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Rodriguez-Fos E, Planas-Fèlix M, Burkert M, Puiggròs M, Toedling J, Thiessen N, Blanc E, Szymansky A, Hertwig F, Ishaque N, Beule D, Torrents D, Eggert A, Koche RP, Schwarz RF, Haase K, Schulte JH, Henssen AG. Mutational topography reflects clinical neuroblastoma heterogeneity. Cell Genom 2023; 3:100402. [PMID: 37868040 PMCID: PMC10589636 DOI: 10.1016/j.xgen.2023.100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 08/11/2023] [Indexed: 10/24/2023]
Abstract
Neuroblastoma is a pediatric solid tumor characterized by strong clinical heterogeneity. Although clinical risk-defining genomic alterations exist in neuroblastomas, the mutational processes involved in their generation remain largely unclear. By examining the topography and mutational signatures derived from all variant classes, we identified co-occurring mutational footprints, which we termed mutational scenarios. We demonstrate that clinical neuroblastoma heterogeneity is associated with differences in the mutational processes driving these scenarios, linking risk-defining pathognomonic variants to distinct molecular processes. Whereas high-risk MYCN-amplified neuroblastomas were characterized by signs of replication slippage and stress, homologous recombination-associated signatures defined high-risk non-MYCN-amplified patients. Non-high-risk neuroblastomas were marked by footprints of chromosome mis-segregation and TOP1 mutational activity. Furthermore, analysis of subclonal mutations uncovered differential activity of these processes through neuroblastoma evolution. Thus, clinical heterogeneity of neuroblastoma patients can be linked to differences in the mutational processes that are active in their tumors.
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Affiliation(s)
- Elias Rodriguez-Fos
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mercè Planas-Fèlix
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Burkert
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Joern Toedling
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nina Thiessen
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Eric Blanc
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Naveed Ishaque
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Angelika Eggert
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes H. Schulte
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Boeddrich A, Haenig C, Neuendorf N, Blanc E, Ivanov A, Kirchner M, Schleumann P, Bayraktaroğlu I, Richter M, Molenda CM, Sporbert A, Zenkner M, Schnoegl S, Suenkel C, Schneider LS, Rybak-Wolf A, Kochnowsky B, Byrne LM, Wild EJ, Nielsen JE, Dittmar G, Peters O, Beule D, Wanker EE. A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease. Genome Med 2023; 15:50. [PMID: 37468900 PMCID: PMC10357615 DOI: 10.1186/s13073-023-01206-2] [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: 03/14/2022] [Accepted: 06/22/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is characterized by the intra- and extracellular accumulation of amyloid-β (Aβ) peptides. How Aβ aggregates perturb the proteome in brains of patients and AD transgenic mouse models, remains largely unclear. State-of-the-art mass spectrometry (MS) methods can comprehensively detect proteomic alterations, providing relevant insights unobtainable with transcriptomics investigations. Analyses of the relationship between progressive Aβ aggregation and protein abundance changes in brains of 5xFAD transgenic mice have not been reported previously. METHODS We quantified progressive Aβ aggregation in hippocampus and cortex of 5xFAD mice and controls with immunohistochemistry and membrane filter assays. Protein changes in different mouse tissues were analyzed by MS-based proteomics using label-free quantification; resulting MS data were processed using an established pipeline. Results were contrasted with existing proteomic data sets from postmortem AD patient brains. Finally, abundance changes in the candidate marker Arl8b were validated in cerebrospinal fluid (CSF) from AD patients and controls using ELISAs. RESULTS Experiments revealed faster accumulation of Aβ42 peptides in hippocampus than in cortex of 5xFAD mice, with more protein abundance changes in hippocampus, indicating that Aβ42 aggregate deposition is associated with brain region-specific proteome perturbations. Generating time-resolved data sets, we defined Aβ aggregate-correlated and anticorrelated proteome changes, a fraction of which was conserved in postmortem AD patient brain tissue, suggesting that proteome changes in 5xFAD mice mimic disease-relevant changes in human AD. We detected a positive correlation between Aβ42 aggregate deposition in the hippocampus of 5xFAD mice and the abundance of the lysosome-associated small GTPase Arl8b, which accumulated together with axonal lysosomal membranes in close proximity of extracellular Aβ plaques in 5xFAD brains. Abnormal aggregation of Arl8b was observed in human AD brain tissue. Arl8b protein levels were significantly increased in CSF of AD patients. CONCLUSIONS We report a comprehensive biochemical and proteomic investigation of hippocampal and cortical brain tissue derived from 5xFAD transgenic mice, providing a valuable resource to the neuroscientific community. We identified Arl8b, with significant abundance changes in 5xFAD and AD patient brains. Arl8b might enable the measurement of progressive lysosome accumulation in AD patients and have clinical utility as a candidate biomarker.
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Affiliation(s)
- Annett Boeddrich
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Christian Haenig
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Nancy Neuendorf
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Andranik Ivanov
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Marieluise Kirchner
- Core Unit Proteomics, Berlin Institute of Health at Charité - University Medicine Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
| | - Philipp Schleumann
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Irem Bayraktaroğlu
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Matthias Richter
- Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Christine Mirjam Molenda
- Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Anje Sporbert
- Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Martina Zenkner
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Sigrid Schnoegl
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Christin Suenkel
- Systems Biology of Gene Regulatory Elements, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Luisa-Sophie Schneider
- Department of Psychiatry, Charité - University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Agnieszka Rybak-Wolf
- Systems Biology of Gene Regulatory Elements, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Bianca Kochnowsky
- Department of Psychiatry, Charité - University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Lauren M Byrne
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Edward J Wild
- UCL Huntington's Disease Centre, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- National Hospital for Neurology & Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Jørgen E Nielsen
- Neurogenetics Clinic & Research Lab, Danish Dementia Research Centre, Rigshospitalet, University of Copenhagen, Section 8008, Inge Lehmanns Vej 8, 2100, Copenhagen, Denmark
| | - Gunnar Dittmar
- Core Unit Proteomics, Berlin Institute of Health at Charité - University Medicine Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Proteomics of Cellular Signalling, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445, Strassen, Luxembourg
| | - Oliver Peters
- Department of Psychiatry, Charité - University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), Charitéplatz 1, 10117, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health at Charité - University Medicine Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Straße 10, 13125, Berlin, Germany.
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Rieke DT, Schröder S, Schafhausen P, Blanc E, Zuljan E, von der Emde B, Beule D, Keller U, Keilholz U, Klinghammer K. Targeted treatment in a case series of AR+, HRAS/PIK3CA co-mutated salivary duct carcinoma. Front Oncol 2023; 13:1107134. [PMID: 37427101 PMCID: PMC10325704 DOI: 10.3389/fonc.2023.1107134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/26/2023] [Indexed: 07/11/2023] Open
Abstract
Background and purpose A subgroup of salivary duct carcinoma (SDC) harbor overexpression of the androgen receptor (AR), and co-occurring mutations in the HRAS- and PIK3CA-genes. The impact of genomic complexity on targeted treatment strategies in advanced cancer is unknown. Materials and methods We analyzed molecular and clinical data from an institutional molecular tumor board (MTB) to identify AR+, HRAS/PIK3CA co-mutated SDC. Follow-up was performed within the MTB registrational study or retrospective chart review after approval by the local ethics committee. Response was assessed by the investigator. A systematic literature search was performed in MEDLINE to identify additional clinically annotated cases. Results 4 patients with AR+ HRAS/PIK3CA co-mutated SDC and clinical follow-up data were identified from the MTB. An additional 9 patients with clinical follow-up were identified from the literature. In addition to AR overexpression and HRAS and PIK3CA-alterations, PD-L1 expression and Tumor Mutational Burden > 10 Mutations per Megabase were identified as additional potentially targetable alterations. Among evaluable patients, androgen deprivation therapy (ADT) was initiated in 7 patients (1 Partial Response (PR), 2 Stable Disease (SD), 3 Progressive Disease (PD), 2 not evaluable), tipifarnib was initiated in 6 patients (1 PR, 4 SD, 1 PD). One patient each was treated with immune checkpoint inhibition (Mixed Response) and combination therapies of tipifarnib and ADT (SD) and alpelisib and ADT (PR). Conclusion Available data further support comprehensive molecular profiling of SDC. Combination therapies, PI3K-inhibitors and immune therapy warrant further investigation, ideally in clinical trials. Future research should consider this rare subgroup of SDC.
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Affiliation(s)
- Damian T. Rieke
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Schröder
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Philippe Schafhausen
- Department of Oncology, Hematology, and Bone Marrow Transplantation with Section of Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eric Blanc
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Erika Zuljan
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Benjamin von der Emde
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrich Keller
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Ulrich Keilholz
- Comprehensive Cancer Center, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konrad Klinghammer
- Department of Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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4
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Winkler W, Farré Díaz C, Blanc E, Napieczynska H, Langner P, Werner M, Walter B, Wollert-Wulf B, Yasuda T, Heuser A, Beule D, Mathas S, Anagnostopoulos I, Rosenwald A, Rajewsky K, Janz M. Mouse models of human multiple myeloma subgroups. Proc Natl Acad Sci U S A 2023; 120:e2219439120. [PMID: 36853944 PMCID: PMC10013859 DOI: 10.1073/pnas.2219439120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/26/2023] [Indexed: 03/01/2023] Open
Abstract
Multiple myeloma (MM), a tumor of germinal center (GC)-experienced plasma cells, comprises distinct genetic subgroups, such as the t(11;14)/CCND1 and the t(4;14)/MMSET subtype. We have generated genetically defined, subgroup-specific MM models by the GC B cell-specific coactivation of mouse Ccnd1 or MMSET with a constitutively active Ikk2 mutant, mimicking the secondary NF-κB activation frequently seen in human MM. Ccnd1/Ikk2ca and MMSET/Ikk2ca mice developed a pronounced, clonally restricted plasma cell outgrowth with age, accompanied by serum M spikes, bone marrow insufficiency, and bone lesions. The transgenic plasma cells could be propagated in vivo and showed distinct transcriptional profiles, resembling their human MM counterparts. Thus, we show that targeting the expression of genes involved in MM subgroup-specific chromosomal translocations into mouse GC B cells translates into distinct MM-like diseases that recapitulate key features of the human tumors, opening the way to a better understanding of the pathogenesis and therapeutic vulnerabilities of different MM subgroups.
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Affiliation(s)
- Wiebke Winkler
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
- Biology of Malignant Lymphomas, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité – Universitätsmedizin Berlin, Berlin13125, Germany
- Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Berlin13125, Germany
| | - Carlota Farré Díaz
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
- Biology of Malignant Lymphomas, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité – Universitätsmedizin Berlin, Berlin13125, Germany
- Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Berlin13125, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin10117, Germany
| | - Hanna Napieczynska
- Animal Phenotyping, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
| | - Patrick Langner
- Animal Phenotyping, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
| | - Marvin Werner
- Biology of Malignant Lymphomas, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité – Universitätsmedizin Berlin, Berlin13125, Germany
- Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Berlin13125, Germany
| | - Barbara Walter
- Biology of Malignant Lymphomas, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité – Universitätsmedizin Berlin, Berlin13125, Germany
- Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Berlin13125, Germany
| | - Brigitte Wollert-Wulf
- Biology of Malignant Lymphomas, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité – Universitätsmedizin Berlin, Berlin13125, Germany
- Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Berlin13125, Germany
| | - Tomoharu Yasuda
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
| | - Arnd Heuser
- Animal Phenotyping, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin10117, Germany
| | - Stephan Mathas
- Biology of Malignant Lymphomas, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité – Universitätsmedizin Berlin, Berlin13125, Germany
- Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Berlin13125, Germany
| | - Ioannis Anagnostopoulos
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken, Würzburg97080, Germany
| | - Andreas Rosenwald
- Institute of Pathology, Universität Würzburg and Comprehensive Cancer Centre Mainfranken, Würzburg97080, Germany
| | - Klaus Rajewsky
- Immune Regulation and Cancer, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
| | - Martin Janz
- Biology of Malignant Lymphomas, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité – Universitätsmedizin Berlin, Berlin13125, Germany
- Hematology, Oncology and Cancer Immunology, Charité – Universitätsmedizin Berlin, Berlin13125, Germany
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5
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Claude L, Bolle S, Morelle M, Huchet A, Vigneron C, Escande A, Chapet S, Leseur J, Bernier V, Carrie C, Barry A, Vizoso S, Blanc E, Laprie A, Supiot S. Hypofractionated stereotactic body radiation therapy (SBRT) in pediatric patients: results of a national prospective multicenter study. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.09.043] [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: 11/16/2022]
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6
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Welters C, Lammoglia Cobo MF, Stein CA, Hsu MT, Ben Hamza A, Penter L, Chen X, Buccitelli C, Popp O, Mertins P, Dietze K, Bullinger L, Moosmann A, Blanc E, Beule D, Gerbitz A, Strobel J, Hackstein H, Rahn HP, Dornmair K, Blankenstein T, Hansmann L. Immune Phenotypes and Target Antigens of Clonally Expanded Bone Marrow T Cells in Treatment-Naïve Multiple Myeloma. Cancer Immunol Res 2022; 10:1407-1419. [PMID: 36122410 PMCID: PMC9627264 DOI: 10.1158/2326-6066.cir-22-0434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/23/2022] [Accepted: 09/09/2022] [Indexed: 01/07/2023]
Abstract
Multiple myeloma is a hematologic malignancy of monoclonal plasma cells that accumulate in the bone marrow. Despite their clinical and pathophysiologic relevance, the roles of bone marrow-infiltrating T cells in treatment-naïve patients are incompletely understood. We investigated whether clonally expanded T cells (i) were detectable in multiple myeloma bone marrow, (ii) showed characteristic immune phenotypes, and (iii) whether dominant clones recognized antigens selectively presented on multiple myeloma cells. Single-cell index sorting and T-cell receptor (TCR) αβ sequencing of bone marrow T cells from 13 treatment-naïve patients showed dominant clonal expansion within CD8+ cytolytic effector compartments, and only a minority of expanded T-cell clones expressed the classic immune-checkpoint molecules PD-1, CTLA-4, or TIM-3. To identify their molecular targets, TCRs of 68 dominant bone marrow clones from five selected patients were reexpressed and incubated with multiple myeloma and non-multiple myeloma cells from corresponding patients. Only 1 of 68 TCRs recognized antigen presented on multiple myeloma cells. This TCR was HLA-C-restricted, self-peptide-specific and could be activated by multiple myeloma cells of multiple patients. The remaining dominant T-cell clones did not recognize multiple myeloma cells and were, in part, specific for antigens associated with chronic viral infections. In conclusion, we showed that dominant bone marrow T-cell clones in treatment-naïve patients rarely recognize antigens presented on multiple myeloma cells and exhibit low expression of classic immune-checkpoint molecules. Our data provide experimental context for experiences from clinical immune-checkpoint inhibition trials and will inform future T cell-dependent therapeutic strategies.
