1
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Eichhoff OM, Stoffel CI, Käsler J, Briker L, Turko P, Karsai G, Zila N, Paulitschke V, Cheng PF, Leitner A, Bileck A, Zamboni N, Irmisch A, Balazs Z, Tastanova A, Pascoal S, Johansen P, Wegmann R, Mena J, Othman A, Viswanathan VS, Wenzina J, Aloia A, Saltari A, Dzung A, Aebersold R, Ak M, Al-Quaddoomi FS, Albert SI, Albinus J, Alborelli I, Andani S, Attinger PO, Bacac M, Baumhoer D, Beck-Schimmer B, Beerenwinkel N, Beisel C, Bernasconi L, Bertolini A, Bodenmiller B, Bonilla X, Bosshard L, Calgua B, Casanova R, Chevrier S, Chicherova N, Coelho R, D'Costa M, Danenberg E, Davidson N, Drãgan MA, Dummer R, Engler S, Erkens M, Eschbach K, Esposito C, Fedier A, Ferreira P, Ficek J, Frei AL, Frey B, Goetze S, Grob L, Gut G, Günther D, Haberecker M, Haeuptle P, Heinzelmann-Schwarz V, Herter S, Holtackers R, Huesser T, Immer A, Irmisch A, Jacob F, Jacobs A, Jaeger TM, Jahn K, James AR, Jermann PM, Kahles A, Kahraman A, Koelzer VH, Kuebler W, Kuipers J, Kunze CP, Kurzeder C, Lehmann KV, Levesque M, Lischetti U, Lugert S, Maass G, Manz MG, Markolin P, Mehnert M, Mena J, Metzler JM, Miglino N, Milani ES, Moch H, Muenst S, Murri R, Ng CK, Nicolet S, Nowak M, Lopez MN, Pedrioli PG, Pelkmans L, Piscuoglio S, Prummer M, Rimmer N, Ritter M, Rommel C, Rosano-González ML, Rätsch G, Santacroce N, Del Castillo JS, Schlenker R, Schwalie PC, Schwan S, Schär T, Senti G, Shao W, Singer F, Sivapatham S, Snijder B, Sobottka B, Sreedharan VT, Stark S, Stekhoven DJ, Tanna T, Theocharides AP, Thomas TM, Tolnay M, Tosevski V, Toussaint NC, Tuncel MA, Tusup M, Van Drogen A, Vetter M, Vlajnic T, Weber S, Weber WP, Wegmann R, Weller M, Wendt F, Wey N, Wicki A, Wildschut MH, Wollscheid B, Yu S, Ziegler J, Zimmermann M, Zoche M, Zuend G, Krauthammer M, Schreiber SL, Hornemann T, Distel M, Snijder B, Dummer R, Levesque MP. ROS Induction Targets Persister Cancer Cells with Low Metabolic Activity in NRAS-Mutated Melanoma. Cancer Res 2023; 83:1128-1146. [PMID: 36946761 DOI: 10.1158/0008-5472.can-22-1826] [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] [Received: 06/03/2022] [Revised: 10/04/2022] [Accepted: 01/24/2023] [Indexed: 03/23/2023]
Abstract
Clinical management of melanomas with NRAS mutations is challenging. Targeting MAPK signaling is only beneficial to a small subset of patients due to resistance that arises through genetic, transcriptional, and metabolic adaptation. Identification of targetable vulnerabilities in NRAS-mutated melanoma could help improve patient treatment. Here, we used multiomics analyses to reveal that NRAS-mutated melanoma cells adopt a mesenchymal phenotype with a quiescent metabolic program to resist cellular stress induced by MEK inhibition. The metabolic alterations elevated baseline reactive oxygen species (ROS) levels, leading these cells to become highly sensitive to ROS induction. In vivo xenograft experiments and single-cell RNA sequencing demonstrated that intratumor heterogeneity necessitates the combination of a ROS inducer and a MEK inhibitor to inhibit both tumor growth and metastasis. Ex vivo pharmacoscopy of 62 human metastatic melanomas confirmed that MEK inhibitor-resistant tumors significantly benefited from the combination therapy. Finally, oxidative stress response and translational suppression corresponded with ROS-inducer sensitivity in 486 cancer cell lines, independent of cancer type. These findings link transcriptional plasticity to a metabolic phenotype that can be inhibited by ROS inducers in melanoma and other cancers. SIGNIFICANCE Metabolic reprogramming in drug-resistant NRAS-mutated melanoma cells confers sensitivity to ROS induction, which suppresses tumor growth and metastasis in combination with MAPK pathway inhibitors.
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Affiliation(s)
- Ossia M Eichhoff
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Corinne I Stoffel
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Jan Käsler
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Luzia Briker
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Patrick Turko
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Gergely Karsai
- Institute for Clinical Chemistry, University Hospital Zurich, Zurich, Switzerland; Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Nina Zila
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Verena Paulitschke
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Phil F Cheng
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | | | - Andrea Bileck
- Joint Metabolome Facility, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Nicola Zamboni
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | - Anja Irmisch
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Zsolt Balazs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Biomedical Informatics, University Hospital of Zurich, Zurich, Switzerland
| | - Aizhan Tastanova
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Susana Pascoal
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Pål Johansen
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Rebekka Wegmann
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | - Julien Mena
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | - Alaa Othman
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | | | - Judith Wenzina
- Skin and Endothelium Research Division, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Andrea Aloia
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | - Annalisa Saltari
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Andreas Dzung
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michael Krauthammer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Biomedical Informatics, University Hospital of Zurich, Zurich, Switzerland
| | | | - Thorsten Hornemann
- Institute for Clinical Chemistry, University Hospital Zurich, Zurich, Switzerland; Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Martin Distel
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Berend Snijder
- Institute for Molecular Systems Biology, ETH Zurich, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
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Crowell HL, Chevrier S, Jacobs A, Sivapatham S, Bodenmiller B, Robinson MD. An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. F1000Res 2022; 9:1263. [PMID: 36072920 PMCID: PMC9411975 DOI: 10.12688/f1000research.26073.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
Mass cytometry (CyTOF) has become a method of choice for in-depth characterization of tissue heterogeneity in health and disease, and is currently implemented in multiple clinical trials, where higher quality standards must be met. Currently, preprocessing of raw files is commonly performed in independent standalone tools, which makes it difficult to reproduce. Here, we present an R pipeline based on an updated version of CATALYST that covers all preprocessing steps required for downstream mass cytometry analysis in a fully reproducible way. This new version of CATALYST is based on Bioconductor’s SingleCellExperiment class and fully unit tested. The R-based pipeline includes file concatenation, bead-based normalization, single-cell deconvolution, spillover compensation and live cell gating after debris and doublet removal. Importantly, this pipeline also includes different quality checks to assess machine sensitivity and staining performance while allowing also for batch correction. This pipeline is based on open source R packages and can be easily be adapted to different study designs. It therefore has the potential to significantly facilitate the work of CyTOF users while increasing the quality and reproducibility of data generated with this technology.
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Affiliation(s)
- Helena L. Crowell
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, 8057, Switzerland
| | - Stéphane Chevrier
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Andrea Jacobs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Sujana Sivapatham
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | | | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Mark D. Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, 8057, Switzerland
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Taeschler P, Adamo S, Deng Y, Cervia C, Zurbuchen Y, Chevrier S, Raeber ME, Hasler S, Bächli E, Rudiger A, Stüssi‐Helbling M, Huber LC, Bodenmiller B, Boyman O, Nilsson J. T-cell recovery and evidence of persistent immune activation 12 months after severe COVID-19. Allergy 2022; 77:2468-2481. [PMID: 35567391 PMCID: PMC9347640 DOI: 10.1111/all.15372] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND T-cell lymphopenia and functional impairment is a hallmark of severe acute coronavirus disease 2019 (COVID-19). How T-cell numbers and function evolve at later timepoints after clinical recovery remains poorly investigated. METHODS We prospectively enrolled and longitudinally sampled 173 individuals with asymptomatic to critical COVID-19 and analyzed phenotypic and functional characteristics of T cells using flow cytometry, 40-parameter mass cytometry, targeted proteomics, and functional assays. RESULTS The extensive T-cell lymphopenia observed particularly in patients with severe COVID-19 during acute infection had recovered 6 months after infection, which was accompanied by a normalization of functional T-cell responses to common viral antigens. We detected persisting CD4+ and CD8+ T-cell activation up to 12 months after infection, in patients with mild and severe COVID-19, as measured by increased HLA-DR and CD38 expression on these cells. Persistent T-cell activation after COVID-19 was independent of administration of a COVID-19 vaccine post-infection. Furthermore, we identified a subgroup of patients with severe COVID-19 that presented with persistently low CD8+ T-cell counts at follow-up and exhibited a distinct phenotype during acute infection consisting of a dysfunctional T-cell response and signs of excessive pro-inflammatory cytokine production. CONCLUSION Our study suggests that T-cell numbers and function recover in most patients after COVID-19. However, we find evidence of persistent T-cell activation up to 12 months after infection and describe a subgroup of severe COVID-19 patients with persistently low CD8+ T-cell counts exhibiting a dysregulated immune response during acute infection.
