1
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Doeleman SE, Reijnders TDY, Joosten SCM, Schuurman AR, van Engelen TSR, Verhoeff J, Léopold V, Brands X, Haak BW, Prins JM, Kanglie MMNP, van den Berk IAH, Faber DR, Douma RA, Stoker J, Saris A, Garcia Vallejo JJ, Wiersinga WJ, van der Poll T. Lymphopenia is associated with broad host response aberrations in community-acquired pneumonia. J Infect 2024; 88:106131. [PMID: 38431153 DOI: 10.1016/j.jinf.2024.106131] [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: 12/16/2023] [Revised: 02/16/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024]
Abstract
OBJECTIVES Lymphopenia at hospital admission occurs in over one-third of patients with community-acquired pneumonia (CAP), yet its clinical relevance and pathophysiological implications remain underexplored. We evaluated outcomes and immune features of patients with lymphopenic CAP (L-CAP), a previously described immunophenotype characterized by admission lymphocyte count <0.724 × 109 cells/L. METHODS Observational study in 149 patients admitted to a general ward for CAP. We measured 34 plasma biomarkers reflective of inflammation, endothelial cell responses, coagulation, and immune checkpoints. We characterized lymphocyte phenotypes in 29 patients using spectral flow cytometry. RESULTS L-CAP occurred in 45 patients (30.2%) and was associated with prolonged time-to-clinical-stability (median 5 versus 3 days), also when we accounted for competing events for reaching clinical stability and adjusted for baseline covariates (subdistribution hazard ratio 0.63; 95% confidence interval 0.45-0.88). L-CAP patients demonstrated a proportional depletion of CD4 T follicular helper cells, CD4 T effector memory cells, naïve CD8 T cells and IgG+ B cells. Plasma biomarker analyses indicated increased activation of the cytokine network and the vascular endothelium in L-CAP. CONCLUSIONS L-CAP patients have a protracted clinical recovery course and a more broadly dysregulated host response. These findings highlight the prognostic and pathophysiological relevance of admission lymphopenia in patients with CAP.
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Affiliation(s)
- Susanne E Doeleman
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Tom D Y Reijnders
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands.
| | - Sebastiaan C M Joosten
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Alex R Schuurman
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Tjitske S R van Engelen
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Jan Verhoeff
- Department of Molecular Cell Biology & Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan, 1117 Amsterdam, the Netherlands
| | - Valentine Léopold
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Xanthe Brands
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Bastiaan W Haak
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Jan M Prins
- Division of Infectious Diseases, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Maadrika M N P Kanglie
- Department of Radiology and Nuclear Medicine, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands; Department of Radiology, Spaarne Gasthuis, Haarlem and Hoofddorp, the Netherlands
| | - Inge A H van den Berk
- Department of Radiology and Nuclear Medicine, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Daniël R Faber
- Department of Internal Medicine, BovenIJ Hospital, Amsterdam, the Netherlands
| | - Renée A Douma
- Department of Internal Medicine, Flevo Hospital, Almere, the Netherlands
| | - Jaap Stoker
- Department of Radiology and Nuclear Medicine, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Anno Saris
- Infectious Disease, Leiden Universitair Medisch Centrum, Leiden, the Netherlands
| | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology & Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan, 1117 Amsterdam, the Netherlands
| | - W Joost Wiersinga
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands; Division of Infectious Diseases, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands; Division of Infectious Diseases, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
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2
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Rodriguez E, Lindijer DV, van Vliet SJ, Garcia Vallejo JJ, van Kooyk Y. The transcriptional landscape of glycosylation-related genes in cancer. iScience 2024; 27:109037. [PMID: 38384845 PMCID: PMC10879703 DOI: 10.1016/j.isci.2024.109037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/12/2023] [Accepted: 01/23/2024] [Indexed: 02/23/2024] Open
Abstract
Changes in glycosylation patterns have been associated with malignant transformation and clinical outcomes in several cancer types, prompting ongoing research into the mechanisms involved and potential clinical applications. In this study, we performed an extensive transcriptomic analysis of glycosylation-related genes and pathways, using publicly available bulk and single cell transcriptomic datasets from tumor samples and cancer cell lines. We identified genes and pathways strongly associated with different tumor types, which may represent novel diagnostic biomarkers. By using single cell RNA-seq data, we characterized the contribution of different cell types to the overall tumor glycosylation. Transcriptomic analysis of cancer cell lines revealed that they present a simplified landscape of genes compared to tissue. Lastly, we describe the association of different genes and pathways with the clinical outcome of patients. These results can serve as a resource for future research aimed to unravel the role of the glyco-code in cancer.
