| | - Anaïs Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
| | - Dimitrios Kyriakis
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Suresh K Poovathingal
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- Single Cell Analytics & Microfluidics Core, Vlaams Instituut voor Biotechnologie-KU Leuven, 3000 Leuven, Belgium
| | - Aurélie Poli
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Arnaud Muller
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Reka Toth
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Barbara Klink
- National Center of Genetics, Laboratoire National de Santé, L-3555 Dudelange, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
- German Cancer Consortium (DKTK), 01307 Dresden, Germany; Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), 01307 Dresden, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Guy Berchem
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
- Centre Hospitalier Luxembourg, 1210 Luxembourg, Luxembourg
| | | | - Frank Hertel
- Centre Hospitalier Luxembourg, 1210 Luxembourg, Luxembourg
| | - Michel Mittelbronn
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Luxembourg
- National Center of Pathology (NCP), Laboratoire National de Santé, L-3555 Dudelange, Luxembourg
| | - Dieter H Heiland
- Microenvironment and Immunology Research Laboratory, Medical Center - University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- Department of Physics and Material Science, University Luxembourg, L-4367 Belvaux, Luxembourg
- Department of Neuroscience, University of California San Diego, La Jolla, CA 92093, USA
| | - Petr V Nazarov
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Alessandro Michelucci
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
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Willekens J, Mosca P, Burt-Oberecken N, Laugeais E, Kaoma T, Bernardin F, Vallar L, Dimofski P, Renaud M, Lambert L, Leheup B, Guéant JL, Leininger-Muller B, Dreumont N. Cross-Talk between miRNAs from the Dlk1-Dio3 Locus and Histone Methylation to Protect Male Cerebellum from Methyl Donor Deficiency. Mol Nutr Food Res 2023; 67:e2300040. [PMID: 37672803 DOI: 10.1002/mnfr.202300040] [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: 01/24/2023] [Revised: 05/12/2023] [Indexed: 09/08/2023]
Abstract
SCOPE Disruption of the one carbon metabolism during development, i.e., following a gestational vitamin B9 and B12 deficiencies, is involved in birth defects and brain development delay. Using a rat nutritional model, consisting of pups born to dams fed a vitamin B9 and B12 deficient diet (MDD), the study previously reports molecular and cellular alterations in the brain, in a sex dependent manner, with females being more affected than males. The study hypothesizes that epigenetic modifications could participate in the sex differences is observed. METHODS AND RESULTS The study investigates lysine methylation of histones and expression of microRNAs in the cerebellum of MDD male and female pups. The study reports a differential regulation of H3K36Me2 and H4K20Me3 between males and females, in response to MDD. Moreover, distinct regulation of Kmt5b and Kdm2a expression by miR-134-5p and miR-369-5p from the Dlk1-Dio3 locus, contributes to the maintenance of expression of genes involved in synaptic plasticity. CONCLUSION These results could explain the neuroprotection to MDD that male pups display. The work will contribute to the understanding of the consequences of vitamin starvation on brain development, as well as how the epigenome is affected by one carbon metabolism disruption.
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Affiliation(s)
- Jeremy Willekens
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
- CINJ, Rutgers Cancer Institute of New Jersey, 195 Little Albany St, New Brunswick, NJ 08901, USA
| | - Pauline Mosca
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
| | | | - Edgar Laugeais
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
| | - Tony Kaoma
- Luxembourg Institute of Health, Bioinformatics Platform, 1 A-B, Luxembourg, L-1445, Luxembourg
| | - François Bernardin
- Department of Cancer Research, Luxembourg Institute of Health, Luxembourg, L-1210, Luxembourg
| | - Laurent Vallar
- Luxembourg Institute of Health, Bioinformatics Platform, 1 A-B, Luxembourg, L-1445, Luxembourg
| | | | - Mathilde Renaud
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
- CHRU Nancy, Hôpital d'enfants, Service de Génétique Clinique, Nancy, F-54000, France
| | - Laetitia Lambert
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
- CHRU Nancy, Hôpital d'enfants, Service de Génétique Clinique, Nancy, F-54000, France
| | - Bruno Leheup
- Université de Lorraine, Inserm, NGERE, Nancy, F-54000, France
- CHRU Nancy, Hôpital d'enfants, Service de Génétique Clinique, Nancy, F-54000, France
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5
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Boulanger M, Aqrouq M, Tempé D, Kifagi C, Ristic M, Akl D, Hallal R, Carusi A, Gabellier L, de Toledo M, Sigurdsson JO, Kaoma T, Andrieu-Soler C, Forné T, Soler E, Hicheri Y, Gueret E, Vallar L, Olsen JV, Cartron G, Piechaczyk M, Bossis G. DeSUMOylation of chromatin-bound proteins limits the rapid transcriptional reprogramming induced by daunorubicin in acute myeloid leukemias. Nucleic Acids Res 2023; 51:8413-8433. [PMID: 37462077 PMCID: PMC10484680 DOI: 10.1093/nar/gkad581] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 09/09/2023] Open
Abstract
Genotoxicants have been used for decades as front-line therapies against cancer on the basis of their DNA-damaging actions. However, some of their non-DNA-damaging effects are also instrumental for killing dividing cells. We report here that the anthracycline Daunorubicin (DNR), one of the main drugs used to treat Acute Myeloid Leukemia (AML), induces rapid (3 h) and broad transcriptional changes in AML cells. The regulated genes are particularly enriched in genes controlling cell proliferation and death, as well as inflammation and immunity. These transcriptional changes are preceded by DNR-dependent deSUMOylation of chromatin proteins, in particular at active promoters and enhancers. Surprisingly, inhibition of SUMOylation with ML-792 (SUMO E1 inhibitor), dampens DNR-induced transcriptional reprogramming. Quantitative proteomics shows that the proteins deSUMOylated in response to DNR are mostly transcription factors, transcriptional co-regulators and chromatin organizers. Among them, the CCCTC-binding factor CTCF is highly enriched at SUMO-binding sites found in cis-regulatory regions. This is notably the case at the promoter of the DNR-induced NFKB2 gene. DNR leads to a reconfiguration of chromatin loops engaging CTCF- and SUMO-bound NFKB2 promoter with a distal cis-regulatory region and inhibition of SUMOylation with ML-792 prevents these changes.
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Affiliation(s)
| | - Mays Aqrouq
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Denis Tempé
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | | | - Marko Ristic
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Dana Akl
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Rawan Hallal
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Aude Carusi
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Ludovic Gabellier
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
- Service d’Hématologie Clinique, CHU de Montpellier, 80 Avenue Augustin Fliche, 34091 Montpellier, France
| | | | - Jon-Otti Sigurdsson
- Proteomics Program, Novo Nordisk Foundation Center For Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Tony Kaoma
- Genomics Research Unit, Luxembourg Institute of Health, 84, Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Charlotte Andrieu-Soler
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
- Université de Paris, Laboratory of Excellence GR-Ex, Paris, France
| | | | - Eric Soler
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
- Université de Paris, Laboratory of Excellence GR-Ex, Paris, France
| | - Yosr Hicheri
- Service d’Hématologie Clinique, CHU de Montpellier, 80 Avenue Augustin Fliche, 34091 Montpellier, France
| | - Elise Gueret
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Laurent Vallar
- Genomics Research Unit, Luxembourg Institute of Health, 84, Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center For Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Guillaume Cartron
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
- Service d’Hématologie Clinique, CHU de Montpellier, 80 Avenue Augustin Fliche, 34091 Montpellier, France
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6
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Zhang L, Fritah S, Nazarov PV, Kaoma T, Van Dyck E. Impact of IDH Mutations, the 1p/19q Co-Deletion and the G-CIMP Status on Alternative Splicing in Diffuse Gliomas. Int J Mol Sci 2023; 24:9825. [PMID: 37372972 DOI: 10.3390/ijms24129825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
By generating protein diversity, alternative splicing provides an important oncogenic pathway. Isocitrate dehydrogenase (IDH) 1 and 2 mutations and 1p/19q co-deletion have become crucial for the novel molecular classification of diffuse gliomas, which also incorporates DNA methylation profiling. In this study, we have carried out a bioinformatics analysis to examine the impact of the IDH mutation, as well as the 1p/19q co-deletion and the glioma CpG island methylator phenotype (G-CIMP) status on alternative splicing in a cohort of 662 diffuse gliomas from The Cancer Genome Atlas (TCGA). We identify the biological processes and molecular functions affected by alternative splicing in the various glioma subgroups and provide evidence supporting the important contribution of alternative splicing in modulating epigenetic regulation in diffuse gliomas. Targeting the genes and pathways affected by alternative splicing might provide novel therapeutic opportunities against gliomas.
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Affiliation(s)
- Lu Zhang
- Bioinformatics Platform, Data Integration and Analysis Unit (DIA), Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Sabrina Fritah
- NorLux Neuro-Oncology Laboratory, Department of Cancer Research (DoCR), Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Petr V Nazarov
- Bioinformatics Platform, Data Integration and Analysis Unit (DIA), Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
- Multiomics Data Science Research Group, DoCR, Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Data Integration and Analysis Unit (DIA), Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Eric Van Dyck
- DNA Repair and Chemoresistance Group, DoCR, Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
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7
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Mgrditchian T, Brown-Clay J, Hoffmann C, Müller T, Filali L, Ockfen E, Mao X, Moreau F, Casellas CP, Kaoma T, Mittelbronn M, Thomas C. Actin cytoskeleton depolymerization increases matrix metalloproteinase gene expression in breast cancer cells by promoting translocation of cysteine-rich protein 2 to the nucleus. Front Cell Dev Biol 2023; 11:1100938. [PMID: 37266453 PMCID: PMC10229898 DOI: 10.3389/fcell.2023.1100938] [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: 11/17/2022] [Accepted: 04/21/2023] [Indexed: 06/03/2023] Open
Abstract
The actin cytoskeleton plays a critical role in cancer cell invasion and metastasis; however, the coordination of its multiple functions remains unclear. Actin dynamics in the cytoplasm control the formation of invadopodia, which are membrane protrusions that facilitate cancer cell invasion by focusing the secretion of extracellular matrix-degrading enzymes, including matrix metalloproteinases (MMPs). In this study, we investigated the nuclear role of cysteine-rich protein 2 (CRP2), a two LIM domain-containing F-actin-binding protein that we previously identified as a cytoskeletal component of invadopodia, in breast cancer cells. We found that F-actin depolymerization stimulates the translocation of CRP2 into the nucleus, resulting in an increase in the transcript levels of pro-invasive and pro-metastatic genes, including several members of the MMP gene family. We demonstrate that in the nucleus, CRP2 interacts with the transcription factor serum response factor (SRF), which is crucial for the expression of MMP-9 and MMP-13. Our data suggest that CRP2 and SRF cooperate to modulate of MMP expression levels. Furthermore, Kaplan-Meier analysis revealed a significant association between high-level expression of SRF and shorter overall survival and distant metastasis-free survival in breast cancer patients with a high CRP2 expression profile. Our findings suggest a model in which CRP2 mediates the coordination of cytoplasmic and nuclear processes driven by actin dynamics, ultimately resulting in the induction of invasive and metastatic behavior in breast cancer cells.
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Affiliation(s)
- Takouhie Mgrditchian
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Joshua Brown-Clay
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Céline Hoffmann
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Tanja Müller
- Department of Cancer Research, Luxembourg Centre of Neuropathology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Liza Filali
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Elena Ockfen
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Xianqing Mao
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Flora Moreau
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Carla Pou Casellas
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Luxembourg, Luxembourg
| | - Michel Mittelbronn
- Department of Cancer Research, Luxembourg Centre of Neuropathology, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-surAlzette, Luxembourg
- Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Esch-surAlzette, Luxembourg
- Department of Life Science and Medicine (DLSM), University of Luxembourg, Esch-surAlzette, Luxembourg
- National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
| | - Clément Thomas
- Department of Cancer Research, Cytoskeleton and Cancer Progression, Luxembourg Institute of Health, Luxembourg, Luxembourg
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8
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Yabo YA, Pires-Afonso Y, Moreno-Sanchez PM, Oudin A, Kaoma T, Nazarov PV, Skupin A, Niclou SP, Michelucci A, Golebiewska A. OS05.5.A Glioblastoma-instructed microglia transit to heterogeneous phenotypic states with dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac174.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
A major contributing factor to Glioblastoma (GBM) development and progression is its ability to evade the immune system by creating an immune-suppressive tumor microenvironment (TME). GBM-associated myeloid cells, including resident microglia, macrophages and other peripheral immune cells are generally geared towards tumor-supportive roles. It is however unclear whether such recruited myeloid cells are phenotypically and functionally identical. Here, we aim to understand the heterogeneity of the GBM TME, using an unbiased, marker-free approach to systematically characterize cell type identities at the molecular and functional levels.
Material and Methods
We applied single-cell RNA-sequencing, multicolor flow cytometry, immunohistochemical analyses and functional studies to examine the heterogeneous TME instructed by GBM cells. GBM patient-derived orthotopic xenografts (PDOXs) representing different tumor phenotypes were compared to glioma mouse GL261 model and patient tumors.
Results
We show that PDOX models recapitulate major components of the TME found in human GBM. Human GBM cells reciprocally interact with mouse cells to create a GBM-specific TME. The most prominent transcriptomic adaptations are found in tumor-associated macrophages (TAMs), which are largely of microglial origin. We reveal inter-patient heterogeneity of TAMs and identify key signatures of distinct phenotypic states within the microglia-derived TAMs across distinct GBM landscapes. GBM-educated microglia adapt expression of genes involved in immunosuppression, migration, phagocytosis and antigen presentation, indicating functional cross-talk with GBM cells. We identify novel phenotypic states with astrocytic and endothelial-like features. Identified gene signatures and phenotypic states are confirmed in GBM patient tumor tissue. Finally we show that temozolomide treatment leads to transcriptomic adaptation of not only the GBM tumor cells but also adjacent TME components.
Conclusion
Our data provide insights into the phenotypic adaptation of the heterogeneous TME instructed by GBM tumor. We confirm a crucial role of microglia in supporting the immunosuppressive TME and show that PDOXs allow to monitor the highly plastic GBM ecosystem and its phenotypic adaptations upon treatment. This work further confirms the clinical relevance of PDOX avatars for testing novel therapeutics including modalities designed to target the myeloid compartment.