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Affiliation(s)
- Patrick Taeschler
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Sarah Adamo
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Yun Deng
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Carlo Cervia
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Yves Zurbuchen
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Stéphane Chevrier
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Miro E. Raeber
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Sara Hasler
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Esther Bächli
- Clinic for Internal Medicine, Hirslanden Klinik St. Anna Lucerne Switzerland
| | - Alain Rudiger
- Department of Medicine Limmattal Hospital Schlieren Switzerland
| | | | - Lars C. Huber
- Clinic for Internal Medicine, City Hospital Triemli Zurich Zurich Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Onur Boyman
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
- Faculty of Medicine University of Zurich Zurich Switzerland
| | - Jakob Nilsson
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
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4
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Adamo S, Chevrier S, Cervia C, Zurbuchen Y, Raeber ME, Yang L, Sivapatham S, Jacobs A, Baechli E, Rudiger A, Stüssi‐Helbling M, Huber LC, Schaer DJ, Bodenmiller B, Boyman O, Nilsson J. Profound dysregulation of T cell homeostasis and function in patients with severe COVID-19. Allergy 2021; 76:2866-2881. [PMID: 33884644 PMCID: PMC8251365 DOI: 10.1111/all.14866] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/09/2021] [Accepted: 03/14/2021] [Indexed: 01/08/2023]
Abstract
Background Coronavirus disease 2019 (COVID‐19) is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and shows a broad clinical presentation ranging from asymptomatic infection to fatal disease. A very prominent feature associated with severe COVID‐19 is T cell lymphopenia. However, homeostatic and functional properties of T cells are ill‐defined in COVID‐19. Methods We prospectively enrolled individuals with mild and severe COVID‐19 into our multicenter cohort and performed a cross‐sectional analysis of phenotypic and functional characteristics of T cells using 40‐parameter mass cytometry, flow cytometry, targeted proteomics, and functional assays. Results Compared with mild disease, we observed strong perturbations of peripheral T cell homeostasis and function in severe COVID‐19. Individuals with severe COVID‐19 showed T cell lymphopenia and redistribution of T cell populations, including loss of naïve T cells, skewing toward CD4+T follicular helper cells and cytotoxic CD4+ T cells, and expansion of activated and exhausted T cells. Extensive T cell apoptosis was particularly evident with severe disease and T cell lymphopenia, which in turn was accompanied by impaired T cell responses to several common viral antigens. Patients with severe disease showed elevated interleukin‐7 and increased T cell proliferation. Furthermore, patients sampled at late time points after symptom onset had higher T cell counts and improved antiviral T cell responses. Conclusion Our study suggests that severe COVID‐19 is characterized by extensive T cell dysfunction and T cell apoptosis, which is associated with signs of homeostatic T cell proliferation and T cell recovery.
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Affiliation(s)
- Sarah Adamo
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Stéphane Chevrier
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Carlo Cervia
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Yves Zurbuchen
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Miro E. Raeber
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Liliane Yang
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Sujana Sivapatham
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Andrea Jacobs
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Esther Baechli
- Clinic for Internal Medicine Uster Hospital Uster Switzerland
| | - Alain Rudiger
- Department of Medicine Limmattal Hospital Schlieren Switzerland
| | | | - Lars C. Huber
- Clinic for Internal Medicine City Hospital Triemli Zurich Zurich Switzerland
| | | | - Bernd Bodenmiller
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Onur Boyman
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
- Faculty of Medicine University of Zurich Zurich Switzerland
| | - Jakob Nilsson
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
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5
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Irmisch A, Bonilla X, Chevrier S, Lehmann KV, Singer F, Toussaint NC, Esposito C, Mena J, Milani ES, Casanova R, Stekhoven DJ, Wegmann R, Jacob F, Sobottka B, Goetze S, Kuipers J, Sarabia Del Castillo J, Prummer M, Tuncel MA, Menzel U, Jacobs A, Engler S, Sivapatham S, Frei AL, Gut G, Ficek J, Miglino N, Aebersold R, Bacac M, Beerenwinkel N, Beisel C, Bodenmiller B, Dummer R, Heinzelmann-Schwarz V, Koelzer VH, Manz MG, Moch H, Pelkmans L, Snijder B, Theocharides APA, Tolnay M, Wicki A, Wollscheid B, Rätsch G, Levesque MP. The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support. Cancer Cell 2021; 39:288-293. [PMID: 33482122 DOI: 10.1016/j.ccell.2021.01.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The application and integration of molecular profiling technologies create novel opportunities for personalized medicine. Here, we introduce the Tumor Profiler Study, an observational trial combining a prospective diagnostic approach to assess the relevance of in-depth tumor profiling to support clinical decision-making with an exploratory approach to improve the biological understanding of the disease.