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Affiliation(s)
- Ernesto Rodriguez
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Cancer Immunology, Amsterdam, the Netherlands
| | - Dimitri V. Lindijer
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Cancer Immunology, Amsterdam, the Netherlands
| | - Sandra J. van Vliet
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Cancer Immunology, Amsterdam, the Netherlands
| | - Juan J. Garcia Vallejo
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Cancer Immunology, Amsterdam, the Netherlands
| | - Yvette van Kooyk
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Molecular Cell Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Cancer Immunology, Amsterdam, the Netherlands
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3
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Reijnders TDY, Schuurman AR, Verhoeff J, van den Braber M, Douma RA, Faber DR, Paul AGA, Wiersinga WJ, Saris A, Garcia Vallejo JJ, van der Poll T. High-dimensional phenotyping of the peripheral immune response in community-acquired pneumonia. Front Immunol 2023; 14:1260283. [PMID: 38077404 PMCID: PMC10704504 DOI: 10.3389/fimmu.2023.1260283] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
Background Community-acquired pneumonia (CAP) represents a major health burden worldwide. Dysregulation of the immune response plays an important role in adverse outcomes in patients with CAP. Methods We analyzed peripheral blood mononuclear cells by 36-color spectral flow cytometry in adult patients hospitalized for CAP (n=40), matched control subjects (n=31), and patients hospitalized for COVID-19 (n=35). Results We identified 86 immune cell metaclusters, 19 of which (22.1%) were differentially abundant in patients with CAP versus matched controls. The most notable differences involved classical monocyte metaclusters, which were more abundant in CAP and displayed phenotypic alterations reminiscent of immunosuppression, increased susceptibility to apoptosis, and enhanced expression of chemokine receptors. Expression profiles on classical monocytes, driven by CCR7 and CXCR5, divided patients with CAP into two clusters with a distinct inflammatory response and disease course. The peripheral immune response in patients with CAP was highly similar to that in patients with COVID-19, but increased CCR7 expression on classical monocytes was only present in CAP. Conclusion CAP is associated with profound cellular changes in blood that mainly relate to classical monocytes and largely overlap with the immune response detected in COVID-19.
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Affiliation(s)
- Tom D. Y. Reijnders
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
| | - Alex R. Schuurman
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
| | - Jan Verhoeff
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Marlous van den Braber
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Renée A. Douma
- Department of Internal Medicine, Flevo Hospital, Almere, Netherlands
| | - Daniël R. Faber
- Department of Internal Medicine, BovenIJ Hospital, Amsterdam, Netherlands
| | - Alberta G. A. Paul
- Application Department, Cytek Biosciences, Inc., Fremont, CA, United States
| | - W. Joost Wiersinga
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
| | - Anno Saris
- Infectious Disease, Leiden Universitair Medisch Centrum, Leiden, Netherlands
| | - Juan J. Garcia Vallejo
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
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4
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Steuten J, Bos AV, Kuijper LH, Claireaux M, Olijhoek W, Elias G, Duurland MC, Jorritsma T, Marsman C, Paul AGA, Garcia Vallejo JJ, van Gils MJ, Wieske L, Kuijpers TW, Eftimov F, van Ham SM, Ten Brinke A. Distinct dynamics of antigen-specific induction and differentiation of different CD11c +Tbet + B-cell subsets. J Allergy Clin Immunol 2023; 152:689-699.e6. [PMID: 36858158 DOI: 10.1016/j.jaci.2023.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 12/12/2022] [Revised: 02/01/2023] [Accepted: 02/10/2023] [Indexed: 03/03/2023]
Abstract
BACKGROUND CD11c+Tbet+ B cells are enriched in autoimmunity and chronic infections and also expand on immune challenge in healthy individuals. CD11c+Tbet+ B cells remain an enigmatic B-cell population because of their intrinsic heterogeneity. OBJECTIVES We investigated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen-specific development and differentiation properties of 3 separate CD11c+ B-cell subsets-age-associated B cells (ABCs), double-negative 2 (DN2) B cells, and activated naive B cells-and compared them to their canonical CD11c- counterparts. METHODS Dynamics of the response of the 3 CD11c+ B-cell subsets were assessed at SARS-CoV-2 vaccination in healthy donors by spectral flow cytometry. Distinct CD11c+ B-cell subsets were functionally characterized by optimized in vitro cultures. RESULTS In contrast to a durable expansion of antigen-specific CD11c- memory B cells over time, both ABCs and DN2 cells were strongly expanded shortly after second vaccination and subsequently contracted. Functional characterization of antibody-secreting cell differentiation dynamics revealed that CD11c+Tbet+ B cells were primed for antibody-secreting cell differentiation compared to relevant canonical CD11c- counterparts. CONCLUSION Overall, CD11c+Tbet+ B cells encompass heterogeneous subpopulations, of which primarily ABCs as well as DN2 B cells respond early to immune challenge and display a pre-antibody-secreting cell phenotype.