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Affiliation(s)
- Carlotta Welters
- Department of Hematology, Oncology, and Tumor Immunology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - María Fernanda Lammoglia Cobo
- Department of Hematology, Oncology, and Tumor Immunology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian Alexander Stein
- Department of Hematology, Oncology, and Tumor Immunology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Meng-Tung Hsu
- Molecular Immunology and Gene Therapy, Max-Delbrück-Center for Molecular Medicine (MDC) Berlin, Germany
| | - Amin Ben Hamza
- Department of Hematology, Oncology, and Tumor Immunology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Livius Penter
- Department of Hematology, Oncology, and Tumor Immunology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xiaojing Chen
- Molecular Immunology and Gene Therapy, Max-Delbrück-Center for Molecular Medicine (MDC) Berlin, Germany
| | - Christopher Buccitelli
- Proteomics Platform, Max-Delbrück-Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Oliver Popp
- Proteomics Platform, Max-Delbrück-Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Philipp Mertins
- Proteomics Platform, Max-Delbrück-Center for Molecular Medicine and Berlin Institute of Health, Berlin, Germany
| | - Kerstin Dietze
- Department of Hematology, Oncology, and Tumor Immunology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology, and Tumor Immunology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas Moosmann
- Department of Medicine III, Klinikum der Universität München, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
| | - Armin Gerbitz
- Hans Messner Allogeneic Stem Cell Transplant Program, Princess Margaret Cancer Centre, Toronto, Canada
| | - Julian Strobel
- Department of Transfusion Medicine and Hemostaseology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Holger Hackstein
- Department of Transfusion Medicine and Hemostaseology, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Hans-Peter Rahn
- Preparative Flow Cytometry, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, LMU Munich, Germany
| | - Thomas Blankenstein
- Molecular Immunology and Gene Therapy, Max-Delbrück-Center for Molecular Medicine (MDC) Berlin, Germany
| | - Leo Hansmann
- Department of Hematology, Oncology, and Tumor Immunology, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Corresponding Author: Leo Hansmann, Charité–Universitätsmedizin Berlin (CVK), Department of Hematology, Oncology, and Tumor Immunology, Augustenburger Platz 1, 13353 Berlin, Germany. Phone: 49-(0)30-450-665238; Fax: 49-(0)30-450-553914; E-mail:
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7
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Wirges A, Bunse M, Joedicke JJ, Blanc E, Gudipati V, Moles MW, Shiku H, Beule D, Huppa JB, Höpken UE, Rehm A. EBAG9 silencing exerts an immune checkpoint function without aggravating adverse effects. Mol Ther 2022; 30:3358-3378. [PMID: 35821635 PMCID: PMC9637585 DOI: 10.1016/j.ymthe.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/31/2022] [Accepted: 07/09/2022] [Indexed: 10/17/2022] Open
Abstract
Chimeric antigen receptor (CAR) T cells have revolutionized treatment of B cell malignancies. However, enhancing the efficacy of engineered T cells without compromising their safety is warranted. The estrogen receptor-binding fragment-associated antigen 9 (EBAG9) inhibits release of cytolytic enzymes from cytotoxic T lymphocytes. Here, we examined the potency of EBAG9 silencing for the improvement of adoptive T cell therapy. MicroRNA (miRNA)-mediated EBAG9 downregulation in transplanted cytolytic CD8+ T cells (CTLs) from immunized mice improved their cytolytic competence in a tumor model. In tolerant female recipient mice that received organ transplants, a minor histocompatibility antigen was turned into a rejection antigen by Ebag9 deletion, indicating an immune checkpoint function for EBAG9. Considerably fewer EBAG9-silenced human CAR T cells were needed for tumor growth control in a xenotransplantation model. Transcriptome profiling did not reveal additional risks regarding genotoxicity or aberrant differentiation. A single-step retrovirus transduction process links CAR or TCR expression with miRNA-mediated EBAG9 downregulation. Despite higher cytolytic efficacy, release of cytokines associated with cytokine release syndrome remains unaffected. Collectively, EBAG9 silencing enhances effector capacity of TCR- and CAR-engineered T cells, results in improved tumor eradication, facilitates efficient manufacturing, and decreases the therapeutic dose.
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Affiliation(s)
- Anthea Wirges
- Translational Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Mario Bunse
- Microenvironmental Regulation in Autoimmunity and Cancer, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Jara J Joedicke
- Translational Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, 10117 Berlin, Germany
| | - Venugopal Gudipati
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, 1090 Vienna, Austria
| | - Michael W Moles
- Translational Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Hiroshi Shiku
- Department of Personalized Cancer Immunotherapy, Mie University Graduate School of Medicine, Tsu city, Mie, 514-8507, Japan
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, 10117 Berlin, Germany
| | - Johannes B Huppa
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, 1090 Vienna, Austria
| | - Uta E Höpken
- Microenvironmental Regulation in Autoimmunity and Cancer, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany
| | - Armin Rehm
- Translational Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany.
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8
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Duret S, Bessou A, Skufca J, Blanc E, Pilz A, Gessner B, Stark J, Faucher JF, Nuttens C. Incidence de la borréliose de Lyme en France en médecine générale et en milieu hospitalier entre 2010 et 2019. Rev Epidemiol Sante Publique 2022. [DOI: 10.1016/j.respe.2022.09.028] [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: 11/06/2022] Open
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9
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Papaioannou N, Papageorgiou A, Schultz D, Frydas I, Gabriel C, Karakitsios S, Langouet S, Blanc E, Audouze K, Sarigiannis D. P14-15 Multi-omics integrated analysis reveals significant metabolic disorders from 2D & 3D HepaRG eparg cells after exposure to amiodarone & DEHP. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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10
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Fievez S, Chechoi M, Fabron C, Waeckel A, Blanc E, Bourgeois M, Baffert S. Etude coût-utilité d'une stratégie vaccinale dans la prévention contre les infections à méningocoques de sérogroupe C. Rev Epidemiol Sante Publique 2022. [DOI: 10.1016/j.respe.2022.03.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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11
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Dorel M, Klinger B, Mari T, Toedling J, Blanc E, Messerschmidt C, Nadler-Holly M, Ziehm M, Sieber A, Hertwig F, Beule D, Eggert A, Schulte JH, Selbach M, Blüthgen N. Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance. PLoS Comput Biol 2021; 17:e1009515. [PMID: 34735429 PMCID: PMC8604339 DOI: 10.1371/journal.pcbi.1009515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/19/2021] [Accepted: 10/01/2021] [Indexed: 12/20/2022] Open
Abstract
Very high risk neuroblastoma is characterised by increased MAPK signalling, and targeting MAPK signalling is a promising therapeutic strategy. We used a deeply characterised panel of neuroblastoma cell lines and found that the sensitivity to MEK inhibitors varied drastically between these cell lines. By generating quantitative perturbation data and mathematical modelling, we determined potential resistance mechanisms. We found that negative feedbacks within MAPK signalling and via the IGF receptor mediate re-activation of MAPK signalling upon treatment in resistant cell lines. By using cell-line specific models, we predict that combinations of MEK inhibitors with RAF or IGFR inhibitors can overcome resistance, and tested these predictions experimentally. In addition, phospho-proteomic profiling confirmed the cell-specific feedback effects and synergy of MEK and IGFR targeted treatment. Our study shows that a quantitative understanding of signalling and feedback mechanisms facilitated by models can help to develop and optimise therapeutic strategies. Our findings should be considered for the planning of future clinical trials introducing MEKi in the treatment of neuroblastoma.
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Affiliation(s)
- Mathurin Dorel
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Integrative Research Institute for the Life Sciences and Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Bertram Klinger
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Integrative Research Institute for the Life Sciences and Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tommaso Mari
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Joern Toedling
- Department of Pediatric, Division of Oncology and Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Eric Blanc
- Berlin Institute of Health, Berlin, Germany
| | | | | | - Matthias Ziehm
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Anja Sieber
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Integrative Research Institute for the Life Sciences and Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, Germany
| | - Falk Hertwig
- Department of Pediatric, Division of Oncology and Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Angelika Eggert
- Department of Pediatric, Division of Oncology and Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Johannes H. Schulte
- Department of Pediatric, Division of Oncology and Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | | | - Nils Blüthgen
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Integrative Research Institute for the Life Sciences and Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
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12
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Uhlitz F, Bischoff P, Peidli S, Sieber A, Trinks A, Lüthen M, Obermayer B, Blanc E, Ruchiy Y, Sell T, Mamlouk S, Arsie R, Wei T, Klotz‐Noack K, Schwarz RF, Sawitzki B, Kamphues C, Beule D, Landthaler M, Sers C, Horst D, Blüthgen N, Morkel M. Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer. EMBO Mol Med 2021; 13:e14123. [PMID: 34409732 PMCID: PMC8495451 DOI: 10.15252/emmm.202114123] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 02/11/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 01/07/2023] Open
Abstract
In colorectal cancer, oncogenic mutations transform a hierarchically organized and homeostatic epithelium into invasive cancer tissue lacking visible organization. We sought to define transcriptional states of colorectal cancer cells and signals controlling their development by performing single-cell transcriptome analysis of tumors and matched non-cancerous tissues of twelve colorectal cancer patients. We defined patient-overarching colorectal cancer cell clusters characterized by differential activities of oncogenic signaling pathways such as mitogen-activated protein kinase and oncogenic traits such as replication stress. RNA metabolic labeling and assessment of RNA velocity in patient-derived organoids revealed developmental trajectories of colorectal cancer cells organized along a mitogen-activated protein kinase activity gradient. This was in contrast to normal colon organoid cells developing along graded Wnt activity. Experimental targeting of EGFR-BRAF-MEK in cancer organoids affected signaling and gene expression contingent on predictive KRAS/BRAF mutations and induced cell plasticity overriding default developmental trajectories. Our results highlight directional cancer cell development as a driver of non-genetic cancer cell heterogeneity and re-routing of trajectories as a response to targeted therapy.