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Affiliation(s)
- Y A Yabo
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health , Luxembourg , Luxembourg
| | - Y Pires-Afonso
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health , Luxembourg , Luxembourg
| | - P M Moreno-Sanchez
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health , Luxembourg , Luxembourg
| | - A Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health , Luxembourg , Luxembourg
| | - T Kaoma
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health , Luxembourg , Luxembourg
| | - P V Nazarov
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health , Luxembourg , Luxembourg
| | - A Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg,, Esch-sur-Alzette, Luxembourg
| | - S P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health , Luxembourg , Luxembourg
| | - A Michelucci
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health , Luxembourg , Luxembourg
| | - A Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health , Luxembourg , Luxembourg
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9
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Garcia P, Jürgens‐Wemheuer W, Uriarte Huarte O, Michelucci A, Masuch A, Brioschi S, Weihofen A, Koncina E, Coowar D, Heurtaux T, Glaab E, Balling R, Sousa C, Kaoma T, Nicot N, Pfander T, Schulz‐Schaeffer W, Allouche A, Fischer N, Biber K, Kleine‐Borgmann F, Mittelbronn M, Ostaszewski M, Schmit KJ, Buttini M. Neurodegeneration and neuroinflammation are linked, but independent of alpha‐synuclein inclusions, in a seeding/spreading mouse model of Parkinson's disease. Glia 2022; 70:935-960. [PMID: 35092321 PMCID: PMC9305192 DOI: 10.1002/glia.24149] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 12/22/2020] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 12/16/2022]
Abstract
A key pathological process in Parkinson's disease (PD) is the transneuronal spreading of α‐synuclein. Alpha‐synuclein (α‐syn) is a presynaptic protein that, in PD, forms pathological inclusions. Other hallmarks of PD include neurodegeneration and microgliosis in susceptible brain regions. Whether it is primarily transneuronal spreading of α‐syn particles, inclusion formation, or other mechanisms, such as inflammation, that cause neurodegeneration in PD is unclear. We used a model of spreading of α‐syn induced by striatal injection of α‐syn preformed fibrils into the mouse striatum to address this question. We performed quantitative analysis for α‐syn inclusions, neurodegeneration, and microgliosis in different brain regions, and generated gene expression profiles of the ventral midbrain, at two different timepoints after disease induction. We observed significant neurodegeneration and microgliosis in brain regions not only with, but also without α‐syn inclusions. We also observed prominent microgliosis in injured brain regions that did not correlate with neurodegeneration nor with inclusion load. Using longitudinal gene expression profiling, we observed early gene expression changes, linked to neuroinflammation, that preceded neurodegeneration, indicating an active role of microglia in this process. Altered gene pathways overlapped with those typical of PD. Our observations indicate that α‐syn inclusion formation is not the major driver in the early phases of PD‐like neurodegeneration, but that microglia, activated by diffusible, oligomeric α‐syn, may play a key role in this process. Our findings uncover new features of α‐syn induced pathologies, in particular microgliosis, and point to the necessity for a broader view of the process of α‐syn spreading.
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Affiliation(s)
- Pierre Garcia
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Luxembourg Center of Neuropathology Dudelange Luxembourg
| | - Wiebke Jürgens‐Wemheuer
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Institute of Neuropathology Saarland University Clinic (UKS) Homburg Germany
| | - Oihane Uriarte Huarte
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Luxembourg Center of Neuropathology Dudelange Luxembourg
| | - Alessandro Michelucci
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
| | - Annette Masuch
- Department of Psychiatry University of Freiburg Medical Center Freiburg Germany
| | - Simone Brioschi
- Department of Psychiatry University of Freiburg Medical Center Freiburg Germany
| | | | - Eric Koncina
- Department of Life Science and Medicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Djalil Coowar
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Tony Heurtaux
- Luxembourg Center of Neuropathology Dudelange Luxembourg
- Department of Life Science and Medicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Carole Sousa
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
| | - Tony Kaoma
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
| | - Nathalie Nicot
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
| | - Tatjana Pfander
- Institute of Neuropathology Saarland University Clinic (UKS) Homburg Germany
| | | | | | | | - Knut Biber
- Department of Psychiatry University of Freiburg Medical Center Freiburg Germany
| | - Felix Kleine‐Borgmann
- Luxembourg Center of Neuropathology Dudelange Luxembourg
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
- Faculty of Science, Technology and Medicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Luxembourg Center of Neuropathology Dudelange Luxembourg
- Department of Cancer Research Luxembourg Institute of Health Strassen Luxembourg
- Department of Life Science and Medicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Faculty of Science, Technology and Medicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
| | - Kristopher J. Schmit
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Luxembourg Center of Neuropathology Dudelange Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine University of Luxembourg Esch‐sur‐Alzette Luxembourg
- Luxembourg Center of Neuropathology Dudelange Luxembourg
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10
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Bosc C, Saland E, Bousard A, Gadaud N, Sabatier M, Cognet G, Farge T, Boet E, Gotanègre M, Aroua N, Mouchel PL, Polley N, Larrue C, Kaphan E, Picard M, Sahal A, Jarrou L, Tosolini M, Rambow F, Cabon F, Nicot N, Poillet-Perez L, Wang Y, Su X, Fovez Q, Kluza J, Argüello RJ, Mazzotti C, Avet-Loiseau H, Vergez F, Tamburini J, Fournié JJ, Tiong IS, Wei AH, Kaoma T, Marine JC, Récher C, Stuani L, Joffre C, Sarry JE. Mitochondrial inhibitors circumvent adaptive resistance to venetoclax and cytarabine combination therapy in acute myeloid leukemia. Nat Cancer 2021; 2:1204-1223. [PMID: 35122057 DOI: 10.1038/s43018-021-00264-y] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/31/2021] [Indexed: 04/23/2023]
Abstract
Therapy resistance represents a major clinical challenge in acute myeloid leukemia (AML). Here we define a 'MitoScore' signature, which identifies high mitochondrial oxidative phosphorylation in vivo and in patients with AML. Primary AML cells with cytarabine (AraC) resistance and a high MitoScore relied on mitochondrial Bcl2 and were highly sensitive to venetoclax (VEN) + AraC (but not to VEN + azacytidine). Single-cell transcriptomics of VEN + AraC-residual cell populations revealed adaptive resistance associated with changes in oxidative phosphorylation, electron transport chain complex and the TP53 pathway. Accordingly, treatment of VEN + AraC-resistant AML cells with electron transport chain complex inhibitors, pyruvate dehydrogenase inhibitors or mitochondrial ClpP protease agonists substantially delayed relapse following VEN + AraC. These findings highlight the central role of mitochondrial adaptation during AML therapy and provide a scientific rationale for alternating VEN + azacytidine with VEN + AraC in patients with a high MitoScore and to target mitochondrial metabolism to enhance the sensitivity of AML cells to currently approved therapies.
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Affiliation(s)
- Claudie Bosc
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Estelle Saland
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Aurélie Bousard
- Department of Oncology, Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
| | - Noémie Gadaud
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- University of Toulouse, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Marie Sabatier
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Guillaume Cognet
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Thomas Farge
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Emeline Boet
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Mathilde Gotanègre
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Nesrine Aroua
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Pierre-Luc Mouchel
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- University of Toulouse, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Nathaniel Polley
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Clément Larrue
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Eléonore Kaphan
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Muriel Picard
- Réanimation Polyvalente IUCT-oncopole, CHU de Toulouse, Toulouse, France
| | - Ambrine Sahal
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Latifa Jarrou
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Marie Tosolini
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
| | - Florian Rambow
- Department of Oncology, Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
| | - Florence Cabon
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Nathalie Nicot
- LuxGen, Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Laura Poillet-Perez
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Yujue Wang
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Xiaoyang Su
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Quentin Fovez
- Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277, Lille, France
| | - Jérôme Kluza
- Cancer Heterogeneity Plasticity and Resistance to Therapies (CANTHER), University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277, Lille, France
| | - Rafael José Argüello
- Aix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Céline Mazzotti
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Hervé Avet-Loiseau
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - François Vergez
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- University of Toulouse, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | | | - Jean-Jacques Fournié
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
| | - Ing S Tiong
- Department of Clinical Haematology, The Alfred Hospital and Monash University, Melbourne, Victoria, Australia
| | - Andrew H Wei
- Department of Clinical Haematology, The Alfred Hospital and Monash University, Melbourne, Victoria, Australia
| | - Tony Kaoma
- Computational Biomedicine Research Group, Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Jean-Christophe Marine
- Department of Oncology, Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
| | - Christian Récher
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- University of Toulouse, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Lucille Stuani
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Carine Joffre
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Jean-Emmanuel Sarry
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Toulouse, France.
- LabEx Toucan, Toulouse, France.
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France.
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11
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Stuani L, Sabatier M, Saland E, Cognet G, Poupin N, Bosc C, Castelli FA, Gales L, Turtoi E, Montersino C, Farge T, Boet E, Broin N, Larrue C, Baran N, Cissé MY, Conti M, Loric S, Kaoma T, Hucteau A, Zavoriti A, Sahal A, Mouchel PL, Gotanègre M, Cassan C, Fernando L, Wang F, Hosseini M, Chu-Van E, Le Cam L, Carroll M, Selak MA, Vey N, Castellano R, Fenaille F, Turtoi A, Cazals G, Bories P, Gibon Y, Nicolay B, Ronseaux S, Marszalek JR, Takahashi K, DiNardo CD, Konopleva M, Pancaldi V, Collette Y, Bellvert F, Jourdan F, Linares LK, Récher C, Portais JC, Sarry JE. Mitochondrial metabolism supports resistance to IDH mutant inhibitors in acute myeloid leukemia. J Exp Med 2021; 218:e20200924. [PMID: 33760042 PMCID: PMC7995203 DOI: 10.1084/jem.20200924] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 11/25/2020] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
Mutations in IDH induce epigenetic and transcriptional reprogramming, differentiation bias, and susceptibility to mitochondrial inhibitors in cancer cells. Here, we first show that cell lines, PDXs, and patients with acute myeloid leukemia (AML) harboring an IDH mutation displayed an enhanced mitochondrial oxidative metabolism. Along with an increase in TCA cycle intermediates, this AML-specific metabolic behavior mechanistically occurred through the increase in electron transport chain complex I activity, mitochondrial respiration, and methylation-driven CEBPα-induced fatty acid β-oxidation of IDH1 mutant cells. While IDH1 mutant inhibitor reduced 2-HG oncometabolite and CEBPα methylation, it failed to reverse FAO and OxPHOS. These mitochondrial activities were maintained through the inhibition of Akt and enhanced activation of peroxisome proliferator-activated receptor-γ coactivator-1 PGC1α upon IDH1 mutant inhibitor. Accordingly, OxPHOS inhibitors improved anti-AML efficacy of IDH mutant inhibitors in vivo. This work provides a scientific rationale for combinatory mitochondrial-targeted therapies to treat IDH mutant AML patients, especially those unresponsive to or relapsing from IDH mutant inhibitors.