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Affiliation(s)
- Anja Irmisch
- University Hospital Zurich, Department of Dermatology, University of Zurich, Gloriastrasse 31, 8091 Zurich, Switzerland
| | - Ximena Bonilla
- ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universitätstrasse 6, 8092 Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Hospital Zurich, Biomedical Informatics, Schmelzbergstrasse 26, 8006 Zurich, Switzerland
| | - Stéphane Chevrier
- University of Zurich, Department of Quantitative Biomedicine, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kjong-Van Lehmann
- ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universitätstrasse 6, 8092 Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Hospital Zurich, Biomedical Informatics, Schmelzbergstrasse 26, 8006 Zurich, Switzerland
| | - Franziska Singer
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; ETH Zurich, NEXUS Personalized Health Technologies, John-von-Neumann-Weg 9, 8093 Zurich, Switzerland
| | - Nora C Toussaint
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; ETH Zurich, NEXUS Personalized Health Technologies, John-von-Neumann-Weg 9, 8093 Zurich, Switzerland
| | - Cinzia Esposito
- University of Zurich, Department of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Julien Mena
- ETH Zurich, Department of Biology, Institute of Molecular Systems Biology, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Emanuela S Milani
- ETH Zurich, Department of Health Sciences and Technology, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Ruben Casanova
- University of Zurich, Department of Quantitative Biomedicine, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel J Stekhoven
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; ETH Zurich, NEXUS Personalized Health Technologies, John-von-Neumann-Weg 9, 8093 Zurich, Switzerland
| | - Rebekka Wegmann
- ETH Zurich, Department of Biology, Institute of Molecular Systems Biology, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Francis Jacob
- University Hospital Basel and University of Basel, Department of Biomedicine, Hebelstrasse 20, 4031 Basel, Switzerland
| | - Bettina Sobottka
- University Hospital Zurich, Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | - Sandra Goetze
- ETH Zurich, Department of Health Sciences and Technology, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Jack Kuipers
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Jacobo Sarabia Del Castillo
- University of Zurich, Department of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Michael Prummer
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; ETH Zurich, NEXUS Personalized Health Technologies, John-von-Neumann-Weg 9, 8093 Zurich, Switzerland
| | - Mustafa A Tuncel
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Ulrike Menzel
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Andrea Jacobs
- University of Zurich, Department of Quantitative Biomedicine, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Stefanie Engler
- University of Zurich, Department of Quantitative Biomedicine, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Sujana Sivapatham
- University of Zurich, Department of Quantitative Biomedicine, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anja L Frei
- University Hospital Zurich, Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | - Gabriele Gut
- University of Zurich, Department of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Joanna Ficek
- ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universitätstrasse 6, 8092 Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Hospital Zurich, Biomedical Informatics, Schmelzbergstrasse 26, 8006 Zurich, Switzerland
| | - Nicola Miglino
- University Hospital Zurich, Department of Medical Oncology and Hematology, Rämistrasse 100, 8091 Zurich, Switzerland
| | | | - Rudolf Aebersold
- ETH Zurich, Department of Biology, Institute of Molecular Systems Biology, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Marina Bacac
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Zurich, Wagistrasse 10, 8952 Schlieren, Switzerland
| | - Niko Beerenwinkel
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Christian Beisel
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Bernd Bodenmiller
- University of Zurich, Department of Quantitative Biomedicine, Winterthurerstrasse 190, 8057 Zurich, Switzerland; ETH Zurich, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, 8093 Zurich, Switzerland
| | - Reinhard Dummer
- University Hospital Zurich, Department of Dermatology, University of Zurich, Gloriastrasse 31, 8091 Zurich, Switzerland
| | - Viola Heinzelmann-Schwarz
- University Hospital Basel and University of Basel, Department of Biomedicine, Hebelstrasse 20, 4031 Basel, Switzerland; University Hospital Basel, Gynecological Cancer Center, Spitalstrasse 21, 4031 Basel, Switzerland
| | - Viktor H Koelzer
- University Hospital Zurich, Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | - Markus G Manz
- University Hospital Zurich, Department of Medical Oncology and Hematology, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Holger Moch
- University Hospital Zurich, Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | - Lucas Pelkmans
- University of Zurich, Department of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Berend Snijder
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; ETH Zurich, Department of Biology, Institute of Molecular Systems Biology, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Alexandre P A Theocharides
- University Hospital Zurich, Department of Medical Oncology and Hematology, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Markus Tolnay
- University Hospital Basel, Institute of Medical Genetics and Pathology, Schönbeinstrasse 40, 4031 Basel, Switzerland
| | - Andreas Wicki
- University Hospital Zurich, Department of Medical Oncology and Hematology, Rämistrasse 100, 8091 Zurich, Switzerland; University of Zurich, Faculty of Medicine, Zurich, Switzerland
| | - Bernd Wollscheid
- ETH Zurich, Department of Health Sciences and Technology, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Gunnar Rätsch
- ETH Zurich, Department of Computer Science, Institute of Machine Learning, Universitätstrasse 6, 8092 Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; University Hospital Zurich, Biomedical Informatics, Schmelzbergstrasse 26, 8006 Zurich, Switzerland; ETH Zurich, Department of Biology, Wolfgang-Pauli-Strasse 27, 8093 Zurich, Switzerland.
| | - Mitchell P Levesque
- University Hospital Zurich, Department of Dermatology, University of Zurich, Gloriastrasse 31, 8091 Zurich, Switzerland.
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6
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Stark SG, Ficek J, Locatello F, Bonilla X, Chevrier S, Singer F, Rätsch G, Lehmann KV. SCIM: universal single-cell matching with unpaired feature sets. Bioinformatics 2021; 36:i919-i927. [PMID: 33381818 PMCID: PMC7773480 DOI: 10.1093/bioinformatics/btaa843] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Motivation Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed. Results We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively. Availability and implementation https://github.com/ratschlab/scim. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stefan G Stark
- Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge Bâtiment Amphipôle, 1015 Lausanne, Switzerland.,Life Science Zurich Graduate School, PhD Program Molecular & Translational Biomedicine, 8057 Zürich, Switzerland
| | - Joanna Ficek
- Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge Bâtiment Amphipôle, 1015 Lausanne, Switzerland.,Life Science Zurich Graduate School, PhD Program Molecular & Translational Biomedicine, 8057 Zürich, Switzerland.,Max Planck Institute for Intelligent Systems, Empirical Inference Department, 72076 Tübingen, Germany
| | - Francesco Locatello
- Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland.,Center for Learning Systems, ETH Zürich, 8092 Zürich, Switzerland.,Department of Quantitative Biomedicine, University of Zürich, 8057 Zürich, Switzerland
| | - Ximena Bonilla
- Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge Bâtiment Amphipôle, 1015 Lausanne, Switzerland.,Life Science Zurich Graduate School, PhD Program Molecular & Translational Biomedicine, 8057 Zürich, Switzerland
| | | | - Franziska Singer
- Swiss Institute of Bioinformatics, Quartier Sorge Bâtiment Amphipôle, 1015 Lausanne, Switzerland.,University Hospital Zürich, 8091 Zürich Switzerland
| | | | - Gunnar Rätsch
- Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge Bâtiment Amphipôle, 1015 Lausanne, Switzerland.,Life Science Zurich Graduate School, PhD Program Molecular & Translational Biomedicine, 8057 Zürich, Switzerland.,Department of Quantitative Biomedicine, University of Zürich, 8057 Zürich, Switzerland.,Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Kjong-Van Lehmann
- Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge Bâtiment Amphipôle, 1015 Lausanne, Switzerland.,Life Science Zurich Graduate School, PhD Program Molecular & Translational Biomedicine, 8057 Zürich, Switzerland
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7
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Chevrier S, Zurbuchen Y, Cervia C, Adamo S, Raeber ME, de Souza N, Sivapatham S, Jacobs A, Bachli E, Rudiger A, Stüssi-Helbling M, Huber LC, Schaer DJ, Nilsson J, Boyman O, Bodenmiller B. A distinct innate immune signature marks progression from mild to severe COVID-19. Cell Rep Med 2021; 2:100166. [PMID: 33521697 PMCID: PMC7817872 DOI: 10.1016/j.xcrm.2020.100166] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/11/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022]
Abstract
Coronavirus disease 2019 (COVID-19) manifests with a range of severities, but immune signatures of mild and severe disease are still not fully understood. Here, we use mass cytometry and targeted proteomics to profile the innate immune response of patients with mild or severe COVID-19 and of healthy individuals. Sampling at different stages allows us to reconstruct a pseudo-temporal trajectory of the innate response. A surge of CD169+ monocytes associated with an IFN-γ+MCP-2+ signature rapidly follows symptom onset. At later stages, we observe a persistent inflammatory phenotype in patients with severe disease, dominated by high CCL3 and CCL4 abundance correlating with the re-appearance of CD16+ monocytes, whereas the response of mild COVID-19 patients normalizes. Our data provide insights into the dynamic nature of inflammatory responses in COVID-19 patients and identify sustained innate immune responses as a likely mechanism in severe patients, thus supporting the investigation of targeted interventions in severe COVID-19.
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Affiliation(s)
- Stéphane Chevrier
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Yves Zurbuchen
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Carlo Cervia
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Sarah Adamo
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Miro E. Raeber
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Natalie de Souza
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Institute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Sujana Sivapatham
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Andrea Jacobs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Esther Bachli
- Clinic for Internal Medicine, Uster Hospital, Uster, Switzerland
| | - Alain Rudiger
- Department of Medicine, Limmattal Hospital, Schlieren, Switzerland
| | | | - Lars C. Huber
- Clinic for Internal Medicine, City Hospital Triemli Zurich, Zurich, Switzerland
| | - Dominik J. Schaer
- Department of Internal Medicine, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
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8
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Crowell HL, Chevrier S, Jacobs A, Sivapatham S, Bodenmiller B, Robinson MD. An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. F1000Res 2020; 9:1263. [PMID: 36072920 PMCID: PMC9411975 DOI: 10.12688/f1000research.26073.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/22/2022] [Indexed: 07/20/2023] Open
Abstract
Mass cytometry (CyTOF) has become a method of choice for in-depth characterization of tissue heterogeneity in health and disease, and is currently implemented in multiple clinical trials, where higher quality standards must be met. Currently, preprocessing of raw files is commonly performed in independent standalone tools, which makes it difficult to reproduce. Here, we present an R pipeline based on an updated version of CATALYST that covers all preprocessing steps required for downstream mass cytometry analysis in a fully reproducible way. This new version of CATALYST is based on Bioconductor's SingleCellExperiment class and fully unit tested. The R-based pipeline includes file concatenation, bead-based normalization, single-cell deconvolution, spillover compensation and live cell gating after debris and doublet removal. Importantly, this pipeline also includes different quality checks to assess machine sensitivity and staining performance while allowing also for batch correction. This pipeline is based on open source R packages and can be easily be adapted to different study designs. It therefore has the potential to significantly facilitate the work of CyTOF users while increasing the quality and reproducibility of data generated with this technology.