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Affiliation(s)
- Florian Uhlitz
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- IRI Life SciencesHumboldt University of BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Philip Bischoff
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Stefan Peidli
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- IRI Life SciencesHumboldt University of BerlinBerlinGermany
| | - Anja Sieber
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- IRI Life SciencesHumboldt University of BerlinBerlinGermany
| | - Alexandra Trinks
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- BIH Bioportal Single CellsBerlin Institute of Health at Charité – Universitätsmedizin BerlinBerlinGermany
| | - Mareen Lüthen
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Benedikt Obermayer
- Core Unit Bioinformatics (CUBI)Berlin Institute of Health at Charité Universitätsmedizin – BerlinBerlinGermany
| | - Eric Blanc
- Core Unit Bioinformatics (CUBI)Berlin Institute of Health at Charité Universitätsmedizin – BerlinBerlinGermany
| | - Yana Ruchiy
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Thomas Sell
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- IRI Life SciencesHumboldt University of BerlinBerlinGermany
| | - Soulafa Mamlouk
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Roberto Arsie
- Max Delbrück Center for Molecular MedicineBerlin Institute for Medical Systems Biology (BIMSB)BerlinGermany
| | - Tzu‐Ting Wei
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- Max Delbrück Center for Molecular MedicineBerlin Institute for Medical Systems Biology (BIMSB)BerlinGermany
| | - Kathleen Klotz‐Noack
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- Institute of Medical ImmunologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Roland F Schwarz
- Max Delbrück Center for Molecular MedicineBerlin Institute for Medical Systems Biology (BIMSB)BerlinGermany
- BIFOLD – Berlin Institute for the Foundations of Learning and DataBerlinGermany
| | - Birgit Sawitzki
- Institute of Medical ImmunologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Carsten Kamphues
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of SurgeryCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
| | - Dieter Beule
- Core Unit Bioinformatics (CUBI)Berlin Institute of Health at Charité Universitätsmedizin – BerlinBerlinGermany
| | - Markus Landthaler
- Max Delbrück Center for Molecular MedicineBerlin Institute for Medical Systems Biology (BIMSB)BerlinGermany
| | - Christine Sers
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - David Horst
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Nils Blüthgen
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- IRI Life SciencesHumboldt University of BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Markus Morkel
- Institute of PathologyCharité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany
- German Cancer Consortium (DKTK) Partner Site BerlinGerman Cancer Research Center (DKFZ)HeidelbergGermany
- BIH Bioportal Single CellsBerlin Institute of Health at Charité – Universitätsmedizin BerlinBerlinGermany
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13
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Blanc E, Chaize G, Fievez S, Féger C, Herquelot E, Vainchtock A, Timsit JF, Gaillat J. The impact of comorbidities and their stacking on short- and long-term prognosis of patients over 50 with community-acquired pneumonia. BMC Infect Dis 2021; 21:949. [PMID: 34521380 PMCID: PMC8442401 DOI: 10.1186/s12879-021-06669-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/28/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The prognosis of patients hospitalized with community-acquired pneumonia (CAP) with regards to intensive care unit (ICU) admission, short- and long-term mortality is correlated with patient's comorbidities. For patients hospitalized for CAP, including P-CAP, we assessed the prognostic impact of comorbidities known as at-risk (AR) or high-risk (HR) of pneumococcal CAP (P-CAP), and of the number of combined comorbidities. METHODS Data on hospitalizations for CAP among the French 50+ population were extracted from the 2014 French Information Systems Medicalization Program (PMSI), an exhaustive national hospital discharge database maintained by the French Technical Agency of Information on Hospitalization (ATIH). Their admission diagnosis, comorbidities (nature, risk type and number), other characteristics, and their subsequent hospital stays within the year following their hospitalization for CAP were analyzed. Logistic regression models were used to assess the associations between ICU transfer, short- and 1-year in-hospital mortality and all covariates. RESULTS From 182,858 patients, 149,555 patients aged ≥ 50 years (nonagenarians 17.8%) were hospitalized for CAP in 2014, including 8270 with P-CAP. Overall, 33.8% and 90.5% had ≥ 1 HR and ≥ 1 AR comorbidity, respectively. Cardiac diseases were the most frequent AR comorbidity (all CAP: 77.4%). Transfer in ICU occurred for 5.4% of CAP patients and 19.4% for P-CAP. Short-term and 1-year in-hospital mortality rates were 10.9% and 23% of CAP patients, respectively, significantly lower for P-CAP patients: 9.2% and 19.8% (HR 0.88 [95% CI 0.84-0.93], p < .0001). Both terms of mortality increased mostly with age, and with the number of comorbidities and combination of AR and HR comorbidities, in addition of specific comorbidities. CONCLUSIONS Not only specific comorbidities, but also the number of combined comorbidities and the combination of AR and HR comorbidities may impact the outcome of hospitalized CAP and P-CAP patients.
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Affiliation(s)
| | | | | | - C Féger
- EMIBiotech, Paris, France
- ICUREsearch, Paris, France
| | | | | | - J F Timsit
- Medical and Infectious Diseases ICU, Bichat-Claude Bernard Hospital, APHP, Paris, France
- UMR 1137-IAME Team 5-DeSCID: Decision SCiences in Infectious Diseases Control and Care INSERM/University of Paris, Paris, France
| | - J Gaillat
- Infectious Diseases Department, Annecy-Genevois Hospital, Annecy, France.
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14
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Blanc E. Teacher Strikes and the Fight for the Common. 10 14746/prt 2021. [DOI: 10.14746/prt2020.4.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To celebrate the 10th anniversary of Praktyka Teoretyczna journal, we have invited our long-lasting collaborators and comrades to reflect once again on the concept of the common and it’s possible futures by posing the following questions: a) what is the most important aspect of the current struggles for the common?; b) what are the biggest challenges for the commonist politics of the future?; and c) where in the ongoing struggles do you see a potential for scaling-up and spreading organisation based on the common? In his reply, Eric Blanc draws our attention to contemporary teachers strikes as a movement with radical potentialities that greatly exceed merely reversing the privatization process of education.
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15
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Martel-Lafay I, Danhier S, Blanc E, Monnet I, Gallocher O, Salem N, Berard H, Bykicki O. PO-1015: SBRT after CT-RT for stage III unresectable NSCLC with peripheral primary tumor (GFPC 01-14 study). Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)01032-x] [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: 11/30/2022]
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16
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Rieke DT, Klinghammer KF, Obermayer B, Blanc E, Messerschmidt C, Jöhrens K, Klauschen F, Tinhofer I, Beule D, Keilholz U, Ochsenreither S. Association of a STK11/KEAP1-mutation gene expression signature in lung adenocarcinoma with immune desertion in squamous cell carcinomas and mediation by NFE2L2 deregulation. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3082 Background: KEAP1 and STK11 mutations are associated with resistance to immune checkpoint inhibition (ICI) in non-small cell lung cancer (NSCLC). Mechanisms are currently unknown. Methods: We examined mutation, methylation, copy number and gene expression data from the cancer genome atlas (TCGA) lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LSCC), head and neck squamous cell carcinoma (HNSCC) and cervical carcinoma (CESC) data sets as well as public single cell gene expression data from a HNSCC cohort. Pathway annotations were performed using gene set enrichment analysis. A previously published cohort of NSCLC patients treated with ICI was analyzed for the predictive value of NFE2L2 mutations on PFS. Results: Annotation of STK11 and KEAP1 mutant LUAD revealed identical gene set enrichment for mitochondrial metabolism and downregulation of the STING-pathway, immune checkpoints, and interferon signaling. A STK11/KEAP1-mutation derived gene expression signature was established in LUAD and found to be driven by NFE2L2-regulated genes. This gene expression signature was independently predictive of immune desertion in LSCC, CESC and HNSCC and associated with STING-pathway downregulation in single cell sequencing analyses in HNSCC. KEAP1 and STK11 mutations were less frequent in LSCC, CESC and HNSCC but NFE2L2 mutations were identified in 15, 6 and 5%, respectively. NFE2L2 mutant SCC exhibited upregulation of the 15-gene- signature as well as immune desertion. In NSCLC, NFE2L2 mutations were associated with significantly worse PFS with ICI. Conclusions: Alterations of KEAP1, STK11, NFE2L2 and other related genes are linked to NFE2L2 target gene upregulation and immune desertion in LUAD, CESC, LSCC and HNSCC alike. The NFE2L2 pathway should be investigated clinically as a putative negative predictive biomarker for ICI and a potential therapeutic target.
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Affiliation(s)
- Damian Tobias Rieke
- Department of Hematology and Oncology - Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | | | - Eric Blanc
- Core Unit Bioinformatics-Berlin Institute of Health, Berlin, Germany
| | | | - Korinna Jöhrens
- Institute of Pathology, Charité Universitätsmedizin, Berlin, Germany
| | | | - Inge Tinhofer
- Department of Radiooncology and Radiotherapy, Charité University Hospital, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics-Berlin Institute of Health, Berlin, Germany
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17
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Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Garcia HD, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Publisher Correction: Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet 2020; 52:464. [PMID: 32107479 DOI: 10.1038/s41588-020-0598-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Elias Rodriguez-Fos
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Konstantin Helmsauer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Burkert
- Department of Biology, Humboldt University, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ian C MacArthur
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jesper Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rocio Chamorro
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalia Munoz-Perez
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yi Bei
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Röefzaad
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Victor Bardinet
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Winkler
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Theresa Thole
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalie Timme
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Katharina Kasack
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Fuchs
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Filippos Klironomos
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Eric Blanc
- Berlin Institute of Health, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdörfer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolina Rosswog
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica Theissen
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hedwig Deubzer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Joern Toedling
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland F Schwarz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Johannes H Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany. .,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.
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18
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Lamping M, Benary M, Leyvraz S, Messerschmidt C, Blanc E, Kessler T, Schütte M, Lenze D, Jöhrens K, Burock S, Klinghammer K, Ochsenreither S, Sers C, Schäfer R, Tinhofer I, Beule D, Klauschen F, Yaspo ML, Keilholz U, Rieke DT. Support of a molecular tumour board by an evidence-based decision management system for precision oncology. Eur J Cancer 2020; 127:41-51. [PMID: 31982633 DOI: 10.1016/j.ejca.2019.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Reliable and reproducible interpretation of molecular aberrations constitutes a bottleneck of precision medicine. Evidence-based decision management systems may improve rational therapy recommendations. To cope with an increasing amount of complex molecular data in the clinical care of patients with cancer, we established a workflow for the interpretation of molecular analyses. METHODS A specialized physician screened results from molecular analyses for potential biomarkers, irrespective of the diagnostic modality. Best available evidence was retrieved and categorized through establishment of an in-house database and interrogation of publicly available databases. Annotated biomarkers were ranked using predefined evidence levels and subsequently discussed at a molecular tumour board (MTB), which generated treatment recommendations. Subsequent translation into patient treatment and clinical outcomes were followed up. RESULTS One hundred patients were discussed in the MTB between January 2016 and May 2017. Molecular data were obtained for 70 of 100 patients (50 whole exome/RNA sequencing, 18 panel sequencing, 2 immunohistochemistry (IHC)/microsatellite instability analysis). The MTB generated a median of two treatment recommendations each for 63 patients. Thirty-nine patients were treated: 6 partial responses and 12 stable diseases were achieved as best responses. Genetic counselling for germline events was recommended for seven patients. CONCLUSION The development of an evidence-based workflow allowed for the clinical interpretation of complex molecular data and facilitated the translation of personalized treatment strategies into routine clinical care. The high number of treatment recommendations in patients with comprehensive genomic data and promising responses in patients treated with combination therapy warrant larger clinical studies.
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Affiliation(s)
- Mario Lamping
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany.
| | - Manuela Benary
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; IRI Life Sciences, Humboldt-Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany
| | - Serge Leyvraz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Clemens Messerschmidt
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | - Thomas Kessler
- Alacris Theranostics GmbH, Max Planck Straße 3, 12489, Berlin, Germany
| | - Moritz Schütte
- Alacris Theranostics GmbH, Max Planck Straße 3, 12489, Berlin, Germany
| | - Dido Lenze
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Korinna Jöhrens
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Susen Burock
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Konrad Klinghammer
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Sebastian Ochsenreither
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Christine Sers
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Reinhold Schäfer
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ingeborg Tinhofer
- German Cancer Consortium (DKTK) and German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany; Department of Radiooncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | - Frederick Klauschen
- Department of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany
| | - Marie-Laure Yaspo
- Alacris Theranostics GmbH, Max Planck Straße 3, 12489, Berlin, Germany; Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Ihnestraße 63, 14195, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; German Cancer Consortium (DKTK) and German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Damian T Rieke
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Charitéplatz 1, 10117, Berlin, Germany; Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, 12203 Berlin, Germany; Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany.