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MESH Headings
- Acute Disease
- Aminopyridines/pharmacology
- Animals
- Cell Line, Tumor
- Doxycycline/pharmacology
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Enzyme Inhibitors/pharmacology
- Epigenesis, Genetic/drug effects
- Glycine/analogs & derivatives
- Glycine/pharmacology
- HL-60 Cells
- Humans
- Isocitrate Dehydrogenase/antagonists & inhibitors
- Isocitrate Dehydrogenase/genetics
- Isocitrate Dehydrogenase/metabolism
- Isoenzymes/antagonists & inhibitors
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Leukemia, Myeloid/drug therapy
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/metabolism
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Mitochondria/drug effects
- Mitochondria/genetics
- Mitochondria/metabolism
- Mutation
- Oxadiazoles/pharmacology
- Oxidative Phosphorylation/drug effects
- Piperidines/pharmacology
- Pyridines/pharmacology
- Triazines/pharmacology
- Xenograft Model Antitumor Assays/methods
- Mice
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Affiliation(s)
- Lucille Stuani
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Marie Sabatier
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Estelle Saland
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Guillaume Cognet
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Nathalie Poupin
- UMR1331 Toxalim, Université de Toulouse, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Ecole Nationale Vétérinaire de Toulouse, INP-Purpan, Université Paul Sabatier, Toulouse, France
| | - Claudie Bosc
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Florence A. Castelli
- CEA/DSV/iBiTec-S/SPI, Laboratoire d’Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Gif-sur-Yvette, France
| | - Lara Gales
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des sciences appliquées, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Evgenia Turtoi
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Institut Régional du Cancer Montpellier, Montpellier, France
- Montpellier Alliance for Metabolomics and Metabolism Analysis, Platform for Translational Oncometabolomics, Biocampus, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Montpellier, France
| | - Camille Montersino
- Aix-Marseille University, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Institut Paoli-Calmettes, Centre de Recherches en Cancérologie de Marseille, Marseille, France
| | - Thomas Farge
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Emeline Boet
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Nicolas Broin
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Clément Larrue
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Natalia Baran
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Madi Y. Cissé
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Institut Régional du Cancer Montpellier, Montpellier, France
| | - Marc Conti
- Institut National de la Santé et de la Recherché Médicale U938, Hôpital St Antoine, Paris, France
- Integracell, Longjumeau, France
| | - Sylvain Loric
- Institut National de la Santé et de la Recherché Médicale U938, Hôpital St Antoine, Paris, France
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Alexis Hucteau
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Aliki Zavoriti
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Ambrine Sahal
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Pierre-Luc Mouchel
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Mathilde Gotanègre
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Cédric Cassan
- UMR1332 Biologie du Fruit et Pathologie, Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d'Ornon, France
| | - Laurent Fernando
- UMR1331 Toxalim, Université de Toulouse, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Ecole Nationale Vétérinaire de Toulouse, INP-Purpan, Université Paul Sabatier, Toulouse, France
| | - Feng Wang
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Mohsen Hosseini
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Emeline Chu-Van
- CEA/DSV/iBiTec-S/SPI, Laboratoire d’Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Gif-sur-Yvette, France
| | - Laurent Le Cam
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Institut Régional du Cancer Montpellier, Montpellier, France
| | - Martin Carroll
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mary A. Selak
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Norbert Vey
- Aix-Marseille University, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Institut Paoli-Calmettes, Centre de Recherches en Cancérologie de Marseille, Marseille, France
| | - Rémy Castellano
- Aix-Marseille University, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Institut Paoli-Calmettes, Centre de Recherches en Cancérologie de Marseille, Marseille, France
| | - François Fenaille
- CEA/DSV/iBiTec-S/SPI, Laboratoire d’Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Gif-sur-Yvette, France
| | - Andrei Turtoi
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Institut Régional du Cancer Montpellier, Montpellier, France
| | - Guillaume Cazals
- Laboratoire de Mesures Physiques, Université de Montpellier, Montpellier, France
| | - Pierre Bories
- Réseau Régional de Cancérologie Onco-Occitanie, Toulouse, France
| | - Yves Gibon
- UMR1332 Biologie du Fruit et Pathologie, Plateforme Métabolome Bordeaux, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d'Ornon, France
| | | | | | - Joseph R. Marszalek
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Koichi Takahashi
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Courtney D. DiNardo
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Marina Konopleva
- Departments of Leukemia and Genomic Medicine, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Véra Pancaldi
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Yves Collette
- Aix-Marseille University, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Institut Paoli-Calmettes, Centre de Recherches en Cancérologie de Marseille, Marseille, France
| | - Floriant Bellvert
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des sciences appliquées, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Fabien Jourdan
- UMR1331 Toxalim, Université de Toulouse, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Ecole Nationale Vétérinaire de Toulouse, INP-Purpan, Université Paul Sabatier, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Laetitia K. Linares
- Institut de Recherche en Cancérologie de Montpellier, Institut National de la Santé et de la Recherché Médicale, Université de Montpellier, Institut Régional du Cancer Montpellier, Montpellier, France
| | - Christian Récher
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Jean-Charles Portais
- Toulouse Biotechnology Institute, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut National des sciences appliquées, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
- STROMALab, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Jean-Emmanuel Sarry
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Institut National de la Santé et de la Recherché Médicale, Centre National de la Recherche Scientifique, Toulouse, France
- LabEx Toucan, Toulouse, France
- Equipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Toulouse, France
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12
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Bejjani F, Tolza C, Boulanger M, Downes D, Romero R, Maqbool M, Zine El Aabidine A, Andrau JC, Lebre S, Brehelin L, Parrinello H, Rohmer M, Kaoma T, Vallar L, Hughes J, Zibara K, Lecellier CH, Piechaczyk M, Jariel-Encontre I. Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers. Nucleic Acids Res 2021; 49:2488-2508. [PMID: 33533919 PMCID: PMC7968996 DOI: 10.1093/nar/gkab053] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 12/21/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
The ubiquitous family of dimeric transcription factors AP-1 is made up of Fos and Jun family proteins. It has long been thought to operate principally at gene promoters and how it controls transcription is still ill-understood. The Fos family protein Fra-1 is overexpressed in triple negative breast cancers (TNBCs) where it contributes to tumor aggressiveness. To address its transcriptional actions in TNBCs, we combined transcriptomics, ChIP-seqs, machine learning and NG Capture-C. Additionally, we studied its Fos family kin Fra-2 also expressed in TNBCs, albeit much less. Consistently with their pleiotropic effects, Fra-1 and Fra-2 up- and downregulate individually, together or redundantly many genes associated with a wide range of biological processes. Target gene regulation is principally due to binding of Fra-1 and Fra-2 at regulatory elements located distantly from cognate promoters where Fra-1 modulates the recruitment of the transcriptional co-regulator p300/CBP and where differences in AP-1 variant motif recognition can underlie preferential Fra-1- or Fra-2 bindings. Our work also shows no major role for Fra-1 in chromatin architecture control at target gene loci, but suggests collaboration between Fra-1-bound and -unbound enhancers within chromatin hubs sometimes including promoters for other Fra-1-regulated genes. Our work impacts our view of AP-1.
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Affiliation(s)
- Fabienne Bejjani
- IGMM, Univ Montpellier, CNRS, Montpellier, France
- PRASE, DSST, ER045, Lebanese University, Beirut, Lebanon
| | - Claire Tolza
- IGMM, Univ Montpellier, CNRS, Montpellier, France
| | | | - Damien Downes
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Raphaël Romero
- IMAG, Univ Montpellier, CNRS, Montpellier, France
- LIRMM, Univ Montpellier, CNRS, Montpellier, France
| | | | | | | | - Sophie Lebre
- IMAG, Univ Montpellier, CNRS, Montpellier, France
| | | | - Hughes Parrinello
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Marine Rohmer
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Tony Kaoma
- Computational Biomedecine, Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Laurent Vallar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Jim R Hughes
- Medical Research Council, Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Kazem Zibara
- PRASE, DSST, ER045, Lebanese University, Beirut, Lebanon
- Biology Department, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Charles-Henri Lecellier
- IGMM, Univ Montpellier, CNRS, Montpellier, France
- LIRMM, Univ Montpellier, CNRS, Montpellier, France
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13
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Hendrickx DM, Garcia P, Ashrafi A, Sciortino A, Schmit KJ, Kollmus H, Nicot N, Kaoma T, Vallar L, Buttini M, Glaab E. A New Synuclein-Transgenic Mouse Model for Early Parkinson's Reveals Molecular Features of Preclinical Disease. Mol Neurobiol 2021; 58:576-602. [PMID: 32997293 PMCID: PMC8219584 DOI: 10.1007/s12035-020-02085-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022]
Abstract
Understanding Parkinson's disease (PD), in particular in its earliest phases, is important for diagnosis and treatment. However, human brain samples are collected post-mortem, reflecting mainly end-stage disease. Because brain samples of mouse models can be collected at any stage of the disease process, they are useful in investigating PD progression. Here, we compare ventral midbrain transcriptomics profiles from α-synuclein transgenic mice with a progressive, early PD-like striatal neurodegeneration across different ages using pathway, gene set, and network analysis methods. Our study uncovers statistically significant altered genes across ages and between genotypes with known, suspected, or unknown function in PD pathogenesis and key pathways associated with disease progression. Among those are genotype-dependent alterations associated with synaptic plasticity and neurotransmission, as well as mitochondria-related genes and dysregulation of lipid metabolism. Age-dependent changes were among others observed in neuronal and synaptic activity, calcium homeostasis, and membrane receptor signaling pathways, many of which linked to G-protein coupled receptors. Most importantly, most changes occurred before neurodegeneration was detected in this model, which points to a sequence of gene expression events that may be relevant for disease initiation and progression. It is tempting to speculate that molecular changes similar to those changes observed in our model happen in midbrain dopaminergic neurons before they start to degenerate. In other words, we believe we have uncovered molecular changes that accompany the progression from preclinical to early PD.
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Affiliation(s)
- Diana M. Hendrickx
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
- Laboratoire National de Santé (LNS), Neuropathology Unit, Dudelange, Luxembourg
| | - Amer Ashrafi
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
- Present Address: Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Alessia Sciortino
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Kristopher J. Schmit
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Heike Kollmus
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Nathalie Nicot
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Tony Kaoma
- Department of Oncology, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Laurent Vallar
- Genomics Research Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
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14
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Golebiewska A, Hau AC, Oudin A, Stieber D, Yabo YA, Baus V, Barthelemy V, Klein E, Bougnaud S, Keunen O, Wantz M, Michelucci A, Neirinckx V, Muller A, Kaoma T, Nazarov PV, Azuaje F, De Falco A, Flies B, Richart L, Poovathingal S, Arns T, Grzyb K, Mock A, Herold-Mende C, Steino A, Brown D, May P, Miletic H, Malta TM, Noushmehr H, Kwon YJ, Jahn W, Klink B, Tanner G, Stead LF, Mittelbronn M, Skupin A, Hertel F, Bjerkvig R, Niclou SP. Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology. Acta Neuropathol 2020; 140:919-949. [PMID: 33009951 PMCID: PMC7666297 DOI: 10.1007/s00401-020-02226-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [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: 07/30/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 11/29/2022]
Abstract
Patient-based cancer models are essential tools for studying tumor biology and for the assessment of drug responses in a translational context. We report the establishment a large cohort of unique organoids and patient-derived orthotopic xenografts (PDOX) of various glioma subtypes, including gliomas with mutations in IDH1, and paired longitudinal PDOX from primary and recurrent tumors of the same patient. We show that glioma PDOXs enable long-term propagation of patient tumors and represent clinically relevant patient avatars that retain histopathological, genetic, epigenetic, and transcriptomic features of parental tumors. We find no evidence of mouse-specific clonal evolution in glioma PDOXs. Our cohort captures individual molecular genotypes for precision medicine including mutations in IDH1, ATRX, TP53, MDM2/4, amplification of EGFR, PDGFRA, MET, CDK4/6, MDM2/4, and deletion of CDKN2A/B, PTCH, and PTEN. Matched longitudinal PDOX recapitulate the limited genetic evolution of gliomas observed in patients following treatment. At the histological level, we observe increased vascularization in the rat host as compared to mice. PDOX-derived standardized glioma organoids are amenable to high-throughput drug screens that can be validated in mice. We show clinically relevant responses to temozolomide (TMZ) and to targeted treatments, such as EGFR and CDK4/6 inhibitors in (epi)genetically defined subgroups, according to MGMT promoter and EGFR/CDK status, respectively. Dianhydrogalactitol (VAL-083), a promising bifunctional alkylating agent in the current clinical trial, displayed high therapeutic efficacy, and was able to overcome TMZ resistance in glioblastoma. Our work underscores the clinical relevance of glioma organoids and PDOX models for translational research and personalized treatment studies and represents a unique publicly available resource for precision oncology.
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Affiliation(s)
- Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Ann-Christin Hau
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Anaïs Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Daniel Stieber
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
- National Center of Genetics, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
| | - Yahaya A Yabo
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Virginie Baus
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Vanessa Barthelemy
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Eliane Klein
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Sébastien Bougnaud
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Olivier Keunen
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
- Quantitative Biology Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - May Wantz
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Alessandro Michelucci
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
- Neuro-Immunology Group, Department of Oncology, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Virginie Neirinckx
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
| | - Arnaud Muller
- Quantitative Biology Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Tony Kaoma
- Quantitative Biology Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Francisco Azuaje
- Quantitative Biology Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Alfonso De Falco
- National Center of Genetics, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4367, Belvaux, Luxembourg
- Luxembourg Center of Neuropathology, Luxembourg, Luxembourg
| | - Ben Flies
- National Center of Genetics, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
| | - Lorraine Richart
- Faculty of Science, Technology and Medicine, University of Luxembourg, 4367, Belvaux, Luxembourg
- Luxembourg Center of Neuropathology, Luxembourg, Luxembourg
- National Center of Pathology, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
- Department of Oncology, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Suresh Poovathingal
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Thais Arns
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Andreas Mock
- Division of Experimental Neurosurgery, Department of Neurosurgery, University of Heidelberg, 69120, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, 69120, Heidelberg, Germany
- German Cancer Research Center (DKFZ) Heidelberg, 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University of Heidelberg, 69120, Heidelberg, Germany
| | - Anne Steino
- DelMar Pharmaceuticals, Inc., Vancouver, BC, Canada
- DelMar Pharmaceuticals, Inc., Menlo Park, CA, USA
| | - Dennis Brown
- DelMar Pharmaceuticals, Inc., Vancouver, BC, Canada
- DelMar Pharmaceuticals, Inc., Menlo Park, CA, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Hrvoje Miletic
- Department of Biomedicine, University of Bergen, 5019, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Yong-Jun Kwon
- Department of Oncology, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Winnie Jahn
- German Cancer Consortium (DKTK), 01307, Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
| | - Barbara Klink
- National Center of Genetics, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
- Department of Oncology, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
- German Cancer Consortium (DKTK), 01307, Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), 01307, Dresden, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Georgette Tanner
- Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Lucy F Stead
- Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
- Luxembourg Center of Neuropathology, Luxembourg, Luxembourg
- National Center of Pathology, Laboratoire National de Santé, 3555, Dudelange, Luxembourg
- Department of Oncology, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
| | - Frank Hertel
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4367, Belvaux, Luxembourg
- Department of Neurosurgery, Centre Hospitalier Luxembourg, 1210, Luxembourg, Luxembourg
| | - Rolf Bjerkvig
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg
- Department of Biomedicine, University of Bergen, 5019, Bergen, Norway
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, 84, Val Fleuri, 1526, Luxembourg, Luxembourg.
- Department of Biomedicine, University of Bergen, 5019, Bergen, Norway.
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15
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Scherer M, Nazarov PV, Toth R, Sahay S, Kaoma T, Maurer V, Vedeneev N, Plass C, Lengauer T, Walter J, Lutsik P. Reference-free deconvolution, visualization and interpretation of complex DNA methylation data using DecompPipeline, MeDeCom and FactorViz. Nat Protoc 2020; 15:3240-3263. [PMID: 32978601 DOI: 10.1038/s41596-020-0369-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
DNA methylation profiling offers unique insights into human development and diseases. Often the analysis of complex tissues and cell mixtures is the only feasible option to study methylation changes across large patient cohorts. Since DNA methylomes are highly cell type specific, deconvolution methods can be used to recover cell type-specific information in the form of latent methylation components (LMCs) from such 'bulk' samples. Reference-free deconvolution methods retrieve these components without the need for DNA methylation profiles of purified cell types. Currently no integrated and guided procedure is available for data preparation and subsequent interpretation of deconvolution results. Here, we describe a three-stage protocol for reference-free deconvolution of DNA methylation data comprising: (i) data preprocessing, confounder adjustment using independent component analysis (ICA) and feature selection using DecompPipeline, (ii) deconvolution with multiple parameters using MeDeCom, RefFreeCellMix or EDec and (iii) guided biological inference and validation of deconvolution results with the R/Shiny graphical user interface FactorViz. Our protocol simplifies the analysis and guides the initial interpretation of DNA methylation data derived from complex samples. The harmonized approach is particularly useful to dissect and evaluate cell heterogeneity in complex systems such as tumors. We apply the protocol to lung cancer methylomes from The Cancer Genome Atlas (TCGA) and show that our approach identifies the proportions of stromal cells and tumor-infiltrating immune cells, as well as associations of the detected components with clinical parameters. The protocol takes slightly >3 d to complete and requires basic R skills.