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Affiliation(s)
- Helena L. Crowell
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, 8057, Switzerland
| | - Stéphane Chevrier
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Andrea Jacobs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Sujana Sivapatham
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | | | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Mark D. Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, 8057, Switzerland
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9
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Richard C, Fumet J, Chevrier S, Derangere V, Boidot R, Truntzer C, Ghiringhelli F. EP1.01-25 An Interactive Interface for Prediction of Anti-PD-1 Efficacy in Lung Cancer Patients. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.2000] [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: 10/25/2022]
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10
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Wagner J, Rapsomaniki MA, Chevrier S, Anzeneder T, Langwieder C, Dykgers A, Rees M, Ramaswamy A, Muenst S, Soysal SD, Jacobs A, Windhager J, Silina K, van den Broek M, Dedes KJ, Rodríguez Martínez M, Weber WP, Bodenmiller B. A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer. Cell 2019; 177:1330-1345.e18. [PMID: 30982598 PMCID: PMC6526772 DOI: 10.1016/j.cell.2019.03.005] [Citation(s) in RCA: 450] [Impact Index Per Article: 90.0] [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: 09/06/2018] [Revised: 01/16/2019] [Accepted: 03/01/2019] [Indexed: 12/12/2022]
Abstract
Breast cancer is a heterogeneous disease. Tumor cells and associated healthy cells form ecosystems that determine disease progression and response to therapy. To characterize features of breast cancer ecosystems and their associations with clinical data, we analyzed 144 human breast tumor and 50 non-tumor tissue samples using mass cytometry. The expression of 73 proteins in 26 million cells was evaluated using tumor and immune cell-centric antibody panels. Tumors displayed individuality in tumor cell composition, including phenotypic abnormalities and phenotype dominance. Relationship analyses between tumor and immune cells revealed characteristics of ecosystems related to immunosuppression and poor prognosis. High frequencies of PD-L1+ tumor-associated macrophages and exhausted T cells were found in high-grade ER+ and ER- tumors. This large-scale, single-cell atlas deepens our understanding of breast tumor ecosystems and suggests that ecosystem-based patient classification will facilitate identification of individuals for precision medicine approaches targeting the tumor and its immunoenvironment.
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Affiliation(s)
- Johanna Wagner
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Sciences Ph.D. Program, Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | - Stéphane Chevrier
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Tobias Anzeneder
- Patients' Tumor Bank of Hope (PATH) Biobank, PO 750729, 81337 Munich, Germany
| | - Claus Langwieder
- Institute of Pathology at Josefshaus, Amalienstrasse 21, 44137 Dortmund, Germany
| | - August Dykgers
- Institute of Pathology at Josefshaus, Amalienstrasse 21, 44137 Dortmund, Germany
| | - Martin Rees
- Institute of Pathology at Josefshaus, Amalienstrasse 21, 44137 Dortmund, Germany
| | - Annette Ramaswamy
- Institute of Pathology, University Hospital Giessen and Marburg, Baldingerstrasse, 35043 Marburg, Germany
| | - Simone Muenst
- Institute of Pathology, University Hospital Basel and University of Basel, Schoenbeinstrasse 40, 4031 Basel, Switzerland
| | - Savas Deniz Soysal
- Clarunis, University Hospital Basel and University of Basel, Spitalstrasse 21, 4031 Basel, Switzerland; Breast Cancer Center, University Hospital Basel and University of Basel, Spitalstrasse 21, 4031 Basel, Switzerland
| | - Andrea Jacobs
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jonas Windhager
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Systems Biology Ph.D. Program, Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Karina Silina
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Maries van den Broek
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | | | - Walter Paul Weber
- Breast Cancer Center, University Hospital Basel and University of Basel, Spitalstrasse 21, 4031 Basel, Switzerland; Department of Surgery, University Hospital Basel and University of Basel, Spitalstrasse 21, 4031 Basel, Switzerland
| | - Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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11
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Gangneux JP, Comacle P, Chevrier S, Ruaux C, Jegou F, Robert-Gangneux F. Apport de la PCR et du séquençage au diagnostic de sinusite fongique : à propos de 42 cas diagnostiques au laboratoire de parasitologie-mycologie du CHU de Rennes. J Mycol Med 2014. [DOI: 10.1016/j.mycmed.2014.06.038] [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: 10/24/2022]
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12
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Chevrier S, Emslie D, Shi W, Kratina T, Wellard C, Karnowski A, Erikci E, Smyth GK, Chowdhury K, Tarlinton D, Corcoran LM. The BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity. ACTA ACUST UNITED AC 2014; 211:827-40. [PMID: 24711583 PMCID: PMC4010913 DOI: 10.1084/jem.20131831] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [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] [Indexed: 12/20/2022]
Abstract
Zbtb20 facilitates terminal differentiation of B cells into antibody-secreting cells, and its expression is dependent on Irf4 and independent of Blimp1. The transcriptional network regulating antibody-secreting cell (ASC) differentiation has been extensively studied, but our current understanding is limited. The mechanisms of action of known “master” regulators are still unclear, while the participation of new factors is being revealed. Here, we identify Zbtb20, a Bcl6 homologue, as a novel regulator of late B cell development. Within the B cell lineage, Zbtb20 is specifically expressed in B1 and germinal center B cells and peaks in long-lived bone marrow (BM) ASCs. Unlike Bcl6, an inhibitor of ASC differentiation, ectopic Zbtb20 expression in primary B cells facilitates terminal B cell differentiation to ASCs. In plasma cell lines, Zbtb20 induces cell survival and blocks cell cycle progression. Immunized Zbtb20-deficient mice exhibit curtailed humoral responses and accelerated loss of antigen-specific plasma cells, specifically from the BM pool. Strikingly, Zbtb20 induction does not require Blimp1 but depends directly on Irf4, acting at a newly identified Zbtb20 promoter in ASCs. These results identify Zbtb20 as an important player in late B cell differentiation and provide new insights into this complex process.
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Affiliation(s)
- Stéphane Chevrier
- Molecular Immunology Division, 2 Bioinformatics Division, 3 Immunology Division, The Walter and Eliza Hall Institute, Parkville, Victoria 3052, Australia
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13
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Chopin M, Seillet C, Chevrier S, Wu L, Wang H, Morse HC, Belz GT, Nutt SL. Langerhans cells are generated by two distinct PU.1-dependent transcriptional networks. ACTA ACUST UNITED AC 2013; 210:2967-80. [PMID: 24249112 PMCID: PMC3865480 DOI: 10.1084/jem.20130930] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Langerhans cell homeostasis and differentiation depends on PU.1, the latter via regulation of TGF-β–dependent binding of PU.1 to the regulatory elements of RUNX3. Langerhans cells (LCs) are the unique dendritic cells found in the epidermis. While a great deal of attention has focused on defining the developmental origins of LCs, reports addressing the transcriptional network ruling their differentiation remain sparse. We addressed the function of a group of key DC transcription factors—PU.1, ID2, IRF4, and IRF8—in the establishment of the LC network. We show that although steady-state LC homeostasis depends on PU.1 and ID2, the latter is dispensable for bone marrow–derived LCs. PU.1 controls LC differentiation by regulating the expression of the critical TGF-β responsive transcription factor RUNX3. PU.1 directly binds to the Runx3 regulatory elements in a TGF-β–dependent manner, whereas ectopic expression of RUNX3 rescued LC differentiation in the absence of PU.1 and promoted LC differentiation from PU.1-sufficient progenitors. These findings highlight the dual molecular network underlying LC differentiation, and show the central role of PU.1 in these processes.