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Affiliation(s)
- Juulke Steuten
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Amélie V Bos
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Lisan H Kuijper
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Mathieu Claireaux
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands; Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Wouter Olijhoek
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands; Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - George Elias
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Mariel C Duurland
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Tineke Jorritsma
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Casper Marsman
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection & Immunity and Cancer Center Amsterdam, Amsterdam University Medical Centers, Free University of Amsterdam, Amsterdam, The Netherlands
| | - Marit J van Gils
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands; Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Luuk Wieske
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, The Netherlands; Department of Clinical Neurophysiology, St Antonius Hospital, Nieuwegein, The Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Filip Eftimov
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
| | - S Marieke van Ham
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Anja Ten Brinke
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
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5
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Bachas C, Duetz C, van Spronsen MF, Verhoeff J, Garcia Vallejo JJ, Jansen JH, Cloos J, Westers TM, van de Loosdrecht AA. Characterization of myelodysplastic syndromes hematopoietic stem and progenitor cells using mass cytometry. Cytometry B Clin Cytom 2023; 104:128-140. [PMID: 35289472 DOI: 10.1002/cyto.b.22066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 02/13/2022] [Accepted: 02/28/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) at risk of transformation to acute myeloid leukemia (AML) are difficult to identify. The bone marrows of MDS patients harbor specific hematopoietic stem and progenitor cell (HSPC) abnormalities that may be associated with sub-types and risk-groups. Leukemia-associated characteristics of such cells may identify MDS patients at risk of progression to AML and provide insight in the pathobiology of MDS. METHODS Bone marrow samples from healthy donors (n = 10), low risk (n = 12) and high risk (n = 13) MDS patients were collected, in addition, AML samples for 5 out of 6 MDS patients that progressed. Mass cytometry was applied to assess expression of stem cell subset and leukemia-associated immunophenotype markers. RESULTS We analyzed the data using FlowSOM to cluster cells with similar expression of 10 commonly used stem cell markers. Metaclusters (n = 20) of these clusters represented populations of cells with a related phenotype, largely resembling known stem cell subsets. Within specific subsets, intra-cellular expression levels of pCREB, IkBα, or pS6 differed significantly between healthy bone marrow (HBM) and MDS or consecutive secondary AML samples. CD34, CD44, and CD49f expression was significantly increased in high risk MDS and AML-associated metaclusters. We identified MDS/sAML cells with aberrant phenotypes when compared to HBM. Such cells were observed in clusters of both primary MDS and secondary AML samples. CONCLUSIONS High-dimensional mass cytometry and computational data analyses enabled characterization of HSPC subsets in MDS and identification of leukemia stem cell populations based on their immunophenotype. Stem cells in MDS that display leukemia-associated features may predict the risk of developing AML.
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Affiliation(s)
- Costa Bachas
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Carolien Duetz
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Margot F van Spronsen
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jan Verhoeff
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Joop H Jansen
- Laboratory of Hematology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jacqueline Cloos
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Theresia M Westers
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Arjan A van de Loosdrecht
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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du Chatinier A, Meel MH, Das AI, Metselaar DS, Waranecki P, Bugiani M, Breur M, Simonds EF, Lu ED, Weiss WA, Garcia Vallejo JJ, Hoving EW, Phoenix TN, Hulleman E. MODL-16. Generation of immunocompetent syngeneic allograft mouse models for pediatric diffuse midline glioma. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Diffuse midline gliomas (DMG) are highly aggressive pediatric brain tumors with a grim prognosis. A lack of effective treatment options highlights the critical need to investigate new therapeutic strategies. This includes the use of immunotherapy, which has shown promise in other hard-to-treat tumors. To facilitate immunotherapeutic research in this field, and to complement the existing immunodeficient patient-derived DMG models, we developed three distinct immunocompetent mouse models representing different DMG subtypes, i.e., histone 3 wildtype and histone 3 K27M mutant DMG (H3.3K27M or H3.1K27M), that can be used for preclinical testing of new therapies. We first established primary tumor cell cultures from murine DMG tumors that were generated by brainstem-targeted intra-uterine electroporation (IUE). This method enabled the introduction of DMG-associated mutations within the intact developing brainstem, thereby generating DMG tumors in a spatially and temporally defined manner, while maintaining a genetically identical (isogenic) background. We then created allograft DMG mouse models by orthotopically implanting the established primary cell cultures into syngeneic (C57BL/6) mice. Herewith, we provide an allograft tool that is better suitable for large-scale therapeutic studies and more accessible to the scientific community. Importantly, we demonstrated that these allograft models recapitulate the histopathologic phenotype of human DMG, including their diffuse infiltrative growth and expression of DMG-associated antigens. Furthermore, CyTOF mass cytometry analysis indicated that these murine pontine tumors exhibit a tumor immune microenvironment (TIME) similar to human DMG, characterized by considerable myeloid cell infiltration and a paucity of T-lymphocytes and NK cells. As such, we provide a representative model to further delineate the immune landscape in DMG and to preclinically investigate novel (immuno)therapies. Currently, we are using these immunocompetent models to study the interaction between DMG cells and microglia, and we are investigating how we can modify the immune microenvironment to improve checkpoint inhibition in DMG.