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19
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Khan W, Zugail AS, Blanc E, Neuziller Y, Lebret T. Reasons for intravesical instillation postponement during adjuvant treatment of non-muscle-invasive bladder cancer: A prospective study. Prog Urol 2020; 30:75-79. [PMID: 31953014 DOI: 10.1016/j.purol.2019.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/28/2019] [Accepted: 11/28/2019] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Intravesical instillations for adjuvant treatment of non-muscle-invasive bladder cancer (NMIBC) may be postponed of necessity. However, the frequency and reasons for postponement are unclear. MATERIALS We carried out a prospective, epidemiological study in an Urology department of the Île-de-France, between August 2016 and March 2017, to determine the frequency and reasons for postponement of intravesical instillations during adjuvant treatment of NMIBC. One-hundred consecutive patients treated by intravesical instillations of mitomycin C (MMC) or Bacillus Calmette-Guérin (BCG) were included. At each session and in case of instillation postponement, the medical team completed a specially designed questionnaire. RESULTS A total of 541 instillations were performed in the 100 patients. Twenty-four instillations (4.4%) were postponed in 19 patients. The major cause of postponement was an untreated positive urine analysis and culture (UAC) in 13/24 (54%) cases. The causes of cancellation did not differ significantly between MMC and BCG. The most frequently cancelled instillations were the first in the therapeutic protocol in 26% of cases. The number of instillations preceding those cancelled did not differ significantly between MMC and BCG (2.1±2.0 instillations for MMC vs. 1.5±1.6 for BCG; P=0.64). CONCLUSIONS There was a low rate of postponed instillations (4.4%). The main reasons, namely an untreated UAC and a positive dipstick test, based on the jurisprudence, are not included in the latest CC-AFU guidelines. LEVEL OF EVIDENCE 3.
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Affiliation(s)
- W Khan
- Department of urology, Foch hospital, University of Versailles, Saint-Quentin-en-Yvelines, Suresnes France.
| | - A S Zugail
- Department of surgery, faculty of medicine in Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - E Blanc
- Department of urology, Foch hospital, University of Versailles, Saint-Quentin-en-Yvelines, Suresnes France
| | - Y Neuziller
- Department of urology, Foch hospital, University of Versailles, Saint-Quentin-en-Yvelines, Suresnes France
| | - T Lebret
- Department of urology, Foch hospital, University of Versailles, Saint-Quentin-en-Yvelines, Suresnes France
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20
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Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Dorado Garcia H, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet 2019; 52:29-34. [PMID: 31844324 DOI: 10.1038/s41588-019-0547-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 01/25/2023]
Abstract
Extrachromosomal circularization of DNA is an important genomic feature in cancer. However, the structure, composition and genome-wide frequency of extrachromosomal circular DNA have not yet been profiled extensively. Here, we combine genomic and transcriptomic approaches to describe the landscape of extrachromosomal circular DNA in neuroblastoma, a tumor arising in childhood from primitive cells of the sympathetic nervous system. Our analysis identifies and characterizes a wide catalog of somatically acquired and undescribed extrachromosomal circular DNAs. Moreover, we find that extrachromosomal circular DNAs are an unanticipated major source of somatic rearrangements, contributing to oncogenic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. Cancer-causing lesions can emerge out of circle-derived rearrangements and are associated with adverse clinical outcome. It is highly probable that circle-derived rearrangements represent an ongoing mutagenic process. Thus, extrachromosomal circular DNAs represent a multihit mutagenic process, with important functional and clinical implications for the origins of genomic remodeling in cancer.
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Affiliation(s)
- Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Elias Rodriguez-Fos
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Konstantin Helmsauer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Burkert
- Department of Biology, Humboldt University, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ian C MacArthur
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jesper Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rocio Chamorro
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalia Munoz-Perez
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yi Bei
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Röefzaad
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Victor Bardinet
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Winkler
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Theresa Thole
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalie Timme
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Katharina Kasack
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Fuchs
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Filippos Klironomos
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Eric Blanc
- Berlin Institute of Health, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdörfer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolina Rosswog
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica Theissen
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hedwig Deubzer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Joern Toedling
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland F Schwarz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Johannes H Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany. .,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.
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21
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Blanc E, Holtgrewe M, Dhamodaran A, Messerschmidt C, Willimsky G, Blankenstein T, Beule D. Identification and ranking of recurrent neo-epitopes in cancer. BMC Med Genomics 2019; 12:171. [PMID: 31775766 PMCID: PMC6882202 DOI: 10.1186/s12920-019-0611-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/09/2019] [Accepted: 10/25/2019] [Indexed: 12/25/2022] Open
Abstract
Background Immune escape is one of the hallmarks of cancer and several new treatment approaches attempt to modulate and restore the immune system’s capability to target cancer cells. At the heart of the immune recognition process lies antigen presentation from somatic mutations. These neo-epitopes are emerging as attractive targets for cancer immunotherapy and new strategies for rapid identification of relevant candidates have become a priority. Methods We carefully screen TCGA data sets for recurrent somatic amino acid exchanges and apply MHC class I binding predictions. Results We propose a method for in silico selection and prioritization of candidates which have a high potential for neo-antigen generation and are likely to appear in multiple patients. While the percentage of patients carrying a specific neo-epitope and HLA-type combination is relatively small, the sheer number of new patients leads to surprisingly high reoccurence numbers. We identify 769 epitopes which are expected to occur in 77629 patients per year. Conclusion While our candidate list will definitely contain false positives, the results provide an objective order for wet-lab testing of reusable neo-epitopes. Thus recurrent neo-epitopes may be suitable to supplement existing personalized T cell treatment approaches with precision treatment options.
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Affiliation(s)
- Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Arunraj Dhamodaran
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany
| | - Clemens Messerschmidt
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Gerald Willimsky
- Institute of Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Lindenberger Weg 80, Berlin, 13125, Germany.,Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Thomas Blankenstein
- Institute of Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Lindenberger Weg 80, Berlin, 13125, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany.,Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany. .,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany.
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22
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Ghio A, Giusti L, Blanc E, Pinto S. French adaptation of the "Frenchay Dysarthria Assessment 2" speech intelligibility test. Eur Ann Otorhinolaryngol Head Neck Dis 2019; 137:111-116. [PMID: 31732389 DOI: 10.1016/j.anorl.2019.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Speech intelligibility can be defined as "the degree to which a speaker's intended message is recovered by a listener". Loss of intelligibility is one of the most frequent complaints in patients suffering from speech disorder, impairing communication. Measurement of intelligibility is therefore an important parameter in follow-up. We developed a French version of the "Frenchay Dysarthria Assessment, 2nd edition" (FDA-2), an intelligibility test recognized internationally in its English version. The present study details the construction of the test and its preliminary validation. MATERIALS AND METHODS We first compiled a set of words and phrases in French, based on the criteria defined in FDA-2. In a second step, we validated the test in healthy subjects in normal and noisy conditions, to check sensitivity to speech signal degradation. RESULTS The test proved valid and sensitive, as scores were significantly lower for noise-degraded stimuli. CONCLUSION This French-language intelligibility test can be used to evaluate speech disorder: for example, in dysarthria, head and neck cancer or after cochlear implantation.
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Affiliation(s)
- A Ghio
- Aix-Marseille Université, CNRS, LPL, Aix-en-Provence, France.
| | - L Giusti
- Aix-Marseille Université, CNRS, LPL, Aix-en-Provence, France
| | - E Blanc
- Aix-Marseille Université, CNRS, LPL, Aix-en-Provence, France
| | - S Pinto
- Aix-Marseille Université, CNRS, LPL, Aix-en-Provence, France
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23
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Schumann F, Blanc E, Messerschmidt C, Blankenstein T, Busse A, Beule D. SigsPack, a package for cancer mutational signatures. BMC Bioinformatics 2019; 20:450. [PMID: 31477009 PMCID: PMC6720940 DOI: 10.1186/s12859-019-3043-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/21/2019] [Indexed: 01/10/2023] Open
Abstract
Background Mutational signatures are specific patterns of somatic mutations introduced into the genome by oncogenic processes. Several mutational signatures have been identified and quantified from multiple cancer studies, and some of them have been linked to known oncogenic processes. Identification of the processes contributing to mutations observed in a sample is potentially informative to understand the cancer etiology. Results We present here SigsPack, a Bioconductor package to estimate a sample’s exposure to mutational processes described by a set of mutational signatures. The package also provides functions to estimate stability of these exposures, using bootstrapping. The performance of exposure and exposure stability estimations have been validated using synthetic and real data. Finally, the package provides tools to normalize the mutation frequencies with respect to the tri-nucleotide contents of the regions probed in the experiment. The importance of this effect is illustrated in an example. Conclusion SigsPack provides a complete set of tools for individual sample exposure estimation, and for mutation catalogue & mutational signatures normalization. Electronic supplementary material The online version of this article (10.1186/s12859-019-3043-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Franziska Schumann
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Clemens Messerschmidt
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Thomas Blankenstein
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany.,Insitute of Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Antonia Busse
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany. .,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany. .,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.
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24
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Borgsmüller N, Gloaguen Y, Opialla T, Blanc E, Sicard E, Royer AL, Le Bizec B, Durand S, Migné C, Pétéra M, Pujos-Guillot E, Giacomoni F, Guitton Y, Beule D, Kirwan J. WiPP: Workflow for Improved Peak Picking for Gas Chromatography-Mass Spectrometry (GC-MS) Data. Metabolites 2019; 9:metabo9090171. [PMID: 31438611 PMCID: PMC6780109 DOI: 10.3390/metabo9090171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/18/2019] [Accepted: 08/20/2019] [Indexed: 02/02/2023] Open
Abstract
Lack of reliable peak detection impedes automated analysis of large-scale gas chromatography-mass spectrometry (GC-MS) metabolomics datasets. Performance and outcome of individual peak-picking algorithms can differ widely depending on both algorithmic approach and parameters, as well as data acquisition method. Therefore, comparing and contrasting between algorithms is difficult. Here we present a workflow for improved peak picking (WiPP), a parameter optimising, multi-algorithm peak detection for GC-MS metabolomics. WiPP evaluates the quality of detected peaks using a machine learning-based classification scheme based on seven peak classes. The quality information returned by the classifier for each individual peak is merged with results from different peak detection algorithms to create one final high-quality peak set for immediate down-stream analysis. Medium- and low-quality peaks are kept for further inspection. By applying WiPP to standard compound mixes and a complex biological dataset, we demonstrate that peak detection is improved through the novel way to assign peak quality, an automated parameter optimisation, and results in integration across different embedded peak picking algorithms. Furthermore, our approach can provide an impartial performance comparison of different peak picking algorithms. WiPP is freely available on GitHub (https://github.com/bihealth/WiPP) under MIT licence.
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Affiliation(s)
- Nico Borgsmüller
- Core Unit Bioinformatics, Berlin Institute of Health, 10178 Berlin, Germany
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Yoann Gloaguen
- Core Unit Bioinformatics, Berlin Institute of Health, 10178 Berlin, Germany
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Tobias Opialla
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, 10178 Berlin, Germany
- Charité - Universitätsmedizin Berlin, 10178 Berlin, Germany
| | - Emilie Sicard
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Anne-Lise Royer
- LABERCA, Oniris, INRA, Université Bretagne - Loire, 44307 Nantes, France
| | - Bruno Le Bizec
- LABERCA, Oniris, INRA, Université Bretagne - Loire, 44307 Nantes, France
| | - Stéphanie Durand
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Carole Migné
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Mélanie Pétéra
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Estelle Pujos-Guillot
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Franck Giacomoni
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Yann Guitton
- LABERCA, Oniris, INRA, Université Bretagne - Loire, 44307 Nantes, France
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, 10178 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Charité - Universitätsmedizin Berlin, 10178 Berlin, Germany
| | - Jennifer Kirwan
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany.
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.
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25
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Rosenfarb J, Sforza N, Rujelman R, Morosan Allo Y, Parisi C, Blanc E, Frigerio C, Fossati P, Caruso D, Faingold C, Meroño T, Brenta G. Relevance of TSH evaluation in elderly in-patients with non-thyroidal illness. J Endocrinol Invest 2019; 42:667-671. [PMID: 30367433 DOI: 10.1007/s40618-018-0967-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/13/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND Non-thyroidal illness (NTI) is frequent in hospitalized patients. Its recovery is characterized by a raise in TSH levels. However, the clinical significance of high TSH levels at admission in hospitalized elderly patients with NTI remains uncertain. AIM To explore the relevance of baseline TSH evaluation in hospitalized elderly patients with NTI. METHODS We examined the participants with NTI (n = 123) from our previous study (Sforza, 2017). NTI was defined as: low T3 (< 80 ng/dL) and normal or low total T4 in the presence of TSH values between 0.1 and 6.0 mU/L. Thyroid function tests were performed on day 1 and day 8 of the hospital stay. Positive TSH changes (+ ΔTSH) were considered when the day-8 TSH value increased more than the reference change value for TSH (+ 78%). Multiple logistic regression was used to evaluate the independent association of baseline TSH, sex, clinical comorbidities (by ACE-27) and medications with + ΔTSH. RESULTS Out of 123 patients (77 ± 8 years, 52% female), 34 showed a + ΔTSH. These patients had a lower TSH at admission (p < 0.001) and intra-hospital mortality (p = 0.003) than the others. In multiple logistic regression, TSH > 2.11 mU/L at baseline was associated with reduced odds to show + ΔTSH [odds ratio (95 CI) 0.29 (0.11-0.75); p = 0.011] in a model adjusted by age, sex and ACE-27. DISCUSSION Inappropriately higher TSH levels at admission in hospitalized elderly patients were associated with a reduced ability to raise their TSH levels later on. The present results confront the idea that TSH levels at admission are irrelevant in this clinical context.