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Affiliation(s)
- Michaël Chopin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
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14
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Fillatre P, Chevrier S, Revest M, Gacouin A, Jouneau S, Leroy H, Robert-Gangneux F, Minjolle S, Le Tulzo Y, Tattevin P. Human herpes virus co-infection is associated with mortality in HIV-negative patients with Pneumocystis jirovecii pneumonia. Eur J Clin Microbiol Infect Dis 2012; 32:189-94. [PMID: 22930407 PMCID: PMC7102362 DOI: 10.1007/s10096-012-1730-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 08/09/2012] [Indexed: 01/13/2023]
Abstract
The purpose of this investigation was to characterize the management and prognosis of severe Pneumocystis jirovecii pneumonia (PJP) in human immunodeficiency virus (HIV)-negative patients. An observational cohort study of HIV-negative adults with PJP documented by bronchoalveolar lavage (BAL) through Gomori-Grocott staining or immunofluorescence, admitted to one intensive care unit (ICU) for acute respiratory failure, was undertaken. From 1990 to 2010, 70 patients (24 females, 46 males) were included, with a mean age of 58.6 ± 18.3 years. The mean Simplified Acute Physiology Score (SAPS)-II was 36.9 ± 20.4. Underlying conditions included hematologic malignancies (n = 21), vasculitis (n = 13), and solid tumors (n = 13). Most patients were receiving systemic corticosteroids (n = 63) and cytotoxic drugs (n = 51). Not a single patient received trimethoprim-sulfamethoxazole as PJP prophylaxis. Endotracheal intubation (ETI) was required in 42 patients (60.0 %), including 38 with acute respiratory distress syndrome (ARDS). In-ICU mortality was 52.9 % overall, reaching 80.9 % and 86.8 %, respectively, for patients who required ETI and for patients with ARDS. In the univariate analysis, in-ICU mortality was associated with SAPS-II (p = 0.0131), ARDS (p < 0.0001), shock (p < 0.0001), and herpes simplex virus (HSV) or cytomegalovirus (CMV) on BAL (p = 0.0031). In the multivariate analysis, only ARDS was associated with in-ICU mortality (odds ratio [OR] 23.4 [4.5-121.9], p < 0.0001). PJP in non-HIV patients remains a serious disease with high in-hospital mortality. Pulmonary co-infection with HSV or CMV may contribute to fatal outcome.
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Affiliation(s)
- P. Fillatre
- Service des Maladies Infectieuses et de Réanimation Médicale, CHU Pontchaillou, 2 rue Henri Le Guilloux, 35033 Rennes Cedex, France
| | - S. Chevrier
- Parasitologie-Mycologie, Faculté de Médecine, Université de Rennes 1, IFR140, 35033 Rennes, France
| | - M. Revest
- Service des Maladies Infectieuses et de Réanimation Médicale, CHU Pontchaillou, 2 rue Henri Le Guilloux, 35033 Rennes Cedex, France
- CIC INSERM 0203, Faculté de Médecine, Université de Rennes 1, IFR140, 35033 Rennes, France
| | - A. Gacouin
- Service des Maladies Infectieuses et de Réanimation Médicale, CHU Pontchaillou, 2 rue Henri Le Guilloux, 35033 Rennes Cedex, France
- CIC INSERM 0203, Faculté de Médecine, Université de Rennes 1, IFR140, 35033 Rennes, France
| | - S. Jouneau
- Pneumologie, Hôpital Pontchaillou, 35033 Rennes, France
- IRSET, UMR, INSERM 1085, Université de Rennes 1, IFR140, 35033 Rennes, France
| | - H. Leroy
- Service des Maladies Infectieuses et de Réanimation Médicale, CHU Pontchaillou, 2 rue Henri Le Guilloux, 35033 Rennes Cedex, France
- CIC INSERM 0203, Faculté de Médecine, Université de Rennes 1, IFR140, 35033 Rennes, France
| | - F. Robert-Gangneux
- Parasitologie-Mycologie, Faculté de Médecine, Université de Rennes 1, IFR140, 35033 Rennes, France
- IRSET, UMR, INSERM 1085, Université de Rennes 1, IFR140, 35033 Rennes, France
| | - S. Minjolle
- Virologie, Faculté de Médecine, Université de Rennes 1, IFR140, 35033 Rennes, France
| | - Y. Le Tulzo
- Service des Maladies Infectieuses et de Réanimation Médicale, CHU Pontchaillou, 2 rue Henri Le Guilloux, 35033 Rennes Cedex, France
- CIC INSERM 0203, Faculté de Médecine, Université de Rennes 1, IFR140, 35033 Rennes, France
| | - P. Tattevin
- Service des Maladies Infectieuses et de Réanimation Médicale, CHU Pontchaillou, 2 rue Henri Le Guilloux, 35033 Rennes Cedex, France
- CIC INSERM 0203, Faculté de Médecine, Université de Rennes 1, IFR140, 35033 Rennes, France
- INSERM U835, Faculté de Médecine, Université de Rennes 1, IFR140, 35033 Rennes, France
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15
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Chevrier S, Genton C, Malissen B, Malissen M, Acha-Orbea H. Dominant Role of CD80-CD86 Over CD40 and ICOSL in the Massive Polyclonal B Cell Activation Mediated by LAT(Y136F) CD4(+) T Cells. Front Immunol 2012; 3:27. [PMID: 22566911 PMCID: PMC3342035 DOI: 10.3389/fimmu.2012.00027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 10/27/2011] [Accepted: 02/09/2012] [Indexed: 12/26/2022] Open
Abstract
Coordinated interactions between T and B cells are crucial for inducing physiological B cell responses. Mutant mice in which tyrosine 136 of linker for activation of T cell (LAT) is replaced by a phenylalanine (LatY136F) exhibit a strong CD4+ T cell proliferation in the absence of intended immunization. The resulting effector T cells produce high amounts of TH2 cytokines and are extremely efficient at inducing polyclonal B cell activation. As a consequence, these LatY136F mutant mice showed massive germinal center formations and hypergammaglobulinemia. Here, we analyzed the involvement of different costimulators and their ligands in such T–B interactions both in vitro and in vivo, using blocking antibodies, knockout mice, and adoptive transfer experiments. Surprisingly, we showed in vitro that although B cell activation required contact with T cells, CD40, and inducible T cell costimulator molecule-ligand (ICOSL) signaling were not necessary for this process. These observations were further confirmed in vivo, where none of these molecules were required for the unfolding of the LAT CD4+ T cell expansion and the subsequent polyclonal B cell activation, although, the absence of CD40 led to a reduction of the follicular B cell response. These results indicate that the crucial functions played by CD40 and ICOSL in germinal center formation and isotype switching in physiological humoral responses are partly overcome in LatY136F mice. By comparison, the absence of CD80–CD86 was found to almost completely block the in vitro B cell activation mediated by LatY136F CD4+ T cells. The role of CD80–CD86 in T–B cooperation in vivo remained elusive due to the upstream implication of these costimulatory molecules in the expansion of LatY136F CD4+ T cells. Together, our data suggest that CD80 and CD86 costimulators play a key role in the polyclonal B cell activation mediated by LatY136F CD4+ T cells even though additional costimulatory molecules or cytokines are likely to be required in this process.