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Affiliation(s)
- Michael Scherer
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.,Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Reka Toth
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Shashwat Sahay
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.,Center for Digital Health, Berlin Institute of Health and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tony Kaoma
- Quantitative Biology Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Valentin Maurer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Lengauer
- Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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16
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Yang M, Petralia F, Li Z, Li H, Ma W, Song X, Kim S, Lee H, Yu H, Lee B, Bae S, Heo E, Kaczmarczyk J, Stępniak P, Warchoł M, Yu T, Calinawan AP, Boutros PC, Payne SH, Reva B, Boja E, Rodriguez H, Stolovitzky G, Guan Y, Kang J, Wang P, Fenyö D, Saez-Rodriguez J, Aderinwale T, Afyounian E, Agrawal P, Ali M, Amadoz A, Azuaje F, Bachman J, Bae S, Bhalla S, Carbonell-Caballero J, Chakraborty P, Chaudhary K, Choi Y, Choi Y, Çubuk C, Dhanda SK, Dopazo J, Elo LL, Fóthi Á, Gevaert O, Granberg K, Greiner R, Heo E, Hidalgo MR, Jayaswal V, Jeon H, Jeon M, Kalmady SV, Kambara Y, Kang J, Kang K, Kaoma T, Kaur H, Kazan H, Kesar D, Kesseli J, Kim D, Kim K, Kim SY, Kim S, Kumar S, Lee B, Lee H, Liu Y, Luethy R, Mahajan S, Mahmoudian M, Muller A, Nazarov PV, Nguyen H, Nykter M, Okuda S, Park S, Pal Singh Raghava G, Rajapakse JC, Rantapero T, Ryu H, Salavert F, Saraei S, Sharma R, Siitonen A, Sokolov A, Subramanian K, Suni V, Suomi T, Tranchevent LC, Usmani SS, Välikangas T, Vega R, Zhong H. Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics. Cell Syst 2020; 11:186-195.e9. [DOI: 10.1016/j.cels.2020.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/12/2020] [Accepted: 06/29/2020] [Indexed: 10/23/2022]
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17
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Aroua N, Boet E, Ghisi M, Nicolau-Travers ML, Saland E, Gwilliam R, de Toni F, Hosseini M, Mouchel PL, Farge T, Bosc C, Stuani L, Sabatier M, Mazed F, Larrue C, Jarrou L, Gandarillas S, Bardotti M, Picard M, Syrykh C, Laurent C, Gotanègre M, Bonnefoy N, Bellvert F, Portais JC, Nicot N, Azuaje F, Kaoma T, Joffre C, Tamburini J, Récher C, Vergez F, Sarry JE. Extracellular ATP and CD39 Activate cAMP-Mediated Mitochondrial Stress Response to Promote Cytarabine Resistance in Acute Myeloid Leukemia. Cancer Discov 2020; 10:1544-1565. [PMID: 32641297 DOI: 10.1158/2159-8290.cd-19-1008] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 05/09/2020] [Accepted: 07/02/2020] [Indexed: 11/16/2022]
Abstract
Relapses driven by chemoresistant leukemic cell populations are the main cause of mortality for patients with acute myeloid leukemia (AML). Here, we show that the ectonucleotidase CD39 (ENTPD1) is upregulated in cytarabine-resistant leukemic cells from both AML cell lines and patient samples in vivo and in vitro. CD39 cell-surface expression and activity is increased in patients with AML upon chemotherapy compared with diagnosis, and enrichment in CD39-expressing blasts is a marker of adverse prognosis in the clinics. High CD39 activity promotes cytarabine resistance by enhancing mitochondrial activity and biogenesis through activation of a cAMP-mediated adaptive mitochondrial stress response. Finally, genetic and pharmacologic inhibition of CD39 ecto-ATPase activity blocks the mitochondrial reprogramming triggered by cytarabine treatment and markedly enhances its cytotoxicity in AML cells in vitro and in vivo. Together, these results reveal CD39 as a new residual disease marker and a promising therapeutic target to improve chemotherapy response in AML. SIGNIFICANCE: Extracellular ATP and CD39-P2RY13-cAMP-OxPHOS axis are key regulators of cytarabine resistance, offering a new promising therapeutic strategy in AML.This article is highlighted in the In This Issue feature, p. 1426.
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Affiliation(s)
- Nesrine Aroua
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Emeline Boet
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Margherita Ghisi
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Marie-Laure Nicolau-Travers
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Estelle Saland
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Ryan Gwilliam
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Fabienne de Toni
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Mohsen Hosseini
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Pierre-Luc Mouchel
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Thomas Farge
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Claudie Bosc
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Lucille Stuani
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Marie Sabatier
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Fetta Mazed
- Institut Cochin, Département Développement, Reproduction, Cancer, UMR8104-CNRS, U1016-INSERM, Paris.,Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Clément Larrue
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Latifa Jarrou
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Sarah Gandarillas
- Centre Régional d'Exploration Fonctionnelle et Ressources Expérimentales, Service d'Expérimentation Animale, UMS006, Inserm, Toulouse, France
| | - Massimiliano Bardotti
- Centre Régional d'Exploration Fonctionnelle et Ressources Expérimentales, Service d'Expérimentation Animale, UMS006, Inserm, Toulouse, France
| | - Muriel Picard
- University of Toulouse, Toulouse, France.,Intensive Care Unit, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Charlotte Syrykh
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Anatomopathologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Camille Laurent
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Anatomopathologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Mathilde Gotanègre
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Nathalie Bonnefoy
- Institut de Recherche en Cancérologie de Montpellier, U1194, Inserm, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | | | | | - Nathalie Nicot
- LuxGene, Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Francisco Azuaje
- Computational Biomedicine Research Group, Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Tony Kaoma
- Computational Biomedicine Research Group, Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Carine Joffre
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France
| | - Jérome Tamburini
- Institut Cochin, Département Développement, Reproduction, Cancer, UMR8104-CNRS, U1016-INSERM, Paris.,Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Christian Récher
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - François Vergez
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France.,University of Toulouse, Toulouse, France.,Service d'Hématologie, Institut Universitaire du Cancer de Toulouse-Oncopole, CHU de Toulouse, Toulouse, France
| | - Jean-Emmanuel Sarry
- Centre de Recherches en Cancérologie de Toulouse, UMR1037 Inserm/Université Toulouse III-Paul Sabatier, ERL5294 CNRS, Equipe Labellisée LIGUE 2018, Toulouse, France. .,University of Toulouse, Toulouse, France
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18
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Monzel AS, Hemmer K, Kaoma T, Smits LM, Bolognin S, Lucarelli P, Rosety I, Zagare A, Antony P, Nickels SL, Krueger R, Azuaje F, Schwamborn JC. Machine learning-assisted neurotoxicity prediction in human midbrain organoids. Parkinsonism Relat Disord 2020; 75:105-109. [PMID: 32534431 DOI: 10.1016/j.parkreldis.2020.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 02/03/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Brain organoids are highly complex multi-cellular tissue proxies, which have recently risen as novel tools to study neurodegenerative diseases such as Parkinson's disease (PD). However, with increasing complexity of the system, usage of quantitative tools becomes challenging. OBJECTIVES The primary objective of this study was to develop a neurotoxin-induced PD organoid model and to assess the neurotoxic effect on dopaminergic neurons using microscopy-based phenotyping in a high-content fashion. METHODS We describe a pipeline for a machine learning-based analytical method, allowing for detailed image-based cell profiling and toxicity prediction in brain organoids treated with the neurotoxic compound 6-hydroxydopamine (6-OHDA). RESULTS We quantified features such as dopaminergic neuron count and neuronal complexity and built a machine learning classifier with the data to optimize data processing strategies and to discriminate between different treatment conditions. We validated the approach with high content imaging data from PD patient derived midbrain organoids. CONCLUSIONS The here described model is a valuable tool for advanced in vitro PD modeling and to test putative neurotoxic compounds.
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Affiliation(s)
- Anna S Monzel
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Kathrin Hemmer
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Tony Kaoma
- Computational Biomedicine Research Group, Quantitative Biology Unit, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
| | - Lisa M Smits
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Silvia Bolognin
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Philippe Lucarelli
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Isabel Rosety
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alise Zagare
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Antony
- Clinical and Experimental Neurobiology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sarah L Nickels
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rejko Krueger
- Clinical and Experimental Neurobiology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg; Parkinson's Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg; Luxembourg Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Luxembourg
| | - Francisco Azuaje
- Computational Biomedicine Research Group, Quantitative Biology Unit, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg; Data and Translational Sciences, UCB Celltech, Slough, UK
| | - Jens C Schwamborn
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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19
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Hau AC, Houben L, Klein E, Oudin A, Stieber D, Flies B, Kaoma T, Azuaje F, Fritah S, Bjerkvig R, Mittelbronn M, Hertel F, Golebiewska A, Niclou S. GENE-02. ESTABLISHING PERSONALIZED TREATMENT OPTIONS FOR RECURRENT HIGH-GRADE GLIOMAS. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
BACKGROUND
High grade glioma (HGG) patients develop resistance to standard treatment leading to disease progression and limited life expectancy. Recent advances in the molecular characterisation of treatment-naïve HGGs based on next generation sequencing and DNA methylation analyses have led to a better delineation of HGG-subtypes and identification of distinct genomic abnormalities opening opportunities for personalized treatment strategies.
METHODS
We collected 300 fresh glioma specimen with approximately 100 longitudinal samples of initial and recurrent tumors from 43 matched patients. We succeeded in generating a live-biobank of HGG patient-derived orthotopic xenografts (PDOX) and 3D tumor organoids that neatly recapitulates the mutational spectrum including structural DNA variations and methylation-based subtypes of gliomas. A highlight is the generation of 19 PDOXs of paired initial and relapse HGGs from 9 glioma patients, enabling high-throughput drug screens. We performed comprehensive molecular profiling using arrayCGH, DNA-methylation and targeted DNA sequencing on patient specimen and their derivatives, 3D tumor organoids and PDOXs.
RESULTS
Detailed analysis of the paired longitudinal samples indicated that PDOXs closely recapitulate the evolutionary trajectory of the parental tumors. Furthermore, targeted genomic sequencing of paired HGGs suggests that relapse tumors also accumulate somatic mutations in epigenetic effectors. Based on patient-derived material we carried out drug response screening on 3D tumor organoids using a compound library matching the majority of genes that were assessed with targeted sequencing. Differential drug responses between initial and recurrent tumors were observed and the prevailing primary drug response profiles were essentially recapitulad in the relapse setting.
CONCLUSIONS
Response assessment of treatment-naïve gliomas and their recurrences provides crucial information on the differential sensitivity between initial and relapsed HGGs and offers novel personalized therapeutic options for the relapse setting. Furthermore, in depth correlation of the profiled somatic molecular landscape with drug response will enable pharmacogenomic predictions of potential inhibitors in the clinical setting.
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Affiliation(s)
- Ann-Christin Hau
- NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Linsey Houben
- National Center of Genetics, Laboratoire National de Sante, Luxembourg, Luxembourg
| | - Eliane Klein
- NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anais Oudin
- NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Daniel Stieber
- National Center of Genetics, Laboratoire National de Sante, Luxembourg, Luxembourg
| | - Ben Flies
- National Center of Genetics, Laboratoire National de Sante, Luxembourg, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Fransisco Azuaje
- Bioinformatics Platform, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Sabrina Fritah
- NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Rolf Bjerkvig
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Michel Mittelbronn
- National Center of Pathology, Laboratoire National de Sante, Luxembourg, Luxembourg
| | - Frank Hertel
- Neurosurgery Department, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Anna Golebiewska
- NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Simone Niclou
- NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health, Luxembourg, Luxembourg
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20
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Hau A, Houben L, Klein E, Oudin A, Stieber D, Flies B, Kaoma T, Azuaje F, Fritah S, Bjerkvig R, Hertel F, Mittelbronn M, Golebiewska A, Niclou SP. OS12.2 Targeting epigenetic pathways in the treatment of recurrent high-grade glioma. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz126.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
BACKGROUND
High grade glioma (HGG) patients develop resistance to standard treatment leading to disease progression and limited life expectancy. Advances in the molecular characterisation of treatment-naïve HGGs based on next-generation sequencing and DNA methylation analyses have led to a better delineation of HGG subtypes and the identification of distinct genomic abnormalities. Furthermore, using large patient cohorts of longitudinal tumor samples, comprehensive genomic profiling studies emerged to investigate therapy-associated evolution of gliomas. All together, those studies point out the need for personalised treatment strategies, where applied drugs will be adapted to the unique patient-specific genetic abnormalities.
MATERIAL AND METHODS
We collected fresh samples of more than 800 brain tumors containing almost 300 glioma specimen with approximately 100 longitudinal samples of initial and recurrent tumors from 43 matched patients. By now, we have successfully established 34 patient-derived orthotopic xenografts (PDOXs) in mice. We performed comprehensive molecular profiling using array comparative genomic hybridisation, DNA methylation analysis and targeted DNA sequencing on patient specimen and their derivatives such as 3D tumor organoids and PDOXs. The custom-design sequencing panel comprises 234 genes that reflect both established genetic identifiers for individual glioma subtype classification and novel genes encoding mainly epigenetic effector genes. Based on patient-derived material we carried out drug response screening on 3D tumor organoids using a compound library matching the majority of genes that were assessed by targeted sequencing.
RESULTS
We succeeded in generating a live biobank of HGG patient-derived xenografts and 3D organoids that neatly recapitulates the mutational spectrum including structural DNA variation and methylation-based subtypes of gliomas. A highlight is the generation of 19 PDOXs of paired initial and relapse HGGs from a total of 9 glioma patients. A detailed analysis of the paired longitudinal samples indicated that PDOX models closely recapitulate the evolutionary trajectory of the parental tumors. Targeted sequencing of longitudinal HGG PDOXs suggests that relapse tumors accumulate somatic mutations in epigenetic effectors compared with the Initial. Differential drug responses between initial and relapse tumors were observed after screening of in vitro 3D tumor organoids.
CONCLUSION
Response assessment of naïve initial gliomas and recurrences provides crucial information on the differential sensitivity between initial and relapsed HGGs and offers novel personalised therapeutic options in the relapse setting. Furthermore, in depth correlation of the profiled somatic molecular landscape with drug response will enable pharmacogenomic predictions of potential inhibitors in the clinical setting.