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Affiliation(s)
- J Rosenfarb
- Thyroid Unit, Department of Endocrinology and Metabolism, Unidad Asistencial Dr. César Milstein/PAMI-INSSJP, La Rioja 951, (1221), Buenos Aires, Argentina
| | - N Sforza
- Thyroid Unit, Department of Endocrinology and Metabolism, Unidad Asistencial Dr. César Milstein/PAMI-INSSJP, La Rioja 951, (1221), Buenos Aires, Argentina
| | - R Rujelman
- Thyroid Unit, Department of Endocrinology and Metabolism, Unidad Asistencial Dr. César Milstein/PAMI-INSSJP, La Rioja 951, (1221), Buenos Aires, Argentina
| | - Y Morosan Allo
- Thyroid Unit, Department of Endocrinology and Metabolism, Unidad Asistencial Dr. César Milstein/PAMI-INSSJP, La Rioja 951, (1221), Buenos Aires, Argentina
| | - C Parisi
- Thyroid Unit, Department of Endocrinology and Metabolism, Unidad Asistencial Dr. César Milstein/PAMI-INSSJP, La Rioja 951, (1221), Buenos Aires, Argentina
| | - E Blanc
- Thyroid Unit, Department of Endocrinology and Metabolism, Unidad Asistencial Dr. César Milstein/PAMI-INSSJP, La Rioja 951, (1221), Buenos Aires, Argentina
| | - C Frigerio
- Thyroid Unit, Department of Endocrinology and Metabolism, Unidad Asistencial Dr. César Milstein/PAMI-INSSJP, La Rioja 951, (1221), Buenos Aires, Argentina
| | - P Fossati
- Thyroid Unit, Department of Endocrinology and Metabolism, Unidad Asistencial Dr. César Milstein/PAMI-INSSJP, La Rioja 951, (1221), Buenos Aires, Argentina
| | - D Caruso
- Thyroid Unit, Department of Endocrinology and Metabolism, Unidad Asistencial Dr. César Milstein/PAMI-INSSJP, La Rioja 951, (1221), Buenos Aires, Argentina
| | - C Faingold
- Thyroid Unit, Department of Endocrinology and Metabolism, Unidad Asistencial Dr. César Milstein/PAMI-INSSJP, La Rioja 951, (1221), Buenos Aires, Argentina
| | - T Meroño
- Depto. de Bioquímica Clínica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - G Brenta
- Thyroid Unit, Department of Endocrinology and Metabolism, Unidad Asistencial Dr. César Milstein/PAMI-INSSJP, La Rioja 951, (1221), Buenos Aires, Argentina.
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26
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Rieke DT, Lamping M, Leyvraz S, Kim TD, Brinkmann L, Tessmer A, Fischer L, Busse A, Horak P, Mock A, Tinhofer I, Messerschmidt C, Blanc E, Beule D, Klauschen F, Klinghammer KF, Froehling S, Ochsenreither S, Keilholz U. Precision oncology for the treatment of salivary gland tumors. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e17577] [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: 11/20/2022] Open
Abstract
e17577 Background: Salivary gland tumors (SGT) represent a rare and heterogeneous group of malignancies. No standard treatment exists in the advanced situation and the prognosis is poor. We here report characteristics and clinical outcomes of patients with SGT discussed at the Charité molecular tumor board (MTB). Methods: Patients with advanced cancer and no curative treatment option were discussed at the Charité MTB. Eligible patients underwent fresh tissue sampling and subsequent whole exome (WES) and RNA sequencing (RNA-seq) and immunohistochemical analyses (EGFR, HER2, AR as well as validation tests) or panel sequencing. Results from molecular testing were discussed at the MTB and patients were followed-up after recommendations were made. Results: 24 patients (median age 56 years, 13 male, 11 female) with advanced SGT were presented at the MTB between 2016 and 2019 (9 adenoidcystic carcinomas, 5 adenocarcinomas, 3 mucoepidermoid, 2 carcinosarcoma, 5 miscellaneous). WES/RNA sequencing was performed on tumor tissue from 16 patients. 2 patients were not included in the sequencing program and WES/RNA-Seq was ongoing for another 4 patients at the time of analysis. For another 2 patients, panel sequencing and IHC analysis, respectively was done. Results from analyses were discussed and a median of 2 recommendations, ranked by priority according to prespecified evidence levels, were made for 17 patients, each. Most commonly proposed treatment options by the MTB were FGFR inhibitors in 6 patients, mTOR or PARP inhibitors in 5 each, EGFR, HDAC inhibitors or antiandrogen therapy in 4, each. Treatments following MTB recommendations were initiated in 8 patients, 1 of which received a second recommended therapy after progression (antiandrogen therapy in 4, EGFR inhibitor in 2, a PDGFR, mTOR and PARP inhibitor in 1, each). A clinical benefit (CR = 1; Mixed Response = 1, SD = 3) was achieved in 5 patients, including a complete response in a patient with a metastatic adenocarcinoma of the parotid gland, treated with antiandrogen therapy. Conclusions: Precision oncology represents a feasible treatment strategy in patients with advanced SGT and shows early evidence of activity in a subset of patients. These results suggest further exploration of personalized therapy in these hard-to-treat tumors.
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Affiliation(s)
| | - Mario Lamping
- Charité Comprehensive Cancer Center, Berlin, Germany
| | | | | | | | | | - Lars Fischer
- Zentrum für Onkologie und Urologie Rostock, Rostock, Germany
| | - Antonia Busse
- Department of Hematology and Medical Oncology, Charitè, CBF, Berlin, Germany
| | | | - Andreas Mock
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Inge Tinhofer
- Department of Radiooncology and Radiotherapy, Charité University Hospital and German Cancer Research Center Heidelberg (DKFZ)/German Cancer Consortium (DKTK), Berlin, Germany
| | | | - Eric Blanc
- Core Unit Bioinformatics-Berlin Institute of Health, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics-Berlin Institute of Health, Berlin, Germany
| | | | | | - Stefan Froehling
- National Center for Tumor Diseases and German Cancer Research Center, Department of Translational Oncology, Heidelberg, Germany
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27
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Lamping M, Rieke DT, Klauschen F, Jöhrens K, Anagnostopoulos I, Lenze D, Tinhofer I, Benary M, Ochsenreither S, Klinghammer KF, Burock S, Jann H, Stüven AK, Ditzen D, Beule D, Messerschmidt C, Blanc E, Schäfer R, Keilholz U. Clinical impact of comprehensive versus targeted genomic analysis for precision oncology. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e13033] [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: 11/20/2022] Open
Abstract
e13033 Background: Panel sequencing (PS) has become a standard-of-care in cancer diagnostics. More comprehensive analyses such as whole-exome (WES) or RNA sequencing (RNAseq) allow for the detection of rare and unknown genetic aberrations that are not covered by predefined assays. The clinical impact of targeted versus comprehensive genomic assays were analyzed in patients presented at the Charité Molecular Tumor Board (MTB). Methods: Patients (pts) with advanced and/or metastatic cancer for whom no standard therapy was available were discussed in the MTB to allocate diagnostic profiling and guide biomarker-based treatment (BBT). Pts had to be < 50 years of age or diagnosed with a rare tumor entity to undergo WES/RNAseq, performed on fresh tissue. If ineligible, standard PS was performed on archival tissue. BBT recommendations, ranked by pre-specified evidence levels, were made by the MTB and pts were followed up. Results: 228 patients (median age 49 years, 108 female and 120 male) were discussed in the MTB between January 2016 and February 2019. We assigned 73 and 155 pts to PS and WES/RNAseq and results were obtained for 78.1% (n = 57/73) and 54.8% (n = 85/155) pts, respectively. Sequencing failed for 11 (PS; 15.1%) and 62 (WES/RNAseq; 40%) pts, most commonly due to insufficient tissue (n = 29). Sequencing was ongoing in 5 (PS) and 8 (WES/RNAseq) pts at the time of analysis. A median of 2 BBTs were recommended for 75.4% (43/57) of PS (range r: 1-3) and 90.6% (77/85) of WES/RNAseq pts (r: 1-6) each. 22% (n = 17/77) of WES/RNAseq pts had ≥4 BBTs made by the MTB. Treatment was initiated in 30.2% (n = 13/43) of PS and 40.2% (n = 31/77) of WES/RNAseq pts. Clinical benefit rates (CBRs) were 23.1% (2 PR, 1 SD) for PS and 45.2% (2 CR, 3 PR, 9 SD) for WES/RNAseq pts. Overall survival data was immature at the time of analysis. Conclusions: Utilizing WES/RNAseq is a feasible approach to perform tumor profiling in a heterogeneous cohort. We here show a higher rate of pts receiving confident evidence-based treatment recommendations in the WES/RNAseq group and a higher rate of treatment initiation. The CBR nearly doubled in the WES/RNAseq cohort when compared to standard PS pts, thus emphasizing the need for larger comparative analyses to guide diagnostic decision-making.
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Affiliation(s)
- Mario Lamping
- Charité Comprehensive Cancer Center, Berlin, Germany
| | | | | | - Korinna Jöhrens
- Institute of Pathology, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | | | | | - Inge Tinhofer
- Department of Radiooncology and Radiotherapy, Charité University Hospital and German Cancer Research Center Heidelberg (DKFZ)/German Cancer Consortium (DKTK), Berlin, Germany
| | - Manuela Benary
- Institute for Theoretical Biology-Humboldt University Berlin, Berlin, Germany
| | | | | | | | - Henning Jann
- Department of Gastroenterology - Charité University Medicine Berlin, Berlin, Germany
| | - Anna Kathrin Stüven
- Department of Gastroenterology - Charité University Medicine Berlin, Berlin, Germany
| | - Doreen Ditzen
- Charité - University Medicine Berlin, German Cancer Consortium (DKTK), Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics-Berlin Institute of Health, Berlin, Germany
| | | | - Eric Blanc
- Core Unit Bioinformatics-Berlin Institute of Health, Berlin, Germany
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Negrier S, Rioux-Leclercq N, Ravaud A, Gravis G, Geoffrois L, Chevreau C, Rolland F, Blanc E, Segura-Ferlay C, Perol D, Gross Goupil M, Dermeche S, Flechon A, Albiges L, Escudier B. Efficacy and safety of axitinib in metastatic papillary renal carcinoma (mPRC): Results of a GETUG multicenter phase II trial (Axipap). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy283.079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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29
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Constance WD, Mukherjee A, Fisher YE, Pop S, Blanc E, Toyama Y, Williams DW. Neurexin and Neuroligin-based adhesion complexes drive axonal arborisation growth independent of synaptic activity. eLife 2018; 7:31659. [PMID: 29504935 PMCID: PMC5869020 DOI: 10.7554/elife.31659] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/04/2018] [Indexed: 11/25/2022] Open
Abstract
Building arborisations of the right size and shape is fundamental for neural network function. Live imaging in vertebrate brains strongly suggests that nascent synapses are critical for branch growth during development. The molecular mechanisms underlying this are largely unknown. Here we present a novel system in Drosophila for studying the development of complex arborisations live, in vivo during metamorphosis. In growing arborisations we see branch dynamics and localisations of presynaptic proteins very similar to the ‘synaptotropic growth’ described in fish/frogs. These accumulations of presynaptic proteins do not appear to be presynaptic release sites and are not paired with neurotransmitter receptors. Knockdowns of either evoked or spontaneous neurotransmission do not impact arbor growth. Instead, we find that axonal branch growth is regulated by dynamic, focal localisations of Neurexin and Neuroligin. These adhesion complexes provide stability for filopodia by a ‘stick-and-grow’ based mechanism wholly independent of synaptic activity.