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Affiliation(s)
| | - Michaël H Meel
- Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Arvid I Das
- Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | | | - Piotr Waranecki
- Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | | | - Marjolein Breur
- Amsterdam University Medical Centers , Amsterdam , Netherlands
| | - Erin F Simonds
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco , California , USA
| | - Edbert D Lu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco , California , USA
| | - William A Weiss
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco , California , USA
| | | | - Eelco W Hoving
- Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Timothy N Phoenix
- University of Cincinnati/ Research in Patient Services, Cincinnati Children's Hospital Medical Center , Cincinnati, Ohio , USA
| | - Esther Hulleman
- Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
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7
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du Chatinier A, Meel MH, Das AI, Metselaar DS, Waranecki P, Bugiani M, Breur M, Simonds EF, Lu ED, Weiss WA, Garcia Vallejo JJ, Hoving EW, Phoenix TN, Hulleman E. Generation of Immunocompetent Syngeneic Allograft Mouse Models for Pediatric Diffuse Midline Glioma. Neurooncol Adv 2022; 4:vdac079. [PMID: 35733514 PMCID: PMC9210310 DOI: 10.1093/noajnl/vdac079] [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] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Diffuse midline gliomas (DMG) are highly malignant incurable pediatric brain tumors. A lack of effective treatment options highlights the need to investigate novel therapeutic strategies. This includes the use of immunotherapy, which has shown promise in other hard-to-treat tumors. To facilitate preclinical immunotherapeutic research, immunocompetent mouse models that accurately reflect the unique genetic, anatomical, and histological features of DMG patients are warranted.
Methods
We established cell cultures from primary DMG mouse models (C57BL/6) that were generated by brainstem targeted intra-uterine electroporation (IUE). We subsequently created allograft DMG mouse models by orthotopically implanting these tumor cells into syngeneic mice. Immunohistochemistry and -fluorescence, mass cytometry, and cell-viability assays were then used to verify that these murine tumors recapitulated human DMG.
Results
We generated three genetically distinct allograft models representing histone 3 wildtype (H3 WT) and K27M-mutant DMG (H3.3 K27M and H3.1 K27M). These allograft models recapitulated the histopathologic phenotype of their human counterparts, including their diffuse infiltrative growth and expression of DMG-associated antigens. These murine pontine tumors also exhibited an immune microenvironment similar to human DMG, characterized by considerable myeloid cell infiltration and a paucity of T-lymphocytes and NK cells. Finally, we show that these murine DMG cells display similar sensitivity to histone deacetylase (HDAC) inhibition as patient-derived DMG cells.
Conclusions
We created and validated an accessible method to generate immunocompetent allograft models reflecting different subtypes of DMG. These models adequately recapitulated the histopathology, immune microenvironment, and therapeutic response of human DMG, providing useful tools for future preclinical studies.
