1
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Vaulet T, Callemeyn J, Lamarthée B, Antoranz A, Debyser T, Koshy P, Anglicheau D, Colpaert J, Gwinner W, Halloran PF, Kuypers D, Tinel C, Van Craenenbroeck A, Van Loon E, Marquet P, Bosisio F, Naesens M. The Clinical Relevance of the Infiltrating Immune Cell Composition in Kidney Transplant Rejection. J Am Soc Nephrol 2024:00001751-990000000-00284. [PMID: 38640017 DOI: 10.1681/asn.0000000000000350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/02/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND The link between the histology of kidney transplant rejection, especially Antibody-mediated rejection, T cell-mediated rejection and Mixed rejection, and the types of infiltrating immune cells is currently not well charted. Cost and technical complexity of single cell analysis hinder large scale studies of the relationship between cell infiltrate profiles and histological heterogeneity. METHODS In this cross-sectional study, we assessed the composition of nine intragraft immune cell types by using a validated kidney transplant-specific signature matrix for deconvolution of bulk transcriptomics in three different kidney transplant biopsy datasets (N=403, N=224, N=282). The association and the discrimination of the immune cell types with the Banff histology and the association with graft failure were assessed individually and with multivariable models. Unsupervised clustering algorithms were applied on the overall immune cells composition and compared to the Banff phenotypes. RESULTS Banff-defined rejection was related to high presence of CD8+ effector T cells, Natural Killer cells, monocytes/macrophages and to a lesser extent B cells, whereas CD4+ memory T cells were lower in rejection compared to no rejection. Estimated intragraft effector memory-expressing CD45RA (TEMRA) CD8+ T cells were strongly and consistently associated with graft failure. The large heterogeneity in immune cell composition across rejection types prevented supervised and unsupervised methods to accurately recover the Banff phenotypes based solely on immune cell estimates. The lack of correlation between immune cell composition and Banff-defined rejection types was validated using multiplex immunohistochemistry. CONCLUSIONS Although some specific cell types (FCGR3A+ myeloid cells, CD14+ monocytes/macrophages and NK cells), partly discriminate between rejection phenotypes, the overall estimated immune cell composition of kidney transplants is ill related to main Banff-defined rejection categories and adds to the Banff lesion scoring and evaluation of rejection severity. The estimated intragraft CD8temra cells bear strong and consistent association with graft failure and independent of Banff-grade rejection.
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Affiliation(s)
- Thibaut Vaulet
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Jasper Callemeyn
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Baptiste Lamarthée
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000 Besançon, France
| | - Asier Antoranz
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Tim Debyser
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Priyanka Koshy
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Dany Anglicheau
- Department of Nephrology and Kidney Transplantation, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, Inserm U1151, Necker Enfants-Malades Institute, Paris, France
| | - Jill Colpaert
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Wilfried Gwinner
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Philip F Halloran
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Dirk Kuypers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Claire Tinel
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT, F-25000 Besançon, France
- Department of Nephrology and Kidney Transplantation, Dijon University Hospital, Dijon, France
| | - Amaryllis Van Craenenbroeck
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Elisabet Van Loon
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Pierre Marquet
- Department of Pharmacology and Transplantation, University of Limoges, Inserm U1248, Limoges University Hospital, Limoges, France
| | - Francesca Bosisio
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
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2
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Pozniak J, Pedri D, Landeloos E, Van Herck Y, Antoranz A, Vanwynsberghe L, Nowosad A, Roda N, Makhzami S, Bervoets G, Maciel LF, Pulido-Vicuña CA, Pollaris L, Seurinck R, Zhao F, Flem-Karlsen K, Damsky W, Chen L, Karagianni D, Cinque S, Kint S, Vandereyken K, Rombaut B, Voet T, Vernaillen F, Annaert W, Lambrechts D, Boecxstaens V, Saeys Y, van den Oord J, Bosisio F, Karras P, Shain AH, Bosenberg M, Leucci E, Paschen A, Rambow F, Bechter O, Marine JC. A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma. Cell 2024; 187:166-183.e25. [PMID: 38181739 DOI: 10.1016/j.cell.2023.11.037] [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: 11/10/2022] [Revised: 08/23/2023] [Accepted: 11/29/2023] [Indexed: 01/07/2024]
Abstract
To better understand intrinsic resistance to immune checkpoint blockade (ICB), we established a comprehensive view of the cellular architecture of the treatment-naive melanoma ecosystem and studied its evolution under ICB. Using single-cell, spatial multi-omics, we showed that the tumor microenvironment promotes the emergence of a complex melanoma transcriptomic landscape. Melanoma cells harboring a mesenchymal-like (MES) state, a population known to confer resistance to targeted therapy, were significantly enriched in early on-treatment biopsies from non-responders to ICB. TCF4 serves as the hub of this landscape by being a master regulator of the MES signature and a suppressor of the melanocytic and antigen presentation transcriptional programs. Targeting TCF4 genetically or pharmacologically, using a bromodomain inhibitor, increased immunogenicity and sensitivity of MES cells to ICB and targeted therapy. We thereby uncovered a TCF4-dependent regulatory network that orchestrates multiple transcriptional programs and contributes to resistance to both targeted therapy and ICB in melanoma.
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Affiliation(s)
- Joanna Pozniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium.
| | - Dennis Pedri
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium; Laboratory for Membrane Trafficking, Center for Brain and Disease Research, VIB, Leuven, Belgium
| | - Ewout Landeloos
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium; Department of General Medical Oncology, UZ Leuven, Leuven, Belgium
| | | | - Asier Antoranz
- Laboratory of Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven and UZ Leuven, Leuven, Belgium
| | - Lukas Vanwynsberghe
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Ada Nowosad
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Niccolò Roda
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Samira Makhzami
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Lucas Ferreira Maciel
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Carlos Ariel Pulido-Vicuña
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - Lotte Pollaris
- Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Ruth Seurinck
- Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Fang Zhao
- Laboratory of Molecular Tumor Immunology, Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Karine Flem-Karlsen
- Department of Dermatology, Yale University, 15 York Street, New Haven, CT 05610, USA
| | - William Damsky
- Departments of Dermatology and Pathology, Yale University, 15 York Street, New Haven, CT 05610, USA
| | - Limin