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Affiliation(s)
- William D Constance
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom.,King's-NUS Joint Studentship Program, King's College London, London, United Kingdom
| | - Amrita Mukherjee
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Yvette E Fisher
- Department of Neurobiology, Stanford University, Stanford, United States.,Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Sinziana Pop
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Eric Blanc
- Berlin Institute of Health, Berlin, Germany
| | - Yusuke Toyama
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Temasek Life Sciences Laboratory, Singapore, Singapore.,Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Darren W Williams
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom
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30
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Sforza N, Rosenfarb J, Rujelman R, Rosmarin M, Blanc E, Frigerio C, Fossati P, Caruso D, Faingold C, Meroño T, Brenta G. Hypothyroidism in hospitalized elderly patients: a sign of worse prognosis. J Endocrinol Invest 2017; 40:1303-1310. [PMID: 28534147 DOI: 10.1007/s40618-017-0690-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/10/2017] [Indexed: 12/26/2022]
Abstract
PURPOSE Overt hypothyroidism has adverse clinical consequences and might worsen prognosis in critically ill elderly patients. However, the difficult interpretation of thyroid function tests (TFT) due to non-thyroidal illness (NTI) has led to discouragement of screening for thyroid dysfunction. Our aim was to determine the prevalence of TFT compatible with hypothyroidism and to study its influence on mortality among hospitalized elderly patients. METHODS In this prospective study we consecutively included all patients ≥60 years admitted by the Internal Medicine Department to the hospital ward (n = 451) of the Cesar Milstein Hospital in Buenos Aires, Argentina. TFT were done on day 1 and 8. Thyroid function categories were defined as overt and subclinical hypothyroidism, overt and subclinical hyperthyroidism, euthyroidism and NTI. Stage of chronic kidney disease (CKD), Adult Comorbidity Evaluation (ACE)-27, and intra-hospital mortality were recorded. The association between mortality and TFT categories was studied by Cox regression. RESULTS Out of 451 patients (77.0 ± 7.9 years, 54% females) 76% were categorized as NTI, 4% as overt hypothyroid, 10% as subclinical hypothyroid, 1% as subclinical hyperthyroid and 9% as euthyroid. Overt hypothyroid patients showed significantly higher mortality than the rest of the groups (25%, p < 0.05) while ACE-27 was similar among all of them (p = 0.658). In addition, patients within the overt hypothyroid category showed a higher mortality rate than NTI in a model adjusted by Stage 5-CKD, ACE-27, sex and age [HR 3.1 (1.14-8.41), p < 0.026]. CONCLUSION Overt hypothyroidism during hospitalization was associated with elevated mortality. Further studies would reveal if TFT alterations compatible with hypothyroidism should be diagnosed/treated in hospitalized elderly patients.
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Affiliation(s)
- N Sforza
- Endocrinology Department, Cesar Milstein Hospital, 951 La Rioja St, 1221, Buenos Aires, Argentina
| | - J Rosenfarb
- Endocrinology Department, Cesar Milstein Hospital, 951 La Rioja St, 1221, Buenos Aires, Argentina
| | - R Rujelman
- Endocrinology Department, Cesar Milstein Hospital, 951 La Rioja St, 1221, Buenos Aires, Argentina
| | - M Rosmarin
- Endocrinology Department, Cesar Milstein Hospital, 951 La Rioja St, 1221, Buenos Aires, Argentina
| | - E Blanc
- Endocrinology Department, Cesar Milstein Hospital, 951 La Rioja St, 1221, Buenos Aires, Argentina
| | - C Frigerio
- Biochemistry Department, Cesar Milstein Hospital, 951 La Rioja St, 1221, Buenos Aires, Argentina
| | - P Fossati
- Biochemistry Department, Cesar Milstein Hospital, 951 La Rioja St, 1221, Buenos Aires, Argentina
| | - D Caruso
- Internal Medicine Department, Cesar Milstein Hospital, 951 La Rioja St, 1221, Buenos Aires, Argentina
| | - C Faingold
- Endocrinology Department, Cesar Milstein Hospital, 951 La Rioja St, 1221, Buenos Aires, Argentina
| | - T Meroño
- Clinical Biochemistry Department, Pharmacy and Biochemistry School, 954 Junin St, 1113, Buenos Aires, Argentina
| | - G Brenta
- Endocrinology Department, Cesar Milstein Hospital, 951 La Rioja St, 1221, Buenos Aires, Argentina.
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31
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Cox D, Blanc E, Romieu G, Rios M, Becuwe C, Jouannaud C, Chaigneau L, Arnedos M, Orfeuvre H, Petit T, Quenel Tueux N, Jacquin JP, Ferrero JM, Abadie Lacourtoisie S, Penault-Llorca F, Segura-Ferlay C, Moullet I, Bachelot T, Pivot X. SToRM: A clinical cohort to identify genetic variability related to metastatic phenotypes. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx440.007] [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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Thomas-Jinu S, Gordon PM, Fielding T, Taylor R, Smith BN, Snowden V, Blanc E, Vance C, Topp S, Wong CH, Bielen H, Williams KL, McCann EP, Nicholson GA, Pan-Vazquez A, Fox AH, Bond CS, Talbot WS, Blair IP, Shaw CE, Houart C. Non-nuclear Pool of Splicing Factor SFPQ Regulates Axonal Transcripts Required for Normal Motor Development. Neuron 2017; 94:931. [PMID: 28521142 PMCID: PMC5441113 DOI: 10.1016/j.neuron.2017.04.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Piper MDW, Soultoukis GA, Blanc E, Mesaros A, Herbert SL, Juricic P, He X, Atanassov I, Salmonowicz H, Yang M, Simpson SJ, Ribeiro C, Partridge L. Matching Dietary Amino Acid Balance to the In Silico-Translated Exome Optimizes Growth and Reproduction without Cost to Lifespan. Cell Metab 2017; 25:1206. [PMID: 28467937 PMCID: PMC5422075 DOI: 10.1016/j.cmet.2017.04.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Thomas-Jinu S, Gordon PM, Fielding T, Taylor R, Smith BN, Snowden V, Blanc E, Vance C, Topp S, Wong CH, Bielen H, Williams KL, McCann EP, Nicholson GA, Pan-Vazquez A, Fox AH, Bond CS, Talbot WS, Blair IP, Shaw CE, Houart C. Non-nuclear Pool of Splicing Factor SFPQ Regulates Axonal Transcripts Required for Normal Motor Development. Neuron 2017; 94:322-336.e5. [PMID: 28392072 PMCID: PMC5405110 DOI: 10.1016/j.neuron.2017.03.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/02/2017] [Accepted: 03/17/2017] [Indexed: 12/12/2022]
Abstract
Recent progress revealed the complexity of RNA processing and its association to human disorders. Here, we unveil a new facet of this complexity. Complete loss of function of the ubiquitous splicing factor SFPQ affects zebrafish motoneuron differentiation cell autonomously. In addition to its nuclear localization, the protein unexpectedly localizes to motor axons. The cytosolic version of SFPQ abolishes motor axonal defects, rescuing key transcripts, and restores motility in the paralyzed sfpq null mutants, indicating a non-nuclear processing role in motor axons. Novel variants affecting the conserved coiled-coil domain, so far exclusively found in fALS exomes, specifically affect the ability of SFPQ to localize in axons. They broadly rescue morphology and motility in the zebrafish mutant, but alter motor axon morphology, demonstrating functional requirement for axonal SFPQ. Altogether, we uncover the axonal function of the splicing factor SFPQ in motor development and highlight the importance of the coiled-coil domain in this process. Video Abstract
SFPQ splicing factor is present in motor axons Non-nuclear SFPQ is able to drive axon maturation and connectivity Loss of axonal SFPQ affects axonal morphology Coiled-coil domain of the protein is important for non-nuclear localization
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Affiliation(s)
- Swapna Thomas-Jinu
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Patricia M Gordon
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Triona Fielding
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Richard Taylor
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Victoria Snowden
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Eric Blanc
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Caroline Vance
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Simon Topp
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Chun-Hao Wong
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Holger Bielen
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Kelly L Williams
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily P McCann
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Garth A Nicholson
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; ANZAC Research Institute, University of Sydney, Concord Hospital, Sydney, NSW 2139, Australia
| | - Alejandro Pan-Vazquez
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Archa H Fox
- School of Anatomy, Physiology, and Human Biology, University of Western Australia, Crawley, WA 6009, Australia; Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, University of Western Australia, Crawley, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
| | - William S Talbot
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian P Blair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Corinne Houart
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK.
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Piper MDW, Soultoukis GA, Blanc E, Mesaros A, Herbert SL, Juricic P, He X, Atanassov I, Salmonowicz H, Yang M, Simpson SJ, Ribeiro C, Partridge L. Matching Dietary Amino Acid Balance to the In Silico-Translated Exome Optimizes Growth and Reproduction without Cost to Lifespan. Cell Metab 2017; 25:610-621. [PMID: 28273481 PMCID: PMC5355364 DOI: 10.1016/j.cmet.2017.02.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [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] [Received: 07/26/2016] [Revised: 12/22/2016] [Accepted: 02/09/2017] [Indexed: 11/16/2022]
Abstract
Balancing the quantity and quality of dietary protein relative to other nutrients is a key determinant of evolutionary fitness. A theoretical framework for defining a balanced diet would both reduce the enormous workload to optimize diets empirically and represent a breakthrough toward tailoring diets to the needs of consumers. Here, we report a simple and powerful in silico technique that uses the genome information of an organism to define its dietary amino acid requirements. We show for the fruit fly Drosophila melanogaster that such "exome-matched" diets are more satiating, enhance growth, and increase reproduction relative to non-matched diets. Thus, early life fitness traits can be enhanced at low levels of dietary amino acids that do not impose a cost to lifespan. Exome matching also enhanced mouse growth, indicating that it can be applied to other organisms whose genome sequence is known.
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Affiliation(s)
- Matthew D W Piper
- Institute of Healthy Ageing and Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK.
| | | | - Eric Blanc
- Berlin Institute of Health, Berlin 10117, Germany
| | - Andrea Mesaros
- Max Planck Institute for Biology of Ageing, Köln 50931, Germany
| | - Samantha L Herbert
- Behavior and Metabolism Laboratory, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Paula Juricic
- Max Planck Institute for Biology of Ageing, Köln 50931, Germany
| | - Xiaoli He
- UCL Ear Institute, University College London, London WC1X 8EE, UK
| | - Ilian Atanassov
- Max Planck Institute for Biology of Ageing, Köln 50931, Germany
| | | | - Mingyao Yang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Stephen J Simpson
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney 2050, Australia
| | - Carlos Ribeiro
- Behavior and Metabolism Laboratory, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Linda Partridge
- Institute of Healthy Ageing and Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, UK; Max Planck Institute for Biology of Ageing, Köln 50931, Germany.
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Mamlouk S, Childs LH, Aust D, Heim D, Melching F, Oliveira C, Wolf T, Durek P, Schumacher D, Bläker H, von Winterfeld M, Gastl B, Möhr K, Menne A, Zeugner S, Redmer T, Lenze D, Tierling S, Möbs M, Weichert W, Folprecht G, Blanc E, Beule D, Schäfer R, Morkel M, Klauschen F, Leser U, Sers C. DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer. Nat Commun 2017; 8:14093. [PMID: 28120820 PMCID: PMC5288500 DOI: 10.1038/ncomms14093] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [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: 02/01/2016] [Accepted: 11/28/2016] [Indexed: 02/06/2023] Open
Abstract
Genetic heterogeneity between and within tumours is a major factor determining cancer progression and therapy response. Here we examined DNA sequence and DNA copy-number heterogeneity in colorectal cancer (CRC) by targeted high-depth sequencing of 100 most frequently altered genes. In 97 samples, with primary tumours and matched metastases from 27 patients, we observe inter-tumour concordance for coding mutations; in contrast, gene copy numbers are highly discordant between primary tumours and metastases as validated by fluorescent in situ hybridization. To further investigate intra-tumour heterogeneity, we dissected a single tumour into 68 spatially defined samples and sequenced them separately. We identify evenly distributed coding mutations in APC and TP53 in all tumour areas, yet highly variable gene copy numbers in numerous genes. 3D morpho-molecular reconstruction reveals two clusters with divergent copy number aberrations along the proximal-distal axis indicating that DNA copy number variations are a major source of tumour heterogeneity in CRC.