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Affiliation(s)
| | - Michaël H Meel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Arvid I Das
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Piotr Waranecki
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marianna Bugiani
- Department of Pathology, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marjolein Breur
- Department of Pathology, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Erin F Simonds
- Departments of Neurology, Neurological Surgery, and Pediatrics, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Edbert D Lu
- Departments of Neurology, Neurological Surgery, and Pediatrics, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - William A Weiss
- Departments of Neurology, Neurological Surgery, and Pediatrics, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Eelco W Hoving
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Timothy N Phoenix
- Division of Pharmaceutical Sciences, College of Pharmacy, University of Cincinnati/ Research in Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Esther Hulleman
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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de Krijger M, Hageman IL, Li Yim AYF, Verhoeff J, Garcia Vallejo JJ, van Hamersveld PHP, Levin E, Hakvoort TBM, Wildenberg ME, Henneman P, Ponsioen CY, de Jonge WJ. Epigenetic Signatures Discriminate Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis From Patients With Ulcerative Colitis. Front Immunol 2022; 13:840935. [PMID: 35371111 PMCID: PMC8965896 DOI: 10.3389/fimmu.2022.840935] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 12/21/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Background Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease affecting the intra- and extrahepatic bile ducts, and is strongly associated with ulcerative colitis (UC). In this study, we explored the peripheral blood DNA methylome and its immune cell composition in patients with PSC-UC, UC, and healthy controls (HC) with the aim to develop a predictive assay in distinguishing patients with PSC-UC from those with UC alone. Methods The peripheral blood DNA methylome of male patients with PSC and concomitant UC, UC and HCs was profiled using the Illumina HumanMethylation Infinium EPIC BeadChip (850K) array. Differentially methylated CpG position (DMP) and region (DMR) analyses were performed alongside gradient boosting classification analyses to discern PSC-UC from UC patients. As observed differences in the DNA methylome could be the result of differences in cellular populations, we additionally employed mass cytometry (CyTOF) to characterize the immune cell compositions. Results Genome wide methylation analysis did not reveal large differences between PSC-UC and UC patients nor HCs. Nonetheless, using gradient boosting we were capable of discerning PSC-UC from UC with an area under the receiver operator curve (AUROC) of 0.80. Four CpG sites annotated to the NINJ2 gene were found to strongly contribute to the predictive performance. While CyTOF analyses corroborated the largely similar blood cell composition among patients with PSC-UC, UC and HC, a higher abundance of myeloid cells was observed in UC compared to PSC-UC patients. Conclusion DNA methylation enables discerning PSC-UC from UC patients, with a potential for biomarker development.
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Affiliation(s)
- Manon de Krijger
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Ishtu L Hageman
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Andrew Y F Li Yim
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Jan Verhoeff
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Molecular Cell Biology and Immunology, Amsterdam Infection & Immunity and Cancer Center Amsterdam, Amsterdam University Medical Centers, Free University of Amsterdam, Amsterdam, Netherlands
| | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection & Immunity and Cancer Center Amsterdam, Amsterdam University Medical Centers, Free University of Amsterdam, Amsterdam, Netherlands
| | - Patricia H P van Hamersveld
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Evgeni Levin
- Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Horaizon BV, Delft, Netherlands
| | - Theodorus B M Hakvoort
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Manon E Wildenberg
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Surgery, University Clinic of Bonn, Bonn, Germany
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9
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Andrade Barbosa B, van Asten SD, Oh JW, Farina-Sarasqueta A, Verheij J, Dijk F, van Laarhoven HWM, Ylstra B, Garcia Vallejo JJ, van de Wiel MA, Kim Y. Bayesian log-normal deconvolution for enhanced in silico microdissection of bulk gene expression data. Nat Commun 2021; 12:6106. [PMID: 34671028 PMCID: PMC8528834 DOI: 10.1038/s41467-021-26328-2] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 09/27/2021] [Indexed: 01/29/2023] Open
Abstract
Deconvolution of bulk gene expression profiles into the cellular components is pivotal to portraying tissue's complex cellular make-up, such as the tumor microenvironment. However, the inherently variable nature of gene expression requires a comprehensive statistical model and reliable prior knowledge of individual cell types that can be obtained from single-cell RNA sequencing. We introduce BLADE (Bayesian Log-normAl Deconvolution), a unified Bayesian framework to estimate both cellular composition and gene expression profiles for each cell type. Unlike previous comprehensive statistical approaches, BLADE can handle > 20 types of cells due to the efficient variational inference. Throughout an intensive evaluation with > 700 simulated and real datasets, BLADE demonstrated enhanced robustness against gene expression variability and better completeness than conventional methods, in particular, to reconstruct gene expression profiles of each cell type. In summary, BLADE is a powerful tool to unravel heterogeneous cellular activity in complex biological systems from standard bulk gene expression data.