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Affiliation(s)
- A Hau
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - L Houben
- National Center of Genetics, Laboratoire national de santé, Dudelange, Luxembourg
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - E Klein
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - A Oudin
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - D Stieber
- National Center of Genetics, Laboratoire national de santé, Dudelange, Luxembourg
| | - B Flies
- National Center of Genetics, Laboratoire national de santé, Dudelange, Luxembourg
| | - T Kaoma
- Bioinformatics platform, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - F Azuaje
- Bioinformatics platform, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - S Fritah
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - R Bjerkvig
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - F Hertel
- Neurosurgery Department, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - M Mittelbronn
- National Center of Pathology, Laboratoire national de santé, Dudelange, Luxembourg
| | - A Golebiewska
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - S P Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
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21
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Zeiner PS, Preusse C, Golebiewska A, Zinke J, Iriondo A, Muller A, Kaoma T, Filipski K, Müller-Eschner M, Bernatz S, Blank AE, Baumgarten P, Ilina E, Grote A, Hansmann ML, Verhoff MA, Franz K, Feuerhake F, Steinbach JP, Wischhusen J, Stenzel W, Niclou SP, Harter PN, Mittelbronn M. Distribution and prognostic impact of microglia/macrophage subpopulations in gliomas. Brain Pathol 2019; 29:513-529. [PMID: 30506802 PMCID: PMC6849857 DOI: 10.1111/bpa.12690] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/14/2018] [Indexed: 12/28/2022] Open
Abstract
While the central nervous system is considered an immunoprivileged site and brain tumors display immunosuppressive features, both innate and adaptive immune responses affect glioblastoma (GBM) growth and treatment resistance. However, the impact of the major immune cell population in gliomas, represented by glioma‐associated microglia/macrophages (GAMs), on patients’ clinical course is still unclear. Thus, we aimed at assessing the immunohistochemical expression of selected microglia and macrophage markers in 344 gliomas (including gliomas from WHO grade I–IV). Furthermore, we analyzed a cohort of 241 IDH1R132H‐non‐mutant GBM patients for association of GAM subtypes and patient overall survival. Phenotypical properties of GAMs, isolated from high‐grade astrocytomas by CD11b‐based magnetic cell sorting, were analyzed by immunocytochemistry, mRNA microarray, qRT‐PCR and bioinformatic analyses. A higher amount of CD68‐, CD163‐ and CD206‐positive GAMs in the vital tumor core was associated with beneficial patient survival. The mRNA expression profile of GAMs displayed an upregulation of factors that are considered as pro‐inflammatory M1 (eg, CCL2, CCL3L3, CCL4, PTGS2) and anti‐inflammatory M2 polarization markers (eg, MRC1, LGMN, CD163, IL10, MSR1), the latter rather being associated with phagocytic functions in the GBM microenvironment. In summary, we present evidence that human GBMs contain mixed M1/M2‐like polarized GAMs and that the levels of different GAM subpopulations in the tumor core are positively associated with overall survival of patients with IDH1R132H‐non‐mutant GBMs.
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Affiliation(s)
- Pia S Zeiner
- Edinger Institute, Institute of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany.,Department of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany.,Dr. Senckenberg Institute of Neurooncology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Corinna Preusse
- Department of Neuropathology, Charité Berlin, Berlin, Germany
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg
| | - Jenny Zinke
- Edinger Institute, Institute of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ane Iriondo
- Edinger Institute, Institute of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Arnaud Muller
- Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg
| | - Tony Kaoma
- Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg
| | - Katharina Filipski
- Edinger Institute, Institute of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Monika Müller-Eschner
- Institute of Neuroradiology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Simon Bernatz
- Edinger Institute, Institute of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anna-Eva Blank
- Edinger Institute, Institute of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Peter Baumgarten
- Edinger Institute, Institute of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany.,Department of Neurosurgery, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Elena Ilina
- Edinger Institute, Institute of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany.,NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg
| | - Anne Grote
- Institute of Pathology and Neuropathology, Medical University Hannover, Hannover, Germany
| | - Martin L Hansmann
- Senckenberg Institute of Pathology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marcel A Verhoff
- Institute of Legal Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kea Franz
- Dr. Senckenberg Institute of Neurooncology, Goethe University Frankfurt, Frankfurt am Main, Germany.,Department of Neurosurgery, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Friedrich Feuerhake
- Institute of Pathology and Neuropathology, Medical University Hannover, Hannover, Germany.,Institute of Neuropathology, University Clinic Freiburg, Freiburg, Germany
| | - Joachim P Steinbach
- Dr. Senckenberg Institute of Neurooncology, Goethe University Frankfurt, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg Wischhusen
- Department of Gynecology, University of Wuerzburg, Wuerzburg, Germany
| | - Werner Stenzel
- Department of Neuropathology, Charité Berlin, Berlin, Germany
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg.,KG Jebsen Brain Tumour Research Center, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Patrick N Harter
- Edinger Institute, Institute of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michel Mittelbronn
- Edinger Institute, Institute of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany.,NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg.,Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg.,Laboratoire national de santé (LNS), Dudelange, Luxembourg
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22
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Azuaje F, Kaoma T, Jeanty C, Nazarov PV, Muller A, Kim SY, Dittmar G, Golebiewska A, Niclou SP. Hub genes in a pan-cancer co-expression network show potential for predicting drug responses. F1000Res 2018; 7:1906. [PMID: 30881689 PMCID: PMC6406180 DOI: 10.12688/f1000research.17149.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/22/2019] [Indexed: 12/15/2022] Open
Abstract
Background: The topological analysis of networks extracted from different types of "omics" data is a useful strategy for characterizing biologically meaningful properties of the complex systems underlying these networks. In particular, the biological significance of highly connected genes in diverse molecular networks has been previously determined using data from several model organisms and phenotypes. Despite such insights, the predictive potential of candidate hubs in gene co-expression networks in the specific context of cancer-related drug experiments remains to be deeply investigated. The examination of such associations may offer opportunities for the accurate prediction of anticancer drug responses. Methods: Here, we address this problem by: a) analyzing a co-expression network obtained from thousands of cancer cell lines, b) detecting significant network hubs, and c) assessing their capacity to predict drug sensitivity using data from thousands of drug experiments. We investigated the prediction capability of those genes using a multiple linear regression model, independent datasets, comparisons with other models and our own in vitro experiments. Results: These analyses led to the identification of 47 hub genes, which are implicated in a diverse range of cancer-relevant processes and pathways. Overall, encouraging agreements between predicted and observed drug sensitivities were observed in public datasets, as well as in our in vitro validations for four glioblastoma cell lines and four drugs. To facilitate further research, we share our hub-based drug sensitivity prediction model as an online tool. Conclusions: Our research shows that co-expression network hubs are biologically interesting and exhibit potential for predicting drug responses in vitro. These findings motivate further investigations about the relevance and application of our unbiased discovery approach in pre-clinical, translationally-oriented research.
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Affiliation(s)
| | - Tony Kaoma
- Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Céline Jeanty
- Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | | | - Arnaud Muller
- Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Sang-Yoon Kim
- Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Gunnar Dittmar
- Luxembourg Institute of Health (LIH), Strassen, Luxembourg
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23
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Azuaje F, Kaoma T, Jeanty C, Nazarov PV, Muller A, Kim SY, Dittmar G, Golebiewska A, Niclou SP. Hub genes in a pan-cancer co-expression network show potential for predicting drug responses. F1000Res 2018; 7:1906. [PMID: 30881689 PMCID: PMC6406180 DOI: 10.12688/f1000research.17149.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/30/2018] [Indexed: 10/07/2023] Open
Abstract
Background: The topological analysis of networks extracted from different types of "omics" data is a useful strategy for characterizing biologically meaningful properties of the complex systems underlying these networks. In particular, the biological significance of highly connected genes in diverse molecular networks has been previously determined using data from several model organisms and phenotypes. Despite such insights, the predictive potential of candidate hubs in gene co-expression networks in the specific context of cancer-related drug experiments remains to be deeply investigated. The examination of such associations may offer opportunities for the accurate prediction of anticancer drug responses. Methods: Here, we address this problem by: a) analyzing a co-expression network obtained from thousands of cancer cell lines, b) detecting significant network hubs, and c) assessing their capacity to predict drug sensitivity using data from thousands of drug experiments. We investigated the prediction capability of those genes using a multiple linear regression model, independent datasets, comparisons with other models and our own in vitro experiments. Results: These analyses led to the identification of 47 hub genes, which are implicated in a diverse range of cancer-relevant processes and pathways. Overall, encouraging agreements between predicted and observed drug sensitivities were observed in public datasets, as well as in our in vitro validations for four glioblastoma cell lines and four drugs. To facilitate further research, we share our hub-based drug sensitivity prediction model as an online tool. Conclusions: Our research shows that co-expression network hubs are biologically interesting and exhibit potential for predicting drug responses in vitro. These findings motivate further investigations about the relevance and application of our unbiased discovery approach in pre-clinical, translationally-oriented research.
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Affiliation(s)
| | - Tony Kaoma
- Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Céline Jeanty
- Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | | | - Arnaud Muller
- Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Sang-Yoon Kim
- Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Gunnar Dittmar
- Luxembourg Institute of Health (LIH), Strassen, Luxembourg
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24
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Hau AC, Golebiewska A, Oudin A, Houben L, Stieber D, Azuaje F, Kaoma T, Muller A, Hertel F, Mittelbronn M, Bjerkvig R, Niclou S. TMOD-29. MOLECULAR CHARACTERIZATION OF GLIOMA PATIENT-DERIVED ORTHOTOPIC XENOGRAFTS: FROM BASIC RESEARCH TO PRECLINICAL STUDIES. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.1141] [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: 11/12/2022] Open
Affiliation(s)
- Ann-Christin Hau
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anna Golebiewska
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anais Oudin
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Linsey Houben
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Daniel Stieber
- Department of Genetics, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Francisco Azuaje
- Genomics and Proteomics Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Tony Kaoma
- Genomics and Proteomics Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Arnaud Muller
- Genomics and Proteomics Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Frank Hertel
- Neurosurgical National Department of Luxembourg, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Michel Mittelbronn
- Department of Anatomic and Molecular Pathology, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Rolf Bjerkvig
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Simone Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
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25
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Sousa C, Golebiewska A, Poovathingal SK, Kaoma T, Pires-Afonso Y, Martina S, Coowar D, Azuaje F, Skupin A, Balling R, Biber K, Niclou SP, Michelucci A. Single-cell transcriptomics reveals distinct inflammation-induced microglia signatures. EMBO Rep 2018; 19:embr.201846171. [PMID: 30206190 PMCID: PMC6216255 DOI: 10.15252/embr.201846171] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/17/2018] [Accepted: 08/22/2018] [Indexed: 01/10/2023] Open
Abstract
Microglia are specialized parenchymal‐resident phagocytes of the central nervous system (CNS) that actively support, defend and modulate the neural environment. Dysfunctional microglial responses are thought to worsen CNS diseases; nevertheless, their impact during neuroinflammatory processes remains largely obscure. Here, using a combination of single‐cell RNA sequencing and multicolour flow cytometry, we comprehensively profile microglia in the brain of lipopolysaccharide (LPS)‐injected mice. By excluding the contribution of other immune CNS‐resident and peripheral cells, we show that microglia isolated from LPS‐injected mice display a global downregulation of their homeostatic signature together with an upregulation of inflammatory genes. Notably, we identify distinct microglial activated profiles under inflammatory conditions, which greatly differ from neurodegenerative disease‐associated profiles. These results provide insights into microglial heterogeneity and establish a resource for the identification of specific phenotypes in CNS disorders, such as neuroinflammatory and neurodegenerative diseases.
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Affiliation(s)
- Carole Sousa
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg.,Doctoral School of Science and Technology, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Suresh K Poovathingal
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg.,Single Cell Analytics & Microfluidics Core, Vlaams Instituut voor Biotechnologie-KU Leuven, Leuven, Belgium
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Yolanda Pires-Afonso
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Doctoral School of Science and Technology, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Silvia Martina
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Djalil Coowar
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Francisco Azuaje
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg.,National Centre for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA
| | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Knut Biber
- Section Molecular Psychiatry, Department for Psychiatry and Psychotherapy, Laboratory of Translational Psychiatry, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Section Medical Physiology, Department of Neuroscience, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Department of Biomedicine, KG Jebsen Brain Tumour Research Center, University of Bergen, Bergen, Norway
| | - Alessandro Michelucci
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg .,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-Belval, Luxembourg
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26
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Tranchevent LC, Nazarov PV, Kaoma T, Schmartz GP, Muller A, Kim SY, Rajapakse JC, Azuaje F. Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach. Biol Direct 2018; 13:12. [PMID: 29880025 PMCID: PMC5992838 DOI: 10.1186/s13062-018-0214-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 05/04/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND One of the main current challenges in computational biology is to make sense of the huge amounts of multidimensional experimental data that are being produced. For instance, large cohorts of patients are often screened using different high-throughput technologies, effectively producing multiple patient-specific molecular profiles for hundreds or thousands of patients. RESULTS We propose and implement a network-based method that integrates such patient omics data into Patient Similarity Networks. Topological features derived from these networks were then used to predict relevant clinical features. As part of the 2017 CAMDA challenge, we have successfully applied this strategy to a neuroblastoma dataset, consisting of genomic and transcriptomic data. In particular, we observe that models built on our network-based approach perform at least as well as state of the art models. We furthermore explore the effectiveness of various topological features and observe, for instance, that redundant centrality metrics can be combined to build more powerful models. CONCLUSION We demonstrate that the networks inferred from omics data contain clinically relevant information and that patient clinical outcomes can be predicted using only network topological data. REVIEWERS This article was reviewed by Yang-Yu Liu, Tomislav Smuc and Isabel Nepomuceno.