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Affiliation(s)
- Soulafa Mamlouk
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Liam Harold Childs
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Daniela Aust
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany.,NCT Biobank Dresden, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Daniel Heim
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Friederike Melching
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Cristiano Oliveira
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Thomas Wolf
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Pawel Durek
- Experimental Rheumatology, German Rheumatism Research Centre, Berlin 10117, Germany
| | - Dirk Schumacher
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | | | - Bastian Gastl
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,BSIO Berlin School of Integrative Oncology, University Medicine Charité, Berlin 13353, Germany
| | - Kerstin Möhr
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Andrea Menne
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Silke Zeugner
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Torben Redmer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dido Lenze
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Sascha Tierling
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken 66123, Germany
| | - Markus Möbs
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,Institute of Pathology, Technical University Munich, Munich 81675, Germany
| | - Gunnar Folprecht
- University Hospital Carl Gustav Carus, University Cancer Center/Medical Dpt. I, Dresden 01307, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany.,Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Reinhold Schäfer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany.,German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Markus Morkel
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Frederick Klauschen
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Christine Sers
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany.,German Cancer Consortium (DKTK), Heidelberg 69120, Germany
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Moyle LA, Blanc E, Jaka O, Prueller J, Banerji CR, Tedesco FS, Harridge SD, Knight RD, Zammit PS. Ret function in muscle stem cells points to tyrosine kinase inhibitor therapy for facioscapulohumeral muscular dystrophy. eLife 2016; 5. [PMID: 27841748 PMCID: PMC5108591 DOI: 10.7554/elife.11405] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 09/01/2016] [Indexed: 12/16/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) involves sporadic expression of DUX4, which inhibits myogenesis and is pro-apoptotic. To identify target genes, we over-expressed DUX4 in myoblasts and found that the receptor tyrosine kinase Ret was significantly up-regulated, suggesting a role in FSHD. RET is dynamically expressed during myogenic progression in mouse and human myoblasts. Constitutive expression of either RET9 or RET51 increased myoblast proliferation, whereas siRNA-mediated knockdown of Ret induced myogenic differentiation. Suppressing RET activity using Sunitinib, a clinically-approved tyrosine kinase inhibitor, rescued differentiation in both DUX4-expressing murine myoblasts and in FSHD patient-derived myoblasts. Importantly, Sunitinib also increased engraftment and differentiation of FSHD myoblasts in regenerating mouse muscle. Thus, DUX4-mediated activation of Ret prevents myogenic differentiation and could contribute to FSHD pathology by preventing satellite cell-mediated repair. Rescue of DUX4-induced pathology by Sunitinib highlights the therapeutic potential of tyrosine kinase inhibitors for treatment of FSHD. DOI:http://dx.doi.org/10.7554/eLife.11405.001
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Affiliation(s)
- Louise A Moyle
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.,Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Eric Blanc
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.,Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany.,Institute of Pathology, Charite Universitatsmedizin Berlin, Berlin, Germany
| | - Oihane Jaka
- Centre of Human and Aerospace Physiological Sciences, King's College London, London, United Kingdom
| | - Johanna Prueller
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Christopher Rs Banerji
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | | | - Stephen Dr Harridge
- Centre of Human and Aerospace Physiological Sciences, King's College London, London, United Kingdom
| | - Robert D Knight
- Craniofacial Development and Stem Cell Biology, King's College London, London, United Kingdom
| | - Peter S Zammit
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
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Vincenot J, Kocot A, Vignot A, Chavrier F, Blanc E, Dupré A, Rivoire M, Chapelon J, Melodelima D. Toroidal Transducer for Intraoperative Thermal Ablation of Pancreatic Tumours by High-Intensity Focused Ultrasound. First In Vitro Experiments. Ing Rech Biomed 2016. [DOI: 10.1016/j.irbm.2016.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Bachelot T, Lavergne E, Romieu G, Rios M, Heudel PE, Roemer-Becuwe C, Jouannaud C, Tredan O, Chaigneau L, Arnedos M, Orfeuvre H, Petit T, Quenel-Tueux N, Jacquin JP, Ferrero JM, Moullet I, Abadie-Lacourtoisie S, Penault-Llorca F, Blanc E, Cox D. Abstract P1-08-06: SToRM: A prospective clinical trial of 1502 metastatic breast cancer (mBC) patients with detail of clinical presentation, molecular subtype, treatment modalities, prognosis and GWAS genotyping. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p1-08-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Due to better molecular classification and new treatment options, epidemiology and prognosis of mBC is rapidly changing. Clinical data extracted from randomized studies are only relevant to specific subpopulations and retrospective studies are prone to selection bias. SToRM is a prospective clinical trial that aims to create a cohort of 1500 mBC patients, with the ultimate goal of identifying germ line polymorphisms associated with prognosis of breast cancer (BC) and response to treatment in the metastatic phase.
Material and methods: Any newly (within 1 year) diagnosed mBC patients were eligible. Whole blood samples were drawn and germline DNA extracted for genetic analysis. Extensive epidemiologic data, disease history from primary diagnosis to metastatic spread, pathological characteristics and ER, PR and HER2 status were collected. Patients are prospectively followed until death. Genotyping using the HumanCoreExome chipset from Illumina is currently underway and will be completed in early summer 2015.
Results: 1502 patients were included from March 2012 to May 2014 from 71 French institutions. Median age at metastatic relapse was 60 years (range 26-93). Median time from primary diagnosis to metastatic relapse was 30 months (range 0-473) with 24% of patients already metastatic at initial diagnosis. 78% of patients were ER+, 18% were HER2+ and only 16% were triple negative. Molecular subtype classification derived from pathological data following St Gallen consensus recommendations is presented below:
n (%)Luminal A like261 (22.2%)Luminal B like HER2 negative476 (40.5%)Luminal B like HER2 positive134 (11.4%)HER2 positive non Luminal (ER-)111 (9.5%)Triple negative193 (16.4%)Missing data327
64% of the patients had received previous adjuvant treatment, among which 81% received adjuvant chemotherapy and 9% trastuzumab.
At metastatic relapse, loco-regional progression, liver, lung and bone metastasis were documented in 301 (20%), 494 (33%), 410 (27%) and 1017 (68%) patients respectively. 313 patients (21%) had bone only metastatic disease. First line treatment included: chemotherapy (71%), endocrine therapy (50%) and anti-HER2 treatments (17%). Survival data will be presented at the meeting.
Conclusion: Despite a theoretically better prognosis and widespread use of adjuvant hormonal treatment, ER+/HER2- breast cancer still account for more than 60% of mBC. The proportion of patients with HER2+ disease (18%) and triple negative disease (16%) is consistent with percentages observed in early BC populations. In comparison with a cohort of "cured", localized cancer, such as the SIGNAL/PHARE study, GWAS analysis will allow for the identification of genetic polymorphisms correlated with treatment resistance. Fundamentally, such variants will provide insight into the molecular mechanisms responsible for host-genetic influence on BC progression. From a clinical perspective, genetic variants that predispose to metastatic disease can serve as stratification variables in future clinical trials, particularly as the development of new treatment options for resistant BC is needed.
Citation Format: Bachelot T, Lavergne E, Romieu G, Rios M, Heudel P-E, Roemer-Becuwe C, Jouannaud C, Tredan O, Chaigneau L, Arnedos M, Orfeuvre H, Petit T, Quenel-Tueux N, Jacquin J-P, Ferrero J-M, Moullet I, Abadie-Lacourtoisie S, Penault-Llorca F, Blanc E, Cox D. SToRM: A prospective clinical trial of 1502 metastatic breast cancer (mBC) patients with detail of clinical presentation, molecular subtype, treatment modalities, prognosis and GWAS genotyping. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-08-06.
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Affiliation(s)
- T Bachelot
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - E Lavergne
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - G Romieu
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - M Rios
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - P-E Heudel
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - C Roemer-Becuwe
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - C Jouannaud
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - O Tredan
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - L Chaigneau
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - M Arnedos
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - H Orfeuvre
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - T Petit
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - N Quenel-Tueux
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - J-P Jacquin
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - J-M Ferrero
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - I Moullet
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - S Abadie-Lacourtoisie
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - F Penault-Llorca
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - E Blanc
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
| | - D Cox
- Centre Leon Berard, Lyon cedex 08, France; Institut Régional du Cancer Montpellier (ICM), Montpellier Cedex, France; Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy Cedex, France; Centre d'Oncologie de Gentilly, Nancy, France; Institut Jean Godinot, Reims Cedex, France; CHU de Besançon - Hopital Jean Minjoz, Besançon, France; Gustave Roussy Cancer Campus, Villejuif Cedex, France; Hôpital Fleyriat - Centre Hospitalier de Bourg-en-Bresse, Bourg-en-Bresse Cedex, France; Centre Paul Strauss, Strasbourg Cedex, France; Institut Bergonié, Bordeaux Cedex, France; Institut de Cancérologie Lucien Neuwirth, Saint-Priest-en-Jarez, France; Centre Antoine Lacassagne, Nice Cedex 02, France; Clinique de la Sauvegarde, Lyon, France; Institut de Cancérologie de l'Ouest - Paul Papin, Angers Cedex 09, France; Centre Jean Perrin, Clermont-Ferrand Cedex, France
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Santos CXC, Hafstad AD, Beretta M, Zhang M, Molenaar C, Kopec J, Fotinou D, Murray TV, Cobb AM, Martin D, Zeh Silva M, Anilkumar N, Schröder K, Shanahan CM, Brewer AC, Brandes RP, Blanc E, Parsons M, Belousov V, Cammack R, Hider RC, Steiner RA, Shah AM. Targeted redox inhibition of protein phosphatase 1 by Nox4 regulates eIF2α-mediated stress signaling. EMBO J 2016; 35:319-34. [PMID: 26742780 PMCID: PMC4741303 DOI: 10.15252/embj.201592394] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 12/02/2015] [Indexed: 01/25/2023] Open
Abstract
Phosphorylation of translation initiation factor 2α (eIF2α) attenuates global protein synthesis but enhances translation of activating transcription factor 4 (ATF4) and is a crucial evolutionarily conserved adaptive pathway during cellular stresses. The serine–threonine protein phosphatase 1 (PP1) deactivates this pathway whereas prolonging eIF2α phosphorylation enhances cell survival. Here, we show that the reactive oxygen species‐generating NADPH oxidase‐4 (Nox4) is induced downstream of ATF4, binds to a PP1‐targeting subunit GADD34 at the endoplasmic reticulum, and inhibits PP1 activity to increase eIF2α phosphorylation and ATF4 levels. Other PP1 targets distant from the endoplasmic reticulum are unaffected, indicating a spatially confined inhibition of the phosphatase. PP1 inhibition involves metal center oxidation rather than the thiol oxidation that underlies redox inhibition of protein tyrosine phosphatases. We show that this Nox4‐regulated pathway robustly enhances cell survival and has a physiologic role in heart ischemia–reperfusion and acute kidney injury. This work uncovers a novel redox signaling pathway, involving Nox4–GADD34 interaction and a targeted oxidative inactivation of the PP1 metal center, that sustains eIF2α phosphorylation to protect tissues under stress.
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Affiliation(s)
- Celio X C Santos
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Anne D Hafstad
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK Cardiovascular Research Group, Department of Medical Biology, The Arctic University of Norway, Tromsø, Norway
| | - Matteo Beretta
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Min Zhang
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Chris Molenaar
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Jola Kopec
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK Randall Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Dina Fotinou
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK Randall Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Thomas V Murray
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Andrew M Cobb
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Daniel Martin
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Maira Zeh Silva
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK Randall Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Narayana Anilkumar
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Katrin Schröder
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany
| | - Catherine M Shanahan
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Alison C Brewer
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany
| | - Eric Blanc
- MRC Centre for Developmental Neurobiology, King's College London, London, UK
| | - Maddy Parsons
- Randall Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Vsevelod Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Richard Cammack
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - Robert C Hider
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - Roberto A Steiner
- Randall Division, King's College London British Heart Foundation Centre of Excellence, London, UK
| | - Ajay M Shah
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence, London, UK
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Dyer C, Blanc E, Stanley RJ, Knight RD. Dissecting the role of Wnt signaling and its interactions with FGF signaling during midbrain neurogenesis. Neurogenesis (Austin) 2015; 2:e1057313. [PMID: 27606327 PMCID: PMC4973611 DOI: 10.1080/23262133.2015.1057313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/07/2015] [Accepted: 05/27/2015] [Indexed: 11/14/2022]
Abstract
Interactions between FGF and Wnt/ bcat signaling control development of the midbrain. The nature of this interaction and how these regulate patterning, growth and differentiation is less clear, as it has not been possible to temporally dissect the effects of one pathway relative to the other. We have employed pharmacological and genetic tools to probe the temporal and spatial roles of FGF and Wnt in controlling the specification of early midbrain neurons. We identify a β-catenin (bcat) independent role for GSK-3 in modulating FGF activity and hence neuronal patterning. This function is complicated by an overlap with bcat-dependent regulation of FGF signaling, through the regulation of sprouty4. Additionally we reveal how attenuation of Axin protein function can promote fluctuating levels of bcat activity that are dependent on FGF activity. This highlights the complex nature of the interactions between FGF and Wnt/ bcat and reveals that they act at multiple levels to control each others activity in the midbrain.