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Affiliation(s)
- Bárbara Andrade Barbosa
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Saskia D van Asten
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Molecular Cell Biology & Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
| | - Ji Won Oh
- Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, South Korea
- Bio-Medical Research Institute, Kyungpook National University Hospital, Daegu, South Korea
| | | | - Joanne Verheij
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Frederike Dijk
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Hanneke W M van Laarhoven
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology & Immunology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
| | - Mark A van de Wiel
- Department of Epidemiology and Data Science, Amsterdam Public Health research institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
| | - Yongsoo Kim
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
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10
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Saris A, Reijnders TDY, Nossent EJ, Schuurman AR, Verhoeff J, Asten SV, Bontkes H, Blok S, Duitman J, Bogaard HJ, Heunks L, Lutter R, van der Poll T, Garcia Vallejo JJ. Distinct cellular immune profiles in the airways and blood of critically ill patients with COVID-19. Thorax 2021; 76:1010-1019. [PMID: 33846275 PMCID: PMC8050882 DOI: 10.1136/thoraxjnl-2020-216256] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/09/2021] [Accepted: 02/27/2021] [Indexed: 01/08/2023]
Abstract
Background Knowledge of the pathophysiology of COVID-19 is almost exclusively derived from studies that examined the immune response in blood. We here aimed to analyse the pulmonary immune response during severe COVID-19 and to compare this with blood responses. Methods This was an observational study in patients with COVID-19 admitted to the intensive care unit (ICU). Mononuclear cells were purified from bronchoalveolar lavage fluid (BALF) and blood, and analysed by spectral flow cytometry; inflammatory mediators were measured in BALF and plasma. Findings Paired blood and BALF samples were obtained from 17 patients, four of whom died in the ICU. Macrophages and T cells were the most abundant cells in BALF, with a high percentage of T cells expressing the ƴδ T cell receptor. In the lungs, both CD4 and CD8 T cells were predominantly effector memory cells (87·3% and 83·8%, respectively), and these cells expressed higher levels of the exhaustion marker programmad death-1 than in peripheral blood. Prolonged ICU stay (>14 days) was associated with a reduced proportion of activated T cells in peripheral blood and even more so in BALF. T cell activation in blood, but not in BALF, was higher in fatal COVID-19 cases. Increased levels of inflammatory mediators were more pronounced in BALF than in plasma. Interpretation The bronchoalveolar immune response in COVID-19 has a unique local profile that strongly differs from the immune profile in peripheral blood. Fully elucidating COVID-19 pathophysiology will require investigation of the pulmonary immune response.
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Affiliation(s)
- Anno Saris
- Center for Experimental and Molecular Medicine, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands .,Infectious Disease, Leiden Universitair Medisch Centrum, Leiden, The Netherlands
| | - Tom D Y Reijnders
- Center for Experimental and Molecular Medicine, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Esther J Nossent
- Department of Pulmonary Medicine, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands.,Amsterdam Cardiovascular Sciences Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Alex R Schuurman
- Center for Experimental and Molecular Medicine, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Jan Verhoeff
- Department of Molecular Cell Biology & Immunology, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands.,Amsterdam institute for infection and immunity, Amsterdam, Netherlands
| | - Saskia van Asten
- Department of Molecular Cell Biology & Immunology, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands.,Amsterdam institute for infection and immunity, Amsterdam, Netherlands
| | - Hetty Bontkes
- Medical Immunology Laboratory, Department of Clinical Chemistry, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - Siebe Blok
- Department of Pulmonary Medicine, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - Janwillem Duitman
- Center for Experimental and Molecular Medicine, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Harm-Jan Bogaard
- Department of Pulmonary Medicine, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands.,Amsterdam Cardiovascular Sciences Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Leo Heunks
- Department of Intensive Care Medicine, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
| | - Rene Lutter
- Department of Pulmonary Medicine, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands.,Department of Experimental Immunology, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam UMC Locatie AMC, Amsterdam, The Netherlands.,Department of Infectious Diseases, Amsterdam UMC, Amsterdam, Netherlands
| | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology & Immunology, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands.,Amsterdam institute for infection and immunity, Amsterdam, Netherlands
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11
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van Olst L, Verhoeff J, Schetters ST, Hulshof LA, van Dijk R, van der Pol SM, Schouten M, Vallejo JJG, van Der Flier W, Teunissen CE, Middeldorp J, de Vries HE. Single‐cell profiling of circulating and brain‐resident immune cells in a mouse model for amyloidosis and in aged mice. Alzheimers Dement 2020. [DOI: 10.1002/alz.041789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lynn van Olst
- Amsterdam Neuroscience Amsterdam Netherlands
- Amsterdam Infection & Immunity Institute Amsterdam Netherlands
- Alzheimer Center Amsterdam Amsterdam Netherlands
- Vrije Universiteit Amsterdam Amsterdam Netherlands
- Amsterdam UMC Amsterdam Netherlands
| | - Jan Verhoeff
- Amsterdam Infection & Immunity Institute Amsterdam Netherlands
- Vrije Universiteit Amsterdam Amsterdam Netherlands
- Amsterdam UMC Amsterdam Netherlands
- Cancer Center Amsterdam Amsterdam Netherlands
| | - Sjoerd T.T. Schetters
- Amsterdam Infection & Immunity Institute Amsterdam Netherlands
- Vrije Universiteit Amsterdam Amsterdam Netherlands
- Amsterdam UMC Amsterdam Netherlands
- Cancer Center Amsterdam Amsterdam Netherlands
- VIB Center for Inflammation Research Gent Belgium
| | - Lianne A. Hulshof
- UMC Utrecht Brain Center University Medical Center Utrecht, Utrecht University Utrecht Netherlands
| | - Roland van Dijk
- UMC Utrecht Brain Center University Medical Center Utrecht, Utrecht University Utrecht Netherlands
| | | | - Marijn Schouten
- Amsterdam Neuroscience Amsterdam Netherlands
- Alzheimer Center Amsterdam Amsterdam Netherlands
- Vrije Universiteit Amsterdam Amsterdam Netherlands
- Amsterdam UMC Amsterdam Netherlands
| | - Juan J. Garcia Vallejo
- Amsterdam Infection & Immunity Institute Amsterdam Netherlands
- Vrije Universiteit Amsterdam Amsterdam Netherlands
- Amsterdam UMC Amsterdam Netherlands
- Cancer Center Amsterdam Amsterdam Netherlands
| | - Wiesje van Der Flier
- Amsterdam Neuroscience Amsterdam Netherlands
- Alzheimer Center Amsterdam Amsterdam Netherlands
- Vrije Universiteit Amsterdam Amsterdam Netherlands
- Amsterdam UMC Amsterdam Netherlands
| | - Charlotte E. Teunissen
- Amsterdam Neuroscience Amsterdam Netherlands
- Amsterdam UMC Amsterdam Netherlands
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC Vrije Universiteit Amsterdam Amsterdam Netherlands
- Amsterdam Neuroscience Vrije Universiteit Amsterdam, Amsterdam UMC Amsterdam Netherlands
| | - Jinte Middeldorp
- UMC Utrecht Brain Center University Medical Center Utrecht, Utrecht University Utrecht Netherlands
| | - Helga E. de Vries
- Amsterdam Neuroscience Amsterdam Netherlands
- Vrije Universiteit Amsterdam Amsterdam Netherlands
- Amsterdam UMC Amsterdam Netherlands
- University of Amsterdam, Amsterdam Cardiovascular Sciences Amsterdam Netherlands
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12
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Back JB, Chadick CH, Garcia Vallejo JJ, Orlowski-Oliver E, Patel R, Roe CE, Srivastava J, Walker RV. Shared Resource Laboratory Operations: Changes Made During Initial Global COVID-19 Lockdown of 2020. Cytometry A 2020; 99:22-32. [PMID: 33175466 PMCID: PMC7898323 DOI: 10.1002/cyto.a.24261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/15/2020] [Accepted: 11/03/2020] [Indexed: 11/16/2022]
Abstract
Undoubtedly, the global pandemic caused by the SARS‐CoV‐2 virus has had a significant impact on Shared Resource Laboratories (SRL) operations worldwide. Unlike other crises (e.g., natural disasters, acts of war, or terrorism) which often result in a sudden and sustained cessation of scientific research usually affecting one or two cities at a time, this impact is being seen simultaneously in every SRL worldwide albeit to a varying degree. The alterations to SRL operations caused by the COVID‐19 pandemic can generally be divided into three categories: (1) complete shutdown, (2) partial shutdown, and (3) uninterrupted operations. In many cases, SRLs that remained partially or fully operational during the initial wave of global infections saw a concurrent increase in COVID‐19‐related research coming through their facilities. This forced SRLs to make rapid adjustments to core operations at the same time as infectious disease experts were still developing recommendations for the safety of frontline medical workers. Although many SRLs already had contingency plans in place, this pandemic has highlighted the importance of having such plans for continuity of service, if possible, during a crisis. Immediate changes have occurred in the way SRLs operate due to potential virus transmission and in line with this new “Best Practices” have been established, that is,social distancing, remote working, and technology‐based meetings and training. Many of these changes are likely to be in place for some time with the threat of further waves of infections toward the end of 2020 and into 2021. Some of these best practices, such as having many training resources recorded and available online, are likely to remain long‐term. Although many changes have been made in haste, these will alter the future operations of SRLs. In addition, we have learnt how to deal with future crises that may be encountered in the workplace. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Jessica B Back