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Affiliation(s)
- Léon-Charles Tranchevent
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Petr V. Nazarov
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Georges P. Schmartz
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
- Bioinformatics bachelor program, Universität des Saarlandes, Saarbrücken, Germany
| | - Arnaud Muller
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Sang-Yoon Kim
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
| | - Jagath C. Rajapakse
- Bioinformatics Research Center, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Francisco Azuaje
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445 Luxembourg
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27
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Bosseler M, Marani V, Broukou A, Lequeux A, Kaoma T, Schlesser V, François JH, Palissot V, Berchem GJ, Aouali N, Janji B. Inhibition of HIF1α-Dependent Upregulation of Phospho-l-Plastin Resensitizes Multiple Myeloma Cells to Frontline Therapy. Int J Mol Sci 2018; 19:ijms19061551. [PMID: 29882856 PMCID: PMC6032243 DOI: 10.3390/ijms19061551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/08/2018] [Accepted: 05/12/2018] [Indexed: 12/18/2022] Open
Abstract
The introduction of novel frontline agents in multiple myeloma (MM), like immunomodulatory drugs and proteasome inhibitors, has improved the overall survival of patients. Yet, MM is still not curable, and drug resistance (DR) remains the main challenge. To improve the understanding of DR in MM, we established a resistant cell line (MOLP8/R). The exploration of DR mechanisms yielded an overexpression of HIF1α, due to impaired proteasome activity of MOLP8/R. We show that MOLP8/R, like other tumor cells, overexpressing HIF1α, have an increased resistance to the immune system. By exploring the main target genes regulated by HIF1α, we could not show an overexpression of these targets in MOLP8/R. We, however, show that MOLP8/R cells display a very high overexpression of LCP1 gene (l-Plastin) controlled by HIF1α, and that this overexpression also exists in MM patient samples. The l-Plastin activity is controlled by its phosphorylation in Ser5. We further show that the inhibition of l-Plastin phosphorylation restores the sensitivity of MOLP8/R to immunomodulatory drugs (IMiDs) and proteasome inhibitors (PIs). Our results reveal a new target gene of DR, controlled by HIF1α.
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Affiliation(s)
- Manon Bosseler
- Laboratory of Experimental Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg City, Luxembourg.
| | - Vanessa Marani
- Laboratory of Experimental Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg City, Luxembourg.
| | - Angelina Broukou
- Laboratory of Experimental Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg City, Luxembourg.
| | - Amandine Lequeux
- Laboratory of Experimental Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg City, Luxembourg.
| | - Tony Kaoma
- Bioinformatics and Modelling, Luxembourg Institute of Health (LIH), L-1526 Luxembourg City, Luxembourg.
| | - Vincent Schlesser
- Laboratory of Hematology, Centre Hospitalier de Luxembourg (CHL), L-1526 Luxembourg City, Luxembourg.
| | - Jean-Hugues François
- Laboratory of Hematology, Centre Hospitalier de Luxembourg (CHL), L-1526 Luxembourg City, Luxembourg.
| | - Valérie Palissot
- Laboratory of Oncolytic-Virus-Immuno-Therapeutics, Luxembourg Institute of Health (LIH), L-1526 Luxembourg City, Luxembourg.
| | - Guy J Berchem
- Laboratory of Experimental Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg City, Luxembourg.
- Laboratory of Hematology, Centre Hospitalier de Luxembourg (CHL), L-1526 Luxembourg City, Luxembourg.
| | - Nasséra Aouali
- Laboratory of Experimental Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg City, Luxembourg.
| | - Bassam Janji
- Laboratory of Experimental Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg City, Luxembourg.
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Gauchotte G, Hergalant S, Vigouroux C, Casse JM, Houlgatte R, Kaoma T, Helle D, Brochin L, Rech F, Peyre M, Labrousse F, Vallar L, Guéant JL, Vignaud JM, Battaglia-Hsu SF. Cytoplasmic overexpression of RNA-binding protein HuR is a marker of poor prognosis in meningioma, and HuR knockdown decreases meningioma cell growth and resistance to hypoxia. J Pathol 2017; 242:421-434. [PMID: 28493484 DOI: 10.1002/path.4916] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/19/2017] [Accepted: 04/26/2017] [Indexed: 11/11/2022]
Abstract
HuR regulates cytoplasmic mRNA stability and translatability, and the HuR expression level has been shown to correlate with poor disease outcome in several cancer types; however, the prognostic value and potential pro-oncogenic properties of HuR in meningioma remain unclear. Thus, in the present study, we analysed 85 meningioma tissue samples to establish the relationship between HuR expression, tumour cell proliferation, and/or patient survival. In addition, we examined the anti-proliferative effects of HuR knockdown in two meningioma cell lines (IOMM-Lee and Ben-Men-1) and conducted transcriptome-wide analyses (IOMM-Lee cells) to elucidate the molecular consequences of HuR knockdown. The results of the present study showed HuR cytoplasmic expression to correlate positively with tumour grade (p = 1.2 × 10-8 ) and negatively with progression-free and overall survival (p = 0.01) time in human meningioma tissues. In vitro, siHuR-induced HuR knockdown was shown to reduce the growth of both Ben-Men-1 (p = 2 × 10-8 ) and IOMM-Lee (p = 4 × 10-9 ) cells. Transcriptome analyses revealed HuR knockdown in IOMM-Lee cells to deregulate the HIF1A signalling pathway (p = 1.5 × 10-6 ) and to up-regulate the expression of genes essential for the assembly of the cytoplasmic mRNA processing body, global genome nucleotide-excision repair, poly(A)-specific ribonuclease activity, the positive regulation of apoptosis and of cell cycle arrest, and the negative regulation of RNA splicing [p(FDR) < 0.001]. Interestingly, HuR knockdown under hypoxic culture conditions further potentiated the effects of HuR knockdown on cell growth, apoptosis, and HIF1A expression. We thus conclude that cytoplasmic HuR expression is a marker of poor prognosis in meningioma and that HuR is a promising potential therapeutic target for use in tumours refractory to standard therapies. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Guillaume Gauchotte
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Pathology, CHRU, Nancy, France
| | - Sébastien Hergalant
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | | | - Jean-Matthieu Casse
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Pathology, CHRU, Nancy, France
| | - Rémi Houlgatte
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Déborah Helle
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | | | - Fabien Rech
- Department of Neurosurgery, CHRU, Nancy, France.,Institut des Neurosciences, INSERM U1051, Montpellier, France
| | - Matthieu Peyre
- Sorbonne Université, UPMC University Paris 06, INSERM, CNRS, UM 75, U 1127, UMR 7225, ICM, Paris, France.,Department of Neurosurgery, Groupe Hospitalier Pitié Salpêtrière, AP-HP, Paris, France
| | | | - Laurent Vallar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Jean-Louis Guéant
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France.,M2TP, Division of Biochemistry and Molecular Biology, CHRU, Vandoeuvre-lès-Nancy, France
| | - Jean-Michel Vignaud
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Pathology, CHRU, Nancy, France.,Centre de Ressources Biologiques, BB-0033-00035, CHRU Nancy, France
| | - Shyue-Fang Battaglia-Hsu
- INSERM U954, Faculty of Medicine, Université de Lorraine, Vandoeuvre-lès-Nancy, France.,M2TP, Division of Biochemistry and Molecular Biology, CHRU, Vandoeuvre-lès-Nancy, France
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29
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Farge T, Saland E, de Toni F, Aroua N, Hosseini M, Perry R, Bosc C, Sugita M, Stuani L, Fraisse M, Scotland S, Larrue C, Boutzen H, Féliu V, Nicolau-Travers ML, Cassant-Sourdy S, Broin N, David M, Serhan N, Sarry A, Tavitian S, Kaoma T, Vallar L, Iacovoni J, Linares LK, Montersino C, Castellano R, Griessinger E, Collette Y, Duchamp O, Barreira Y, Hirsch P, Palama T, Gales L, Delhommeau F, Garmy-Susini BH, Portais JC, Vergez F, Selak M, Danet-Desnoyers G, Carroll M, Récher C, Sarry JE. Chemotherapy-Resistant Human Acute Myeloid Leukemia Cells Are Not Enriched for Leukemic Stem Cells but Require Oxidative Metabolism. Cancer Discov 2017; 7:716-735. [PMID: 28416471 PMCID: PMC5501738 DOI: 10.1158/2159-8290.cd-16-0441] [Citation(s) in RCA: 512] [Impact Index Per Article: 73.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/15/2016] [Accepted: 04/12/2017] [Indexed: 12/12/2022]
Abstract
Chemotherapy-resistant human acute myeloid leukemia (AML) cells are thought to be enriched in quiescent immature leukemic stem cells (LSC). To validate this hypothesis in vivo, we developed a clinically relevant chemotherapeutic approach treating patient-derived xenografts (PDX) with cytarabine (AraC). AraC residual AML cells are enriched in neither immature, quiescent cells nor LSCs. Strikingly, AraC-resistant preexisting and persisting cells displayed high levels of reactive oxygen species, showed increased mitochondrial mass, and retained active polarized mitochondria, consistent with a high oxidative phosphorylation (OXPHOS) status. AraC residual cells exhibited increased fatty-acid oxidation, upregulated CD36 expression, and a high OXPHOS gene signature predictive for treatment response in PDX and patients with AML. High OXPHOS but not low OXPHOS human AML cell lines were chemoresistant in vivo. Targeting mitochondrial protein synthesis, electron transfer, or fatty-acid oxidation induced an energetic shift toward low OXPHOS and markedly enhanced antileukemic effects of AraC. Together, this study demonstrates that essential mitochondrial functions contribute to AraC resistance in AML and are a robust hallmark of AraC sensitivity and a promising therapeutic avenue to treat AML residual disease.Significance: AraC-resistant AML cells exhibit metabolic features and gene signatures consistent with a high OXPHOS status. In these cells, targeting mitochondrial metabolism through the CD36-FAO-OXPHOS axis induces an energetic shift toward low OXPHOS and strongly enhanced antileukemic effects of AraC, offering a promising avenue to design new therapeutic strategies and fight AraC resistance in AML. Cancer Discov; 7(7); 716-35. ©2017 AACR.See related commentary by Schimmer, p. 670This article is highlighted in the In This Issue feature, p. 653.
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Affiliation(s)
- Thomas Farge
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
- Consortium IMODI "Innovative MODels Initiative against Cancer," France
| | - Estelle Saland
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
- Consortium IMODI "Innovative MODels Initiative against Cancer," France
| | - Fabienne de Toni
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
- Consortium IMODI "Innovative MODels Initiative against Cancer," France
| | - Nesrine Aroua
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
- Consortium IMODI "Innovative MODels Initiative against Cancer," France
| | - Mohsen Hosseini
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
| | - Robin Perry
- Division of Hematology & Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Claudie Bosc
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
| | - Mayumi Sugita
- Division of Hematology & Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lucille Stuani
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
| | - Marine Fraisse
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
| | - Sarah Scotland
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
| | - Clément Larrue
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
| | - Héléna Boutzen
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
| | - Virginie Féliu
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
- Sorbonne Universités, UPMC Université Paris 06, UMR-S 938, CDR Saint-Antoine, Paris, France
| | - Marie-Laure Nicolau-Travers
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse Oncopole, Toulouse, France
| | | | - Nicolas Broin
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
| | - Marion David
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
| | - Nizar Serhan
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
| | - Audrey Sarry
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse Oncopole, Toulouse, France.
| | - Suzanne Tavitian
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse Oncopole, Toulouse, France
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Laurent Vallar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Jason Iacovoni
- Inserm, Institut des Maladies Métaboliques et Cardiovasculaires, U1048, Toulouse, France
| | - Laetitia K Linares
- Inserm, Institut de Recherche en Cancérologie de Montpellier, U1194, Montpellier, France
- Université de Montpellier, Montpellier, France
- Institut Régional du Cancer Montpellier, Montpellier, France
| | - Camille Montersino
- Inserm, Centre de Recherche en Cancérologie de Marseille, U1068, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, Marseille, France
| | - Rémy Castellano
- Inserm, Centre de Recherche en Cancérologie de Marseille, U1068, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, Marseille, France
| | | | - Yves Collette
- Inserm, Centre de Recherche en Cancérologie de Marseille, U1068, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- Université Aix-Marseille, Marseille, France
- CNRS, UMR7258, Marseille, France
| | - Olivier Duchamp
- Consortium IMODI "Innovative MODels Initiative against Cancer," France
- Oncodesign, Dijon, France
| | - Yara Barreira
- Consortium IMODI "Innovative MODels Initiative against Cancer," France
- Inserm, Service d'Expérimentation Animale, UMS006, Toulouse, France
| | - Pierre Hirsch
- Sorbonne Universités, UPMC Université Paris 06, UMR-S 938, CDR Saint-Antoine, Paris, France
- Inserm, UMR-S938, CDR Saint-Antoine, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, GRC n°07, Groupe de Recherche Clinique sur les Myéloproliférations Aiguës et Chroniques MyPAC, Paris, France
- AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Tony Palama
- Université de Toulouse III Paul Sabatier, INSA, UPS, INP, LISBP, Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques & des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
| | - Lara Gales
- Université de Toulouse III Paul Sabatier, INSA, UPS, INP, LISBP, Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques & des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
| | - François Delhommeau
- Sorbonne Universités, UPMC Université Paris 06, UMR-S 938, CDR Saint-Antoine, Paris, France
- Inserm, UMR-S938, CDR Saint-Antoine, Paris, France
- Sorbonne Universités, UPMC Université Paris 06, GRC n°07, Groupe de Recherche Clinique sur les Myéloproliférations Aiguës et Chroniques MyPAC, Paris, France
- AP-HP, Hôpital Saint-Antoine, Paris, France
| | - Barbara H Garmy-Susini
- Inserm, Institut des Maladies Métaboliques et Cardiovasculaires, U1048, Toulouse, France
| | - Jean-Charles Portais
- Université de Toulouse III Paul Sabatier, INSA, UPS, INP, LISBP, Toulouse, France
- INRA, UMR792, Ingénierie des Systèmes Biologiques & des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
| | - François Vergez
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
- Consortium IMODI "Innovative MODels Initiative against Cancer," France
| | - Mary Selak
- Division of Hematology & Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gwenn Danet-Desnoyers
- Division of Hematology & Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Martin Carroll
- Division of Hematology & Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Christian Récher
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France
- Université de Toulouse, Toulouse, France
- Consortium IMODI "Innovative MODels Initiative against Cancer," France
- Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse Oncopole, Toulouse, France
| | - Jean-Emmanuel Sarry
- Inserm, Cancer Research Center of Toulouse, U1037, Toulouse, France.