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Affiliation(s)
- Stéphane Chevrier
- Department of Biochemistry, University of Lausanne Lausanne, Switzerland
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16
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Boidot R, Végran F, Jacob D, Chevrier S, Cadouot M, Feron O, Solary E, Lizard-Nacol S. The transcription factor GATA-1 is overexpressed in breast carcinomas and contributes to survivin upregulation via a promoter polymorphism. Oncogene 2010; 29:2577-84. [DOI: 10.1038/onc.2009.525] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [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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17
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Salvador Alonso R, Lahbabi I, Ben Hassel M, Boisselier P, Chaari N, Lesimple T, Chevrier S, de Crevoisier R. Carcinome à cellules de Merkel : prise en charge et place de la radiothérapie. Cancer Radiother 2008; 12:352-9. [DOI: 10.1016/j.canrad.2008.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2008] [Revised: 04/07/2008] [Accepted: 04/16/2008] [Indexed: 11/29/2022]
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18
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Salvador Alonso R, Lahbabi I, Ben Hassel M, Boisselier P, Chaari N, Lesimple T, Chevrier S, de Crevoisier R. Recurrences of Non Metastatic Merkel Cell Carcinoma after Surgery and Radiotherapy Occur More Frequently Outside the Irradiated Fields. Int J Radiat Oncol Biol Phys 2008. [DOI: 10.1016/j.ijrobp.2008.06.1480] [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: 10/21/2022]
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Patrat-Delon S, Drogoul AS, Le Ho H, Biziraguzenyuka J, Rabier V, Arvieux C, Michelet C, Chevrier S, Tattevin P. [Recurrent tick-borne fever: a possible diagnosis in patients returning from Senegal]. Med Mal Infect 2008; 38:396-9. [PMID: 18602236 DOI: 10.1016/j.medmal.2008.03.005] [Citation(s) in RCA: 5] [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] [Received: 11/30/2007] [Revised: 12/20/2007] [Accepted: 03/03/2008] [Indexed: 11/16/2022]
Abstract
In Senegal, tick-borne relapsing fever caused by the spirochetes Borrelia crucidurae is the most common cause of fever after malaria in rural areas. However, this is only rarely diagnosed in France, probably because: i) the diagnosis relies on investigations that are not routinely done; ii) even undiagnosed, borreliosis may be cured with empirical antibiotic treatment. We report four observations of tick-borne relapsing fever in patients returning from Senegal: In two patients, the diagnosis relied on the observation of spirochetes in blood smears; in the other two, the diagnosis relied on typical clinico-biological signs, borreliosis serology and exposure. These four cases diagnosed over a four year period in one institution suggest that relapsing fever is not rare in patients returning from West Africa. Patients who return form Senegal with unexplained fever should be investigated with careful examination of blood smears and PCR on blood samples.
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Affiliation(s)
- S Patrat-Delon
- Service de maladies infectieuses et réanimation médicale, CHU Pontchaillou, 2, rue Henri-Le-Guilloux, 35033 Rennes cedex, France
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20
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Roussey M, Chevrier S, Giroux F, Desrues B, Belleguic C, Deneuville E, Guiguen C, Gangneux J. Clinical value of Aspergillus detection in sputum obtained from 84 patients with cystic fibrosis. J Cyst Fibros 2008. [DOI: 10.1016/s1569-1993(08)60187-3] [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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21
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Wang Y, Kissenpfennig A, Mingueneau M, Richelme S, Perrin P, Chevrier S, Genton C, Lucas B, DiSanto JP, Acha-Orbea H, Malissen B, Malissen M. Th2 lymphoproliferative disorder of LatY136F mutant mice unfolds independently of TCR-MHC engagement and is insensitive to the action of Foxp3+ regulatory T cells. J Immunol 2008; 180:1565-75. [PMID: 18209052 DOI: 10.4049/jimmunol.180.3.1565] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mutant mice where tyrosine 136 of linker for activation of T cells (LAT) was replaced with a phenylalanine (Lat(Y136F) mice) develop a fast-onset lymphoproliferative disorder involving polyclonal CD4 T cells that produce massive amounts of Th2 cytokines and trigger severe inflammation and autoantibodies. We analyzed whether the Lat(Y136F) pathology constitutes a bona fide autoimmune disorder dependent on TCR specificity. Using adoptive transfer experiments, we demonstrated that the expansion and uncontrolled Th2-effector function of Lat(Y136F) CD4 cells are not triggered by an MHC class II-driven, autoreactive process. Using Foxp3EGFP reporter mice, we further showed that nonfunctional Foxp3(+) regulatory T cells are present in Lat(Y136F) mice and that pathogenic Lat(Y136F) CD4 T cells were capable of escaping the control of infused wild-type Foxp3(+) regulatory T cells. These results argue against a scenario where the Lat(Y136F) pathology is primarily due to a lack of functional Foxp3(+) regulatory T cells and suggest that a defect intrinsic to Lat(Y136F) CD4 T cells leads to a state of TCR-independent hyperactivity. This abnormal status confers Lat(Y136F) CD4 T cells with the ability to trigger the production of Abs and of autoantibodies in a TCR-independent, quasi-mitogenic fashion. Therefore, despite the presence of autoantibodies causative of severe systemic disease, the pathological conditions observed in Lat(Y136F) mice unfold in an Ag-independent manner and thus do not qualify as a genuine autoimmune disorder.
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Affiliation(s)
- Ying Wang
- Centre d'Immunologie de Marseille-Luminy, INSERM/CNRS, Université de la Méditerranée, Parc Scientifique et Technologique de Luminy, Marseille Cedex 09, France
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Guyomard JL, Chevrier S, Bertholom JL, Guigen C, Charlin JF. [Finding of Strongyloides stercoralis infection, 25 years after leaving the endemic area, upon corticotherapy for ocular trauma]. J Fr Ophtalmol 2007; 30:e4. [PMID: 17318103 DOI: 10.1016/s0181-5512(07)89571-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In the field of ophthalmology, indications for high-dose corticotherapy are various. This paper reports the case of a Caledonian man who presented with intestinal strongyloidiasis, discovered 25 years after he had left the endemic area. A checkup before corticotherapy for traumatic retina edema provided the diagnosis of the infection. The authors emphasize the importance of searching for Strongyloidiasis stercoralis larva before initiating corticotherapy, as it is the main treatment responsible for parasitic dissemination. The most severe form of strongyloidiasis, the disseminated form, has a high mortality rate: 70%-90%. The definitive diagnostic test is enhanced larva recovery, which should be proposed to every patient returning from endemic area, people with precarious hygiene or with high eosinophilia or intestinal symptoms of chronic infection. Delay in diagnosing strongyloidiasis frequently results in death, despite vigorous treatment.
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Affiliation(s)
- J-L Guyomard
- Service d'Ophtalmologie, CHU de Pontchaillou, Rennes.
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23
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Adamski H, Pessel S, Ferraro V, Arvieux C, Chevrier S, Le Gall F, Gangneux JP, Chevrant-Breton J. [Chronic ulceration of the ear caused by Cryptococcus neoformans]. Ann Dermatol Venereol 2007; 134:273-5. [PMID: 17389857 DOI: 10.1016/s0151-9638(07)91513-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Cornillet A, Camus C, Nimubona S, Gandemer V, Tattevin P, Belleguic C, Chevrier S, Meunier C, Lebert C, Aupée M, Caulet-Maugendre S, Faucheux M, Lelong B, Leray E, Guiguen C, Gangneux JP. Comparison of epidemiological, clinical, and biological features of invasive aspergillosis in neutropenic and nonneutropenic patients: a 6-year survey. Clin Infect Dis 2006; 43:577-84. [PMID: 16886149 DOI: 10.1086/505870] [Citation(s) in RCA: 234] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Accepted: 05/10/2006] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Invasive aspergillosis is an opportunistic infection that occurs mainly among patients with prolonged neutropenia. Few data are available on invasive aspergillosis in nonneutropenic patients. METHODS The aim of this survey was to compare neutropenic and nonneutropenic patients who had received a diagnosis of invasive aspergillosis at our institution during a 6-year period. RESULTS Among the 88 cases of invasive aspergillosis analyzed here, 12 were histologically proven, 52 were probable, and 24 were possible. Forty-seven percent of cases were diagnosed in the intensive care unit, and 40% were diagnosed in hematology units. Neutropenia was a risk factor for 52 patients (59%), most of whom had hematological or solid malignancies. Among the 36 nonneutropenic patients (41%), the main underlying conditions were steroid-treated chronic obstructive pulmonary disease, asthma, rheumatoid arthritis, giant-cell arteritis, and microvascular disorders; 10 patients were recipients of solid-organ transplants, and 1 patient was seropositive for human immunodeficiency virus. The distribution of proven and probable invasive aspergillosis was similar for neutropenic and nonneutropenic patients. The mortality rate was 71.5% overall and was significantly higher among nonneutropenic patients than among neutropenic patients (89% vs. 60%; P<.05). Compared with neutropenic patients, nonneutropenic patients were significantly less likely to have symptoms of invasive aspergillosis and more likely to have frequent intercurrent pneumonia due to another microorganism. The sensitivity of mycological examination of bronchoalveolar lavage fluid specimens was higher for nonneutropenic patients than for neutropenic patients (85% vs. 58%; P<.05), whereas the sensitivity of antigenemia was the same for the 2 populations (65% vs. 64%). Findings on thoracic computed tomographs were similar, except that segmental areas of consolidation occurred more frequently among neutropenic patients. CONCLUSION This survey at a whole institution underlines the high number of cases of invasive aspergillosis among nonneutropenic patients, with an overall mortality rate that was significantly higher than that for neutropenic patients.