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Affiliation(s)
- Carlene Dyer
- Craniofacial Development and Stem Cell Biology; King's College London ; London, UK
| | - Eric Blanc
- MRC Centre for Developmental Neurobiology; King's College London ; London, UK
| | - Rob J Stanley
- Department of Cell and Developmental Biology; University College London; London, UK; CoMPLEX; University College London; London, UK
| | - Robert D Knight
- Craniofacial Development and Stem Cell Biology; King's College London ; London, UK
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Piper MDW, Blanc E, Leitão-Gonçalves R, Yang M, He X, Linford NJ, Hoddinott MP, Hopfen C, Soultoukis GA, Niemeyer C, Kerr F, Pletcher SD, Ribeiro C, Partridge L. Erratum: Corrigendum: A holidic medium for Drosophila melanogaster. Nat Methods 2014. [DOI: 10.1038/nmeth0914-971c] [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] [Indexed: 11/09/2022]
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Machado CB, Kanning KC, Kreis P, Stevenson D, Crossley M, Nowak M, Iacovino M, Kyba M, Chambers D, Blanc E, Lieberam I. Reconstruction of phrenic neuron identity in embryonic stem cell-derived motor neurons. Development 2014; 141:784-94. [PMID: 24496616 PMCID: PMC3912827 DOI: 10.1242/dev.097188] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [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] [Indexed: 11/20/2022]
Abstract
Air breathing is an essential motor function for vertebrates living on land. The rhythm that drives breathing is generated within the central nervous system and relayed via specialised subsets of spinal motor neurons to muscles that regulate lung volume. In mammals, a key respiratory muscle is the diaphragm, which is innervated by motor neurons in the phrenic nucleus. Remarkably, relatively little is known about how this crucial subtype of motor neuron is generated during embryogenesis. Here, we used direct differentiation of motor neurons from mouse embryonic stem cells as a tool to identify genes that direct phrenic neuron identity. We find that three determinants, Pou3f1, Hoxa5 and Notch, act in combination to promote a phrenic neuron molecular identity. We show that Notch signalling induces Pou3f1 in developing motor neurons in vitro and in vivo. This suggests that the phrenic neuron lineage is established through a local source of Notch ligand at mid-cervical levels. Furthermore, we find that the cadherins Pcdh10, which is regulated by Pou3f1 and Hoxa5, and Cdh10, which is controlled by Pou3f1, are both mediators of like-like clustering of motor neuron cell bodies. This specific Pcdh10/Cdh10 activity might provide the means by which phrenic neurons are assembled into a distinct nucleus. Our study provides a framework for understanding how phrenic neuron identity is conferred and will help to generate this rare and inaccessible yet vital neuronal subtype directly from pluripotent stem cells, thus facilitating subsequent functional investigations.
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Machado CB, Kanning KC, Kreis P, Stevenson D, Crossley M, Nowak M, Iacovino M, Kyba M, Chambers D, Blanc E, Lieberam I. Reconstruction of phrenic neuron identity in embryonic stem cell-derived motor neurons. Development 2014. [DOI: 10.1242/dev.108803] [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: 11/20/2022]
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Fernandes de Abreu DA, Caballero A, Fardel P, Stroustrup N, Chen Z, Lee K, Keyes WD, Nash ZM, López-Moyado IF, Vaggi F, Cornils A, Regenass M, Neagu A, Ostojic I, Liu C, Cho Y, Sifoglu D, Shen Y, Fontana W, Lu H, Csikasz-Nagy A, Murphy CT, Antebi A, Blanc E, Apfeld J, Zhang Y, Alcedo J, Ch'ng Q. An insulin-to-insulin regulatory network orchestrates phenotypic specificity in development and physiology. PLoS Genet 2014; 10:e1004225. [PMID: 24675767 PMCID: PMC3967928 DOI: 10.1371/journal.pgen.1004225] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 01/22/2014] [Indexed: 12/22/2022] Open
Abstract
Insulin-like peptides (ILPs) play highly conserved roles in development and physiology. Most animal genomes encode multiple ILPs. Here we identify mechanisms for how the forty Caenorhabditis elegans ILPs coordinate diverse processes, including development, reproduction, longevity and several specific stress responses. Our systematic studies identify an ILP-based combinatorial code for these phenotypes characterized by substantial functional specificity and diversity rather than global redundancy. Notably, we show that ILPs regulate each other transcriptionally, uncovering an ILP-to-ILP regulatory network that underlies the combinatorial phenotypic coding by the ILP family. Extensive analyses of genetic interactions among ILPs reveal how their signals are integrated. A combined analysis of these functional and regulatory ILP interactions identifies local genetic circuits that act in parallel and interact by crosstalk, feedback and compensation. This organization provides emergent mechanisms for phenotypic specificity and graded regulation for the combinatorial phenotypic coding we observe. Our findings also provide insights into how large hormonal networks regulate diverse traits.
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Affiliation(s)
| | - Antonio Caballero
- MRC Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Pascal Fardel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Biozentrum, University of Basel, Basel, Basel, Switzerland
| | - Nicholas Stroustrup
- Dept of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zhunan Chen
- Dept of Organismic and Evolutionary Biology, The Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
| | - KyungHwa Lee
- Lewis-Sigler Institute for Integrative Genomics and Dept of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - William D. Keyes
- Lewis-Sigler Institute for Integrative Genomics and Dept of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Zachary M. Nash
- Dept of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isaac F. López-Moyado
- Dept of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Federico Vaggi
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Astrid Cornils
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Martin Regenass
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Anca Neagu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Biozentrum, University of Basel, Basel, Basel, Switzerland
| | - Ivan Ostojic
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Chang Liu
- MRC Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Yongmin Cho
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Deniz Sifoglu
- Dept of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Yu Shen
- Dept of Organismic and Evolutionary Biology, The Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
| | - Walter Fontana
- Dept of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hang Lu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Attila Csikasz-Nagy
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Institute for Mathematical and Molecular Biomedicine, King's College London, London, United Kingdom
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Coleen T. Murphy
- Lewis-Sigler Institute for Integrative Genomics and Dept of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Koeln, Germany
| | - Eric Blanc
- MRC Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Javier Apfeld
- Dept of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yun Zhang
- Dept of Organismic and Evolutionary Biology, The Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
| | - Joy Alcedo
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Dept of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - QueeLim Ch'ng
- MRC Centre for Developmental Neurobiology, King's College London, London, United Kingdom
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46
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Dyer C, Blanc E, Hanisch A, Roehl H, Otto GW, Yu T, Basson MA, Knight R. A bi-modal function of Wnt signalling directs an FGF activity gradient to spatially regulate neuronal differentiation in the midbrain. Development 2013; 141:63-72. [PMID: 24284206 DOI: 10.1242/dev.099507] [Citation(s) in RCA: 27] [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: 12/28/2022]
Abstract
FGFs and Wnts are important morphogens during midbrain development, but their importance and potential interactions during neurogenesis are poorly understood. We have employed a combination of genetic and pharmacological manipulations in zebrafish to show that during neurogenesis FGF activity occurs as a gradient along the anterior-posterior axis of the dorsal midbrain and directs spatially dynamic expression of the Hairy gene her5. As FGF activity diminishes during development, Her5 is lost and differentiation of neuronal progenitors occurs in an anterior-posterior manner. We generated mathematical models to explain how Wnt and FGFs direct the spatial differentiation of neurons in the midbrain through Wnt regulation of FGF signalling. These models suggested that a negative-feedback loop controlled by Wnt is crucial for regulating FGF activity. We tested Sprouty genes as mediators of this regulatory loop using conditional mouse knockouts and pharmacological manipulations in zebrafish. These reveal that Sprouty genes direct the positioning of early midbrain neurons and are Wnt responsive in the midbrain. We propose a model in which Wnt regulates FGF activity at the isthmus by driving both FGF and Sprouty gene expression. This controls a dynamic, posteriorly retracting expression of her5 that directs neuronal differentiation in a precise spatiotemporal manner in the midbrain.
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Affiliation(s)
- Carlene Dyer
- Craniofacial Development and Stem Cell Biology, King's College London, Guy's Hospital, London SE1 9RT, UK
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47
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Piper MDW, Blanc E, Leitão-Gonçalves R, Yang M, He X, Linford NJ, Hoddinott MP, Hopfen C, Soultoukis GA, Niemeyer C, Kerr F, Pletcher SD, Ribeiro C, Partridge L. A holidic medium for Drosophila melanogaster. Nat Methods 2013; 11:100-5. [PMID: 24240321 PMCID: PMC3877687 DOI: 10.1038/nmeth.2731] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 10/10/2013] [Indexed: 11/09/2022]
Abstract
A critical requirement for research using model organisms is an appropriate, well-defined and consistent diet. There is currently no complete chemically defined (holidic) diet available for Drosophila melanogaster. We describe a holidic medium that is equal in performance to an oligidic diet optimized for adult fecundity and lifespan. It is also sufficient to support development over multiple generations, but at a reduced rate. During seven years of experiments, the holidic diet yielded more consistent experimental outcomes than oligidic food for adult fitness traits. Furthermore, nutrients and drugs are more accessible to flies in holidic medium and, similar to dietary restriction on oligidic food, amino acid dilution increases fly lifespan. We also report amino acid specific effects on food choice behavior and that folic acid from the microbiota is sufficient for development. These insights could not be gained using oligidic or meridic diets.
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Affiliation(s)
- Matthew D W Piper
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Eric Blanc
- Medical Research Council (MRC) Centre for Developmental Neurobiology, King's College London, London, UK
| | - Ricardo Leitão-Gonçalves
- Behavior and Metabolism Laboratory, Champalimaud Neuroscience Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Mingyao Yang
- 1] Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK. [2]
| | - Xiaoli He
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Nancy J Linford
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew P Hoddinott
- 1] Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK. [2] Max Planck Institute for Biology of Ageing, Köln, Germany
| | - Corinna Hopfen
- Max Planck Institute for Biology of Ageing, Köln, Germany
| | | | - Christine Niemeyer
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Fiona Kerr
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Scott D Pletcher
- 1] Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA. [2] Geriatrics Center and Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Michigan, Ann Arbor, Michigan, USA
| | - Carlos Ribeiro
- Behavior and Metabolism Laboratory, Champalimaud Neuroscience Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Linda Partridge
- 1] Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK. [2] Max Planck Institute for Biology of Ageing, Köln, Germany
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48
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Mari JM, Bouchoux G, Dillenseger JL, Gimonet S, Birer A, Garnier C, Brasset L, Ke W, Guey JL, Fleury G, Chapelon JY, Blanc E. Study of a dual-mode array integrated in a multi-element transducer for imaging and therapy of prostate cancer. Ing Rech Biomed 2013. [DOI: 10.1016/j.irbm.2013.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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49
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Chen Y, Lee SF, Blanc E, Reuter C, Wertheim B, Martinez-Diaz P, Hoffmann AA, Partridge L. Genome-wide transcription analysis of clinal genetic variation in Drosophila. PLoS One 2012; 7:e34620. [PMID: 22514645 PMCID: PMC3326059 DOI: 10.1371/journal.pone.0034620] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [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: 11/30/2011] [Accepted: 03/02/2012] [Indexed: 11/19/2022] Open
Abstract
Clinal variation in quantitative traits is widespread, but its genetic basis awaits identification. Drosophila melanogaster shows adaptive, clinal variation in traits such as body size along latitudinal gradients on multiple continents. To investigate genome wide transcription differentiation between North and South that might contribute to the clinal phenotypic variation, we compared RNA expression patterns during development of D. melanogaster from tropical northern and temperate southern populations using whole genome tiling arrays. We found that genes that were differentially expressed between the cline ends were generally associated with metabolism and growth, and experimental alteration of expression of a sample of them generally resulted in altered body size in the predicted direction, sometimes significantly so. We further identified the serpent (srp) transcription factor binding sites to be enriched near genes up-regulated in expression in the south. Analysis of clinal populations revealed a significant cline in the expression level of srp. Experimental over-expression of srp increased body size, as predicted from its clinal expression pattern, suggesting that it may be involved in regulating adaptive clinal variation in Drosophila. This study identified a handful of genes that contributed to clinal phenotypic variation through altered gene expression level, yet misexpression of individual gene led to modest body size change.
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Affiliation(s)
- Ying Chen
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- * E-mail: (LP); (YC)
| | - Siu F. Lee
- Bio21 Institute, Department of Genetics, The University of Melbourne, Parkville, Victoria, Australia
| | - Eric Blanc
- MRC Centre for Developmental Neurobiology, King's College, London, United Kingdom
| | - Caroline Reuter
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Bregje Wertheim
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Pedro Martinez-Diaz
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ary A. Hoffmann
- Bio21 Institute, Department of Genetics, The University of Melbourne, Parkville, Victoria, Australia
| | - Linda Partridge
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- * E-mail: (LP); (YC)
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50
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Abstract
Tetartohedral crystal twinning is discussed as a particular case of (pseudo)merohedral twinning when the number of twinned domains is four. Tetartohedrally twinned crystals often possess pseudosymmetry, with the rotational part of the pseudosymmetry operators coinciding with the twinning operators. Tetartohedrally twinned structures from the literature are reviewed and the recent structure determination of tetartohedrally twinned triclinic crystals of human complement factor I is discussed.
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Affiliation(s)
- Pietro Roversi
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, England.
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