- Université de Toulouse, Toulouse, France
- Consortium IMODI "Innovative MODels Initiative against Cancer," France
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Armento A, Ilina EI, Kaoma T, Muller A, Vallar L, Niclou SP, Krüger MA, Mittelbronn M, Naumann U. Carboxypeptidase E transmits its anti-migratory function in glioma cells via transcriptional regulation of cell architecture and motility regulating factors. Int J Oncol 2017; 51:702-714. [DOI: 10.3892/ijo.2017.4051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/06/2017] [Indexed: 11/06/2022] Open
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31
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Nazarov PV, Muller A, Kaoma T, Nicot N, Maximo C, Birembaut P, Tran NL, Dittmar G, Vallar L. RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples. BMC Genomics 2017; 18:443. [PMID: 28587590 PMCID: PMC5461714 DOI: 10.1186/s12864-017-3819-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/25/2017] [Indexed: 01/29/2023] Open
Abstract
Background RNA sequencing (RNA-seq) and microarrays are two transcriptomics techniques aimed at the quantification of transcribed genes and their isoforms. Here we compare the latest Affymetrix HTA 2.0 microarray with Illumina 2000 RNA-seq for the analysis of patient samples - normal lung epithelium tissue and squamous cell carcinoma lung tumours. Protein coding mRNAs and long non-coding RNAs (lncRNAs) were included in the study. Results Both platforms performed equally well for protein-coding RNAs, however the stochastic variability was higher for the sequencing data than for microarrays. This reduced the number of differentially expressed genes and genes with predictive potential for RNA-seq compared to microarray data. Analysis of this variability revealed a lack of reads for short and low abundant genes; lncRNAs, being shorter and less abundant RNAs, were found especially susceptible to this issue. A major difference between the two platforms was uncovered by analysis of alternatively spliced genes. Investigation of differential exon abundance showed insufficient reads for many exons and exon junctions in RNA-seq while the detection on the array platform was more stable. Nevertheless, we identified 207 genes which undergo alternative splicing and were consistently detected by both techniques. Conclusions Despite the fact that the results of gene expression analysis were highly consistent between Human Transcriptome Arrays and RNA-seq platforms, the analysis of alternative splicing produced discordant results. We concluded that modern microarrays can still outperform sequencing for standard analysis of gene expression in terms of reproducibility and cost. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3819-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Petr V Nazarov
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.
| | - Arnaud Muller
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Tony Kaoma
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Nathalie Nicot
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Cristina Maximo
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | | | - Nhan L Tran
- Departments of Cancer Biology and Neurosurgery, Mayo Clinic Arizona, Phoenix, USA
| | - Gunnar Dittmar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Laurent Vallar
- Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
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Golebiewska A, Stieber D, Oudin A, Azuaje F, Kaoma T, Vallar L, Mock A, Herold-Mende C, Bjerkvig R, Niclou SP. P05.01 Patient-derived xenograft (PDX) model of glioblastoma: from basic research to preclinical studies. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now188.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Boutzen H, Saland E, Larrue C, de Toni F, Gales L, Castelli FA, Cathebas M, Zaghdoudi S, Stuani L, Kaoma T, Riscal R, Yang G, Hirsch P, David M, De Mas-Mansat V, Delabesse E, Vallar L, Delhommeau F, Jouanin I, Ouerfelli O, Le Cam L, Linares LK, Junot C, Portais JC, Vergez F, Récher C, Sarry JE. Isocitrate dehydrogenase 1 mutations prime the all-trans retinoic acid myeloid differentiation pathway in acute myeloid leukemia. J Exp Med 2016; 213:483-97. [PMID: 26951332 PMCID: PMC4821643 DOI: 10.1084/jem.20150736] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 02/02/2016] [Indexed: 11/30/2022] Open
Abstract
Boutzen et al. show that the IDH1 mutation and its oncometabolite, (R)-2-hydroxyglutarate, dysregulate downstream target pathways of myeloid-specific TFs, especially CEBPα, priming mutant IDH1-R132H AML blasts to the granulomonocytic lineage. Acute myeloid leukemia (AML) is characterized by the accumulation of malignant blasts with impaired differentiation programs caused by recurrent mutations, such as the isocitrate dehydrogenase (IDH) mutations found in 15% of AML patients. These mutations result in the production of the oncometabolite (R)-2-hydroxyglutarate (2-HG), leading to a hypermethylation phenotype that dysregulates hematopoietic differentiation. In this study, we identified mutant R132H IDH1-specific gene signatures regulated by key transcription factors, particularly CEBPα, involved in myeloid differentiation and retinoid responsiveness. We show that treatment with all-trans retinoic acid (ATRA) at clinically achievable doses markedly enhanced terminal granulocytic differentiation in AML cell lines, primary patient samples, and a xenograft mouse model carrying mutant IDH1. Moreover, treatment with a cell-permeable form of 2-HG sensitized wild-type IDH1 AML cells to ATRA-induced myeloid differentiation, whereas inhibition of 2-HG production significantly reduced ATRA effects in mutant IDH1 cells. ATRA treatment specifically decreased cell viability and induced apoptosis of mutant IDH1 blasts in vitro. ATRA also reduced tumor burden of mutant IDH1 AML cells xenografted in NOD–Scid–IL2rγnull mice and markedly increased overall survival, revealing a potent antileukemic effect of ATRA in the presence of IDH1 mutation. This therapeutic strategy holds promise for this AML patient subgroup in future clinical studies.
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Affiliation(s)
- Héléna Boutzen
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse Oncopole, F-31059 Toulouse, France
| | - Estelle Saland
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France
| | - Clément Larrue
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France
| | - Fabienne de Toni
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France
| | - Lara Gales
- Université de Toulouse III Paul Sabatier, Institut National des Sciences Appliquées, UPS, Institut National Polytechnique, L'Ingénierie des Systèmes Biologiques et des Procédés, F-31077 Toulouse, France Institut National de la Recherche Agronomique (INRA), UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France Centre National de la Recherche Scientifique, UMR5504, F-31400 Toulouse, France
| | - Florence A Castelli
- CEA/DSV/iBiTec-S/SPI, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, F-91191 Gif-sur-Yvette, France
| | - Mathilde Cathebas
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France
| | - Sonia Zaghdoudi
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France
| | - Lucille Stuani
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France
| | - Tony Kaoma
- Genomics Research Unit, Centre de Recherche Public de la Santé, 1526 Luxembourg City, Luxembourg
| | - Romain Riscal
- INSERM, U1194, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France Université de Montpellier, F-34298 Montpellier, France Institut régional du Cancer Montpellier, F-34298 Montpellier, France
| | - Guangli Yang
- Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Pierre Hirsch
- Sorbonne Universités, Université Pierre-et-Marie-Curie (UPMC) Paris VI, UMR-S 938, CDR Saint-Antoine, F-75012 Paris, France INSERM, UMR-S938, CDR Saint-Antoine, F-75012 Paris, France Sorbonne Universités, UPMC Paris VI, GRC n°07, Groupe de Recherche Clinique sur les Myéloproliférations Aiguës et Chroniques MyPAC, F-75012 Paris, France AP-HP, Hôpital Saint-Antoine, F-75012 Paris, France
| | - Marion David
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France
| | - Véronique De Mas-Mansat
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse Oncopole, F-31059 Toulouse, France
| | - Eric Delabesse
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse Oncopole, F-31059 Toulouse, France
| | - Laurent Vallar
- Genomics Research Unit, Centre de Recherche Public de la Santé, 1526 Luxembourg City, Luxembourg
| | - François Delhommeau
- Sorbonne Universités, Université Pierre-et-Marie-Curie (UPMC) Paris VI, UMR-S 938, CDR Saint-Antoine, F-75012 Paris, France INSERM, UMR-S938, CDR Saint-Antoine, F-75012 Paris, France Sorbonne Universités, UPMC Paris VI, GRC n°07, Groupe de Recherche Clinique sur les Myéloproliférations Aiguës et Chroniques MyPAC, F-75012 Paris, France AP-HP, Hôpital Saint-Antoine, F-75012 Paris, France
| | - Isabelle Jouanin
- INRA, UMR1331, Toxalim, Research Centre in Food Toxicology, F-31027 Toulouse, France Université de Toulouse, INP, Toxalim, UMR1331, F-31027 Toulouse, France
| | - Ouathek Ouerfelli
- Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Laurent Le Cam
- INSERM, U1194, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France Université de Montpellier, F-34298 Montpellier, France Institut régional du Cancer Montpellier, F-34298 Montpellier, France
| | - Laetitia K Linares
- INSERM, U1194, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France Université de Montpellier, F-34298 Montpellier, France Institut régional du Cancer Montpellier, F-34298 Montpellier, France
| | - Christophe Junot
- CEA/DSV/iBiTec-S/SPI, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, F-91191 Gif-sur-Yvette, France
| | - Jean-Charles Portais
- Université de Toulouse III Paul Sabatier, Institut National des Sciences Appliquées, UPS, Institut National Polytechnique, L'Ingénierie des Systèmes Biologiques et des Procédés, F-31077 Toulouse, France Institut National de la Recherche Agronomique (INRA), UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France Centre National de la Recherche Scientifique, UMR5504, F-31400 Toulouse, France
| | - François Vergez
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse Oncopole, F-31059 Toulouse, France
| | - Christian Récher
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France Service d'Hématologie, Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer Toulouse Oncopole, F-31059 Toulouse, France
| | - Jean-Emmanuel Sarry
- Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Research Center of Toulouse, U1037, F-31024 Toulouse, France Université de Toulouse, F-31300 Toulouse, France
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El-Khoury V, Pierson S, Kaoma T, Bernardin F, Berchem G. Assessing cellular and circulating miRNA recovery: the impact of the RNA isolation method and the quantity of input material. Sci Rep 2016; 6:19529. [PMID: 26787294 PMCID: PMC4726450 DOI: 10.1038/srep19529] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [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: 08/06/2015] [Accepted: 12/14/2015] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) have emerged as promising cancer biomarkers. However, exploiting their informative potential requires careful optimization of their detection. Here, we compared the efficiency of commonly used RNA extraction kits in miRNA recovery from cells, plasma and urine/plasma-derived exosomes, using single-gene RT-qPCR and miRNA profiling. We used increasing amounts of starting material to investigate the impact of the input material size on miRNA extraction. We showed that miRNA recovery was largely influenced by the isolation method and by the amount of input material. In particular, the miRCURY™ kit provided highly pure RNA. However, its columns poorly recovered miRNAs from limiting amounts of cells and plasma, and rapidly saturated by large RNA species and plasma components, thus impeding miRNA recovery from high input amounts. Overall, the miRNeasy® kit permitted a better miRNA detection despite a less pure extracted RNA. Nevertheless, some miRNAs were preferentially or exclusively isolated by either of the methods. Trizol® LS resulted in very low purity RNA which affected RT-qPCR efficiency. In general, miRCURY™ biofluids kit efficiently extracted miRNAs from plasma. A careful selection of the RNA isolation method and the consideration of the type and size of input material are highly recommended to avoid biased results.
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Affiliation(s)
- Victoria El-Khoury
- Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Sandrine Pierson
- Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Tony Kaoma
- Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - François Bernardin
- Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
| | - Guy Berchem
- Department of Oncology, Luxembourg Institute of Health (LIH), 84 Val Fleuri, L-1526 Luxembourg, Luxembourg.,Centre Hospitalier de Luxembourg, 4 rue Barblé, L-1210 Luxembourg, Luxembourg
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Lommel MJ, Trairatphisan P, Gäbler K, Laurini C, Muller A, Kaoma T, Vallar L, Sauter T, Schaffner-Reckinger E. L-plastin Ser5 phosphorylation in breast cancer cells and in vitro is mediated by RSK downstream of the ERK/MAPK pathway. FASEB J 2015; 30:1218-33. [PMID: 26631483 DOI: 10.1096/fj.15-276311] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 05/21/2015] [Accepted: 11/16/2015] [Indexed: 12/20/2022]
Abstract
Deregulated cell migration and invasion are hallmarks of metastatic cancer cells. Phosphorylation on residue Ser5 of the actin-bundling protein L-plastin activates L-plastin and has been reported to be crucial for invasion and metastasis. Here, we investigate signal transduction leading to L-plastin Ser5 phosphorylation using 4 human breast cancer cell lines. Whole-genome microarray analysis comparing cell lines with different invasive capacities and corresponding variations in L-plastin Ser5 phosphorylation level revealed that genes of the ERK/MAPK pathway are differentially expressed. It is noteworthy that in vitro kinase assays showed that ERK/MAPK pathway downstream ribosomal protein S6 kinases α-1 (RSK1) and α-3 (RSK2) are able to directly phosphorylate L-plastin on Ser5. Small interfering RNA- or short hairpin RNA-mediated knockdown and activation/inhibition studies followed by immunoblot analysis and computational modeling confirmed that ribosomal S6 kinase (RSK) is an essential activator of L-plastin. Migration and invasion assays showed that RSK knockdown led to a decrease of up to 30% of migration and invasion of MDA-MB-435S cells. Although the presence of L-plastin was not necessary for migration/invasion of these cells, immunofluorescence assays illustrated RSK-dependent recruitment of Ser5-phosphorylated L-plastin to migratory structures. Altogether, we provide evidence that the ERK/MAPK pathway is involved in L-plastin Ser5 phosphorylation in breast cancer cells with RSK1 and RSK2 kinases able to directly phosphorylate L-plastin residue Ser5.