- Microscopy, Imaging, and Cytometry Resources Core, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, USA
| | - Cora H Chadick
- Amsterdam UMC, VU Amsterdam, Department of Molecular Cell Biology & Immunology, Amsterdam Infection & Immunity Institute, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Microscopy and Cytometry Core Facility, Amsterdam UMC - Location VUmc, Amsterdam, The Netherlands
| | - Juan J Garcia Vallejo
- Amsterdam UMC, VU Amsterdam, Department of Molecular Cell Biology & Immunology, Amsterdam Infection & Immunity Institute, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Microscopy and Cytometry Core Facility, Amsterdam UMC - Location VUmc, Amsterdam, The Netherlands
| | | | - Radhika Patel
- St Mary's Flow Cytometry Core Facility, National Heart and Lung Institute, Imperial College London, UK
| | - Caroline E Roe
- Mass Cytometry Center of Excellence at Vanderbilt University, Department of Cell and Developmental Biology, Nashville, Tennessee, USA
| | - Jane Srivastava
- Flow Cytometry Core, J. David Gladstone Institutes, San Francisco, California, USA
| | - Rachael V Walker
- Flow Cytometry Core Facility, Babraham Institute, Cambridge, CB22 3AT, UK
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13
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Bolscher JGM, Oudhoff MJ, Nazmi K, Antos JM, Guimaraes CP, Spooner E, Haney EF, Garcia Vallejo JJ, Vogel HJ, van't Hof W, Ploegh HL, Veerman ECI. Sortase A as a tool for high-yield histatin cyclization. FASEB J 2011; 25:2650-8. [PMID: 21525488 DOI: 10.1096/fj.11-182212] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cyclic peptides are highly valued tools in biomedical research. In many cases, they show higher receptor affinity, enhanced biological activity, and improved serum stability. Technical difficulties in producing cyclic peptides, especially larger ones, in appreciable yields have precluded a prolific use in biomedical research. Here, we describe a novel and efficient cyclization method that uses the peptidyl-transferase activity of the Staphylococcus aureus enzyme sortase A to cyclize linear synthetic precursor peptides. As a model, we used histatin 1, a 38-mer salivary peptide with motogenic activity. Chemical cyclization of histatin 1 resulted in ≤ 3% yields, whereas sortase-mediated cyclization provided a yield of >90%. The sortase-cyclized peptide displayed a maximum wound closure activity at 10 nM, whereas the linear peptide displayed maximal activity at 10 μM. Circular dichroism and NMR spectroscopic analysis of the linear and cyclic peptide in solution showed no evidence for conformational changes, suggesting that structural differences due to cyclization only became manifest when these peptides were located in the binding domain of the receptor. The sortase-based cyclization technology provides a general method for easy and efficient manufacturing of large cyclic peptides.
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Affiliation(s)
- Jan G M Bolscher
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU Amsterdam, Gustav Mahlerlaan 3004, 1081 LA, Amsterdam, The Netherlands.
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14
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Aarnoudse CA, Garcia Vallejo JJ, Saeland E, van Kooyk Y. Recognition of tumor glycans by antigen-presenting cells. Curr Opin Immunol 2005; 18:105-11. [PMID: 16303292 DOI: 10.1016/j.coi.2005.11.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [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: 09/15/2005] [Accepted: 11/07/2005] [Indexed: 11/28/2022]
Abstract
C-type lectin receptors on antigen-presenting cells are potent antigen-uptake receptors with specificity for glycan structures. Glycosylation changes during malignant transformation create tumor-specific carbohydrate structures that interact with C-type lectins on dendritic cells. Recent findings revealed that tumor glycoproteins, such as carcinoembryonic antigen and MUC-1, indeed interact with the C-type lectins DC-SIGN and macrophage galactose-type lectin on antigen-presenting cells. The consequences for anti-cancer immunity or tolerance induction can be extrapolated from the function of C-type lectins in pathogen recognition and antigen presentation. In addition, in vivo studies in mice recently demonstrated the potency of targeting antigens to C-type lectins on antigen-presenting cells for anti-tumor vaccination strategies.
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Affiliation(s)
- Corlien A Aarnoudse
- Department of Molecular Cell Biology and Immunology, Vrije Universiteit Medical Center Amsterdam, PO Box 7057, 1081 BT Amsterdam, The Netherlands
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