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Affiliation(s)
- A Cornillet
- Laboratoire de Parasitologie-Mycologie,Hôpital Pontchaillou, Rennes, France
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Revest M, Decaux O, Frouget T, Cazalets C, Albert JD, Chevrier S, Guiguen C, Jego P, Grosbois B. Infections à cryptocoque chez des patients non VIH. À propos de quatre cas et revue de la littérature. Rev Med Interne 2006; 27:203-8. [PMID: 16364503 DOI: 10.1016/j.revmed.2005.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 11/24/2005] [Indexed: 10/25/2022]
Abstract
BACKGROUND Cryptococcal infections are frequent in HIV-infected patients and are regularly looked after. This infection may occur in others immunosuppressives situations and, in those cases, diagnosis is often delayed. METHODS We report four cases of cryptococcal infections in patients whose immunosuppression isn't related with HIV infection but due to chronic lymphocytic leukemia, giant cell temporal arteritis, gastric neoplasm and lupus. Diagnosis, prognostic and treatment are detailed. RESULTS Four patients aged from 25 to 76 presented a cryptococcal infection (three meningitis). A woman died at the admission. Another died seven years later. The two others are still alive under treatment. When infected, all patients were immunodeficiency. CONCLUSION Cryptococcal infection may occur in patients non-HIV-infected patients. Early detection is needed to improve prognostic.
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Affiliation(s)
- M Revest
- Service de Médecine Interne, Département de Médecine de l'Adulte, Hôpital Sud, 16, boulevard de Bulgarie, 35203 Rennes cedex, France
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Abstract
BACKGROUND Primary cutaneous cribriform carcinoma (PCCC) is a rare apocrine tumour occurring in middle-aged people. This neoplasm is often located on the limbs. The histopathological diagnosis is difficult, mainly because this tumour is exceptional. We, in this study, report a patient with PCCC. CASE REPORT The patient was a 37-year-old man who presented with a nodule of the left knee. RESULTS Histopathologic findings showed an asymmetrical deep dermal tumour with a cribriform pattern. The aggregations of neoplastic cells were interconnected and varied in size and shape. The cells were arranged in solid nests or tubular structures. In the lumina of tubules, some papillary protrusion of basophilic cells was seen. The ductal elements were lined by cuboidal or cylindric cells with images of decapitation secretion. The nuclei of the neoplastic cells were pleomorphic. A wide excision was performed with sentinel inguinal node biopsy. After a 2-year follow-up, neither persistence at the local site nor metastasis was observed. CONCLUSIONS Clinical and pathological features of PCCC are reviewed. Differential diagnoses, including cutaneous metastasis of adenocarcinoma, adenoid basal cell carcinoma and adenoid cystic carcinoma, are discussed.
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Affiliation(s)
- Henri Adamski
- Department of Dermatology, University of Rennes, Rennes, France.
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Droitcourt C, Adamski H, Arvieux C, Chevrier S, Le Gall F, Michelet C, Chevrant-Breton J. Cryptococcoses cutanées primitives chez des patients transplantes : à propos de deux observations. Rev Med Interne 2005; 26:157-9. [PMID: 15710267 DOI: 10.1016/j.revmed.2004.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2004] [Accepted: 10/05/2004] [Indexed: 11/24/2022]
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Ben Jemaa H, Chevrier S, Georgieu N, Pailheret JP, Watier E. [Post-inflammatory cutis laxa. A case report]. ANN CHIR PLAST ESTH 2002; 47:647-50. [PMID: 12577797 DOI: 10.1016/s0294-1260(02)00158-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cutis laxa (CL) is a rare disorder in which the skin hangs in loose fields, so that affected individuals appear to be prematurely aged. The changes are more evident when effect the face with a prematurely-aged appearance. The acute form follows an inflammatory skin lesions. Its aetiology is not well known. We report a case of a head acute CL of a 17 years patient, secondary to a generalized skin eruption. The prematurely-aged appearance concern especially forehead, ear lobes and nasolabial folds. A two stages surgical treatment has associated: a forehead lifting associated to a Coleman lipofilling and an ear lobe reduction, a secondary Coleman lipofilling of the nasolabial folds. The skin biopsy confirm the diagnosis. The correction is stable and satisfactory after one year. The confrontation of our findings to those previously described confirm complexity of diagnosis and histological observations of this rare disorder.
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Affiliation(s)
- H Ben Jemaa
- Service de chirurgie plastique, reconstructrice et esthétique, hôpital Sud, 16, boulevard de Bulgarie, BP 90347, 35203 Rennes, France
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Tattevin P, Chevrier S, Arvieux C, Souala F, Chapplain J, Bouget J, Guiguen C, Michelet C. Augmentation du paludisme d’importation à Rennes : étude épidémiologique et analyse de la chimioprophylaxie et des traitements curatifs. Med Mal Infect 2002. [DOI: 10.1016/s0399-077x(02)00394-3] [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: 10/27/2022]
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Abstract
UNLABELLED Reduction mammaplasty (RM) can be performed during adolescence if the functional capacity of the breast is preserved. Future breast feeding must be carefully considered in the therapeutic decision making process. PURPOSE OF THE STUDY Breast feeding after reduction mammaplasty performed during adolescence was assessed to determine surgical factors influencing outcome and patient reception of information concerning breast feeding. METHODS A questionnaire was sent to 109 women who had undergone reduction mammaplasty between 1981 and 1997 when they were 15-17 years old to ascertain their reasons for having surgery, their satisfaction, and their attitude towards breast feeding. RESULTS Sixty-five questionnaires (60%) could be analyzed. Mean delay since surgery was 8.1 years. Seventeen women (26%) had delivered 25 infants (mean 1.5). Mean delay after surgery to first delivery was 7.68 years. Five women (29%) nursed their first infant for a mean 11.3 days. None of the women interrupted breast feeding for a reason related to a nipple anomaly or difficult sucking. Twelve women (71%) did not nurse their first infant, because of the prior breast surgery for six of them. Among the 48 nulliparous women, 24 (50%) stated they would nurse their future infant. Although information on breast feeding was systematically delivered, 41 women (63%) stated they had not been informed. There was no statistical relationship between breast feeding and degree of satisfaction, patient-assessed scar quality, or nipple disorders. CONCLUSION Adolescents who undergo reduction mammaplasty can nurse their future infants with a complication rate similar to that in the general population. Special attention must be given to delivery of information on breast feeding.
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Affiliation(s)
- S Aillet
- Service de Chirurgie Plastique, Reconstructrice et Esthétique, Hôpital Sud, Université de Rennes, 35056 Rennes Cedex, France
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Abstract
UNLABELLED Reduction mammaplasty has now become routine surgery with good results in middle-aged women. However the scars it leaves, its psychological and functional (breastfeeding) impact could limited its indications in teenage girls. AIM The purpose of our study was to report the long-term results of reduction mammaplasty in teenage girls and to assess their consequences. MATERIAL AND METHODS We conducted a retrospective study of 65 reduction mammaplasty carried out between 1981 and 1997 in 15 to 17 years old girls. The study was based on data in their medical records and answers to a questionnaire which was sent to each patient. RESULTS Average followup was 8.1 years. The reduction technique with superior pedicle were mainly used. Average breast tissue excised was 1050 g. Minor complications occurred in three cases. Eleven revisions had to be carried out with 1.6 years on average after primary surgery. The psychological and functional complaints observed preoperatively disappeared in more than 90% of the cases. In over 80% of the cases the patients were pleased or very pleased with the shape, the volume kept and the symmetry. Scars were well accepted in 83% of the cases. Seventeen women were given birth to 25 children. Five of whom breast-fed their babies, while six refused because of their breast surgery history. Although information about breast-feeding after such surgery is systematically given, 41 women claimed they had not received it. CONCLUSION Reduction mammaplasty is reliable in teenage girls. Patients are generally satisfied and the remaining scar is well accepted. Breast-feeding is possible after this surgery and information on that point ought to be better developed.