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Affiliation(s)
- Maiti J Lommel
- *Laboratory of Cytoskeleton and Cell Plasticity and Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg; and Genomics Research Unit, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Panuwat Trairatphisan
- *Laboratory of Cytoskeleton and Cell Plasticity and Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg; and Genomics Research Unit, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Karoline Gäbler
- *Laboratory of Cytoskeleton and Cell Plasticity and Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg; and Genomics Research Unit, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Christina Laurini
- *Laboratory of Cytoskeleton and Cell Plasticity and Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg; and Genomics Research Unit, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Arnaud Muller
- *Laboratory of Cytoskeleton and Cell Plasticity and Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg; and Genomics Research Unit, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Tony Kaoma
- *Laboratory of Cytoskeleton and Cell Plasticity and Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg; and Genomics Research Unit, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Laurent Vallar
- *Laboratory of Cytoskeleton and Cell Plasticity and Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg; and Genomics Research Unit, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Thomas Sauter
- *Laboratory of Cytoskeleton and Cell Plasticity and Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg; and Genomics Research Unit, Luxembourg Institute of Health, Luxembourg City, Luxembourg
| | - Elisabeth Schaffner-Reckinger
- *Laboratory of Cytoskeleton and Cell Plasticity and Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Luxembourg City, Luxembourg; and Genomics Research Unit, Luxembourg Institute of Health, Luxembourg City, Luxembourg
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Pacheco MP, John E, Kaoma T, Heinäniemi M, Nicot N, Vallar L, Bueb JL, Sinkkonen L, Sauter T. Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network. BMC Genomics 2015; 16:809. [PMID: 26480823 PMCID: PMC4617894 DOI: 10.1186/s12864-015-1984-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 10/06/2015] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The reconstruction of context-specific metabolic models from easily and reliably measurable features such as transcriptomics data will be increasingly important in research and medicine. Current reconstruction methods suffer from high computational effort and arbitrary threshold setting. Moreover, understanding the underlying epigenetic regulation might allow the identification of putative intervention points within metabolic networks. Genes under high regulatory load from multiple enhancers or super-enhancers are known key genes for disease and cell identity. However, their role in regulation of metabolism and their placement within the metabolic networks has not been studied. METHODS Here we present FASTCORMICS, a fast and robust workflow for the creation of high-quality metabolic models from transcriptomics data. FASTCORMICS is devoid of arbitrary parameter settings and due to its low computational demand allows cross-validation assays. Applying FASTCORMICS, we have generated models for 63 primary human cell types from microarray data, revealing significant differences in their metabolic networks. RESULTS To understand the cell type-specific regulation of the alternative metabolic pathways we built multiple models during differentiation of primary human monocytes to macrophages and performed ChIP-Seq experiments for histone H3 K27 acetylation (H3K27ac) to map the active enhancers in macrophages. Focusing on the metabolic genes under high regulatory load from multiple enhancers or super-enhancers, we found these genes to show the most cell type-restricted and abundant expression profiles within their respective pathways. Importantly, the high regulatory load genes are associated to reactions enriched for transport reactions and other pathway entry points, suggesting that they are critical regulatory control points for cell type-specific metabolism. CONCLUSIONS By integrating metabolic modelling and epigenomic analysis we have identified high regulatory load as a common feature of metabolic genes at pathway entry points such as transporters within the macrophage metabolic network. Analysis of these control points through further integration of metabolic and gene regulatory networks in various contexts could be beneficial in multiple fields from identification of disease intervention strategies to cellular reprogramming.
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Affiliation(s)
- Maria Pires Pacheco
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
| | - Elisabeth John
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg.
| | - Tony Kaoma
- Genomics Research Unit, Luxembourg Institute of Health, L-1526, Luxembourg, Luxembourg.
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211, Kuopio, Finland.
| | - Nathalie Nicot
- Genomics Research Unit, Luxembourg Institute of Health, L-1526, Luxembourg, Luxembourg.
| | - Laurent Vallar
- Genomics Research Unit, Luxembourg Institute of Health, L-1526, Luxembourg, Luxembourg.
| | - Jean-Luc Bueb
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
| | - Lasse Sinkkonen
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg.
| | - Thomas Sauter
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
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Sanzey M, Abdul Rahim SA, Oudin A, Dirkse A, Kaoma T, Vallar L, Herold-Mende C, Bjerkvig R, Golebiewska A, Niclou SP. Comprehensive analysis of glycolytic enzymes as therapeutic targets in the treatment of glioblastoma. PLoS One 2015; 10:e0123544. [PMID: 25932951 PMCID: PMC4416792 DOI: 10.1371/journal.pone.0123544] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/05/2015] [Indexed: 12/19/2022] Open
Abstract
Major efforts have been put in anti-angiogenic treatment for glioblastoma (GBM), an aggressive and highly vascularized brain tumor with dismal prognosis. However clinical outcome with anti-angiogenic agents has been disappointing and tumors quickly develop escape mechanisms. In preclinical GBM models we have recently shown that bevacizumab, a blocking antibody against vascular endothelial growth factor, induces hypoxia in treated tumors, which is accompanied by increased glycolytic activity and tumor invasiveness. Genome-wide transcriptomic analysis of patient derived GBM cells including stem cell lines revealed a strong up-regulation of glycolysis-related genes in response to severe hypoxia. We therefore investigated the importance of glycolytic enzymes in GBM adaptation and survival under hypoxia, both in vitro and in vivo. We found that shRNA-mediated attenuation of glycolytic enzyme expression interfered with GBM growth under normoxic and hypoxic conditions in all cellular models. Using intracranial GBM xenografts we identified seven glycolytic genes whose knockdown led to a dramatic survival benefit in mice. The most drastic effect was observed for PFKP (PFK1, +21.8%) and PDK1 (+20.9%), followed by PGAM1 and ENO1 (+14.5% each), HK2 (+11.8%), ALDOA (+10.9%) and ENO2 (+7.2%). The increase in mouse survival after genetic interference was confirmed using chemical inhibition of PFK1 with clotrimazole. We thus provide a comprehensive analysis on the importance of the glycolytic pathway for GBM growth in vivo and propose PFK1 and PDK1 as the most promising therapeutic targets to address the metabolic escape mechanisms of GBM.
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Affiliation(s)
- Morgane Sanzey
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (L.I.H.), Luxembourg, Luxembourg
| | - Siti Aminah Abdul Rahim
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (L.I.H.), Luxembourg, Luxembourg
| | - Anais Oudin
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (L.I.H.), Luxembourg, Luxembourg
| | - Anne Dirkse
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (L.I.H.), Luxembourg, Luxembourg
| | - Tony Kaoma
- Genomics Research Unit, Luxembourg Institute of Health (L.I.H.), Luxembourg, Luxembourg
| | - Laurent Vallar
- Genomics Research Unit, Luxembourg Institute of Health (L.I.H.), Luxembourg, Luxembourg
| | - Christel Herold-Mende
- Experimental Neurosurgery, Department of Neurosurgery, University of Heidelberg, Heidelberg, Germany
| | - Rolf Bjerkvig
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (L.I.H.), Luxembourg, Luxembourg
- NorLux Neuro-Oncology Laboratory, Department of Biomedicine, University of Bergen, Bergen, Norway
- KG Jebsen Brain Tumour Research Center, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Anna Golebiewska
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (L.I.H.), Luxembourg, Luxembourg
| | - Simone P. Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (L.I.H.), Luxembourg, Luxembourg
- KG Jebsen Brain Tumour Research Center, Department of Biomedicine, University of Bergen, Bergen, Norway
- * E-mail:
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Naegelen I, Plançon S, Nicot N, Kaoma T, Muller A, Vallar L, Tschirhart EJ, Bréchard S. An essential role of syntaxin 3 protein for granule exocytosis and secretion of IL-1α, IL-1β, IL-12b, and CCL4 from differentiated HL-60 cells. J Leukoc Biol 2014; 97:557-71. [PMID: 25548252 DOI: 10.1189/jlb.3a0514-254rr] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Besides their roles in the killing of pathogens, neutrophils have the capacity to package a variety of cytokines into cytoplasmic granules for subsequent release upon inflammatory conditions. Because the rapid secretion of cytokines orchestrates the action of other immune cells at the infection site and thus, can contribute to the development and chronicity of inflammatory diseases, we aimed to determine the intracellular SNARE machinery responsible for the regulation of cytokine secretion and degranulation. From a constructed gene-expression network, we first selected relevant cytokines for functional validation by the CBA approach. We established a cytokine-secretion profile for human neutrophils and dHL-60 cells, underlining their similar ability to secrete a broad variety of cytokines within proinflammatory conditions mimicked by LPS stimulation. Secondly, after screening of SNARE genes by microarray experiments, we selected STX3 for further functional studies. With the use of a siRNA strategy, we show that STX3 is clearly required for the maximal release of IL-1α, IL-1β, IL-12b, and CCL4 without alteration of other cytokine secretion in dHL-60 cells. In addition, we demonstrate that STX3 is involved in MMP-9 exocytosis from gelatinase granules, where STX3 is partly localized. Our results suggest that the secretion of IL-1α, IL-1β, IL-12b, and CCL4 occurs during gelatinase degranulation, a process controlled by STX3. In summary, these findings provide first evidence that STX3 has an essential role in trafficking pathways of cytokines in neutrophil granulocytes.
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Affiliation(s)
- Isabelle Naegelen
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Sébastien Plançon
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Nathalie Nicot
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Tony Kaoma
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Arnaud Muller
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Laurent Vallar
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Eric J Tschirhart
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
| | - Sabrina Bréchard
- *University of Luxembourg, Life Sciences Research Unit, Calcium Signaling and Inflammation, Luxembourg; and Centre de Recherche Public Santé, Luxembourg
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Bour T, Yang X, Li W, Bernardin F, Kaoma T, Muller A, Vallar L, Steinmetz A. Differential Effects of Antofine N-Oxide on Solid Tumor and Leukemia Cells. Anticancer Agents Med Chem 2014; 14:1315-23. [DOI: 10.2174/1871520614666140624110458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 03/03/2014] [Accepted: 05/15/2014] [Indexed: 11/22/2022]
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Moussay E, Kaoma T, Baginska J, Muller A, Van Moer K, Nicot N, Nazarov PV, Vallar L, Chouaib S, Berchem G, Janji B. The acquisition of resistance to TNFα in breast cancer cells is associated with constitutive activation of autophagy as revealed by a transcriptome analysis using a custom microarray. Autophagy 2014; 7:760-70. [DOI: 10.4161/auto.7.7.15454] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Sleiman M, Brons NHC, Kaoma T, Dogu F, Villa-Forte A, Lenoble P, Hentges F, Kotsch K, Gadola SD, Vilches C, Zimmer J. NK cell killer Ig-like receptor repertoire acquisition and maturation are strongly modulated by HLA class I molecules. J Immunol 2014; 192:2602-10. [PMID: 24554773 DOI: 10.4049/jimmunol.1302843] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The interaction between clonally distributed inhibitory receptors and their activating counterparts on NK cells and HLA class I molecules defines NK cell functions, but the role of HLA class I ligands in the acquisition of their receptors during NK development is still unclear. Although some studies demonstrated that HLA-C affects the expression of killer Ig-like receptors (KIR), other studies showed that NK cells acquire their KIR repertoire in a stochastic manner. Only when infected with human CMV is an expansion of self-specific KIR(+) NKG2C(+) NK cells detected. To gain more insight into this question, we compared the coexpression of different KIR molecules, NKG2A, CD8, and CD57, on NK cells in healthy donors and seven patients with deficient HLA class I expression due to mutations in one of the TAP genes. Our results show a correlation between the presence/absence of HLA class I molecules and the coexpression of their receptors. In an HLA class I low-expression context, an increase in KIR molecules' coexpression is detected on the NKG2A(+) CD8(+) subset. In functional assays, hyporesponsiveness was observed for TAP-deficient NK cells derived from four patients. In contrast, NK cells from patient five were functional, whereas CD107a(+) and IFN-γ(+) CD56(dim) NK cells presented a different pattern of HLA class I receptors compared with healthy donors. Taken together, our results provide strong evidence for the role of HLA class I molecules in NK cell maturation and KIR repertoire acquisition.
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Affiliation(s)
- Marwan Sleiman
- Laboratory of Immunogenetics and Allergology, Public Research Center for Health, L-1526 Luxembourg, Luxembourg
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Ghoneim C, Kaoma T, Nicot N, François B, Nazarov P, Muller A, Birembaut P, Vallar L. Abstract 3905: Identification of new tumor-specific splice variants in NSCL cancers by whole genome exon arrays. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-3905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Although lung cancer is one of the major causes of cancer death in men and women worldwide, the molecular pathogenesis of this disease remains elusive. The contribution of alternative splicing (AS) to cancer pathogenesis and progression is emerging as an area of considerable interest. Cancer-specific splice variants seem to play a key role in disease mechanism and etiology.
In this study, we analyzed 20 matched pairs of tumor specimens of Adenocarcinomas (AC), Squamous Cell Carcinomas (SCC) and adjacent normal tissue using Affymetrix GeneChip Exon microarrays. With this technology, it is possible to profile simultaneously gene expression and alternative splicing patterns for the entire genome using a single array. At the exon level, multiple probes for each exon enable the discrimination among different isoforms of a gene. Total RNA from tumors or normal tissue samples were amplified using the Ambion whole transcript expression kit and were hybridized onto GeneChip Human Exon 1.0 ST Array®. Data generated were normalized using RMA and were subjected to several layers of filtering (DABG filter, Multiple mRNAs filter). The delta splice index (ΔSI) was calculated, and alternative splicing events were detected using MIDAS and Rank Product method. Probesets were ranked based on their SI p-values.
By comparing tumor samples to the corresponding normal subgroups, we generated a list of 1689 splice variant candidates for SCC and 1010 for AC showing significant differential expression between normal and tumor tissues. Top candidates in each tumor subtype were selected based on their ΔSI for manual inspection and further bioinformatics analysis. Study of alternatively spliced candidates revealed that approximately 30 % of the genes were detected in both types of cancer. Gene function analysis combining text mining and knowledge-based approaches indicated that the largest subset (70 %) of these genes was related to cancer. Within this group, 30% of genes were related to lung cancers. Interestingly the major part (85%) of variant candidates was not previously associated with AS events in cancer. We focused our attention on this latter group and, through validation by RT/PCR, confirmed the existence of new specific alternative splicing events occurring in each cancer type. In addition, we identified biological pathways and gene networks that are specifically altered in AC or SCC. The cancer-specific AS variants and pathways identified in our study are promising biomarkers and targets for diagnostic or therapeutic purposes.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3905. doi:10.1158/1538-7445.AM2011-3905
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Affiliation(s)
| | - Tony Kaoma
- 1Microarray center CRP-SANTE, Luxembourg, Luxembourg
| | | | | | - Petr Nazarov
- 1Microarray center CRP-SANTE, Luxembourg, Luxembourg
| | - Arnaud Muller
- 1Microarray center CRP-SANTE, Luxembourg, Luxembourg
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