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Affiliation(s)
- S Aillet
- Service de chirurgie plastique, reconstructrice et esthétique, CHU Rennes, hôpital sud, boulevard de Bulgarie, BP 90347, 35203 Rennes, France
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Watier E, Georgieu N, Chevrier S, Burtin F, Pailheret JP. Squamous cell carcinoma on both palms. European Journal of Plastic Surgery 2000. [DOI: 10.1007/s002380000182] [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: 10/27/2022]
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Watier E, Chevrier S, Georgieu N, Pardo A, Schück S, Pailheret JP. Our experience with ischial pressure sores in a series of 34 patients. European Journal of Plastic Surgery 2000. [DOI: 10.1007/s002380050008] [Citation(s) in RCA: 4] [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: 10/27/2022]
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Pardo A, Watier E, Georgieu N, Chevrier S, Pailheret JP. [Tuberous breast syndrome. Report on a series of 22 operated patients]. ANN CHIR PLAST ESTH 1999; 44:583-92. [PMID: 10675958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The tuberous breast syndrome is a rare unilateral or bilateral breast malformation presenting at the age of mammary development. It requires surgical correction, depending on the severity of the clinical expression, because of its inaesthetic appearance. We report a series of 22 patients (35 breasts) treated and followed up in the plastic and reconstructive surgery department of Rennes over a period of nearly ten years. The average age was 18 +/- 3.2 years (range: 15-26 years old). Long-term results were assessed by the surgical team and the patients on the basis of objective and subjective criteria with an average follow-up of 36 months (12 to 116 months). In our opinion, surgical correction should be proposed after puberty with, whenever possible, section of the basal fibrous ring and glandular plasty via a periareolar incision. The use of mammary implant alone or in combination with breast tissue remodelling must be reserved for hypoplastic cases only.
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Affiliation(s)
- A Pardo
- Service de Chirurgie Plastique Reconstructrice et Esthétique, Hôpital Sud, Rennes, France
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35
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Seguin P, Musellec H, Le Gall F, Chevrier S, Le Bouquin V, Malledant Y. Post-traumatic course complicated by cutaneous infection with Absidia corymbifera. Eur J Clin Microbiol Infect Dis 1999; 18:737-9. [PMID: 10584903 DOI: 10.1007/s100960050389] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cutaneous mucormycosis is a rare but serious infection in trauma patients. Reported here is the case of a young patient with cutaneous mucormycosis due to Absidia corymbifera probably caused by a soil-contaminated wound. Despite daily surgical debridement and amphotericin B therapy, cure could be achieved only by amputation of the lower limb.
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Affiliation(s)
- P Seguin
- Service de Réanimation Chirurgicale, CHR-U Pontchaillou, Rennes, France. yMalledant.rennes@in vivo.edu
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Camin AM, Michelet C, Langanay T, de Place C, Chevrier S, Guého E, Guiguen C. Endocarditis due to Fusarium dimerum four years after coronary artery bypass grafting. Clin Infect Dis 1999; 28:150. [PMID: 10028093 DOI: 10.1086/517184] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- A M Camin
- Department of Parasitology, Pontchaillou Hospital, Rennes, Ille-et-Vilaine, France.
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Lamy T, Bernard M, Courtois A, Jacquelinet C, Chevrier S, Dauriac C, Grulois I, Guiguen C, Le Prise PY. Prophylactic use of itraconazole for the prevention of invasive pulmonary aspergillosis in high risk neutropenic patients. Leuk Lymphoma 1998; 30:163-74. [PMID: 9669686 DOI: 10.3109/10428199809050939] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Invasive pulmonary aspergillosis (IPA) is an increasing cause of morbidity and mortality in patients with hematologic malignancies. A major program of construction work close to our unit prompted us to evaluate the efficacy of itraconazole prophylaxis in preventing IPA in these patients. During September 1994 to December 1995, 77 patients undergoing 96 neutropenic episodes (mean duration, 19.3 days +/- 9.1) received itraconazole as antifungal prophylaxis. All patients were treated in laminar air flow rooms. Itraconazole was administered at a loading dose of 600mg/d, (day 1 to day 3) and 400mg/d on the following days, in 87 instances. In the remaining episodes, the daily dose was 200 or 400mg. Oral doses were adjusted to reach a plasma itraconazole level (PIL) above 1000ng/l. In cases of inadequate PIL or poor oral intake, IV AmphoB was started at a 20 mg daily dose. Five cases of IPA (proven n = 2, probable n = 3) were observed. This represents an incidence of 5.2% of the total number of episodes. One out of 67 (2%) treatment episodes with adequate PIL were associated with IPA as compared to 4 of 29 (14%) episodes with inadequate PIL, (p < 0.02). AmphoB was added in 28 cases because of low PIL (n = 25), and/or antibiotic-resistant fever persistent pulmonary infiltrate (n = 8). These results need to be interpreted with caution, because of the absence of randomization or a control group. The efficacy of Itraconazole in neutropenic patients with high risk IPA has to be confirmed on larger and prospective studies.
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Affiliation(s)
- T Lamy
- Service d'Hématologie clinique, Hopital Pontchaillou, Rennes, France
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38
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Chevrier S, Beaucournu-Saguez F, Ungeheuer M, Beaucournu J. Clinical aspects of simuliidosis in the area of Vaucluse, France. Toxicon 1996. [DOI: 10.1016/0041-0101(96)83707-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: 10/17/2022]
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Betremieux P, Chevrier S, Quindos G, Sullivan D, Polonelli L, Guiguen C. Use of DNA fingerprinting and biotyping methods to study a Candida albicans outbreak in a neonatal intensive care unit. Pediatr Infect Dis J 1994; 13:899-905. [PMID: 7854891 DOI: 10.1097/00006454-199410000-00011] [Citation(s) in RCA: 37] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
During a 15-day period, 7 premature infants hospitalized in a neonatal intensive care unit presented with sepsis caused by Candida albicans. The local environment and hands of all 54 persons involved in the intensive care unit were examined for the presence of this organism. Five techniques were used in the analysis of the isolates recovered from blood cultures of the children, the hands of personnel and 10 control isolates. The methods used were serotype determination, genetic fingerprinting, morphotyping, resistotyping and killer yeast typing. Morphotyping and genetic fingerprinting proved to be the most discriminatory techniques, and only combined analysis of the results obtained with these various methods allowed the source of the outbreak to be identified. An isolate from the hands of a healthy staff member and isolates from infected children all belonged to the same strain.
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Beaucournu-Saguez F, Gilot B, Chevrier S, Branquet F, Hautefort B, Beaucournu JC. [Observation in France of Simulium erythrocephalum De Geer, 1776 as an agent of human simuliidosis]. Ann Parasitol Hum Comp 1993; 68:109-10. [PMID: 8215110 DOI: 10.1051/parasite/1993682109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Second observation of this black-fly in human simuliidosis. The country is the department of Vaucluse.
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Abstract
The problem of the human Simuliidosis (caused by black flies) is reviewed for the France: important and, perhaps, relatively recent increase from the known human attacks by black flies. Countries and anthropophilic species are cited.
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Affiliation(s)
- J C Beaucournu
- Laboratoire de Parasitologie médicale, Faculté de Médecine, Rennes
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43
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Couatarmanac'h A, Le Foll F, Perrier D, Chevrier S, Pinel J, Doby J. Maladie de lyme. Etude de 42 Cas observes dans l'Ouest de la France. Med Mal Infect 1989. [DOI: 10.1016/s0399-077x(89)80282-3] [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: 10/25/2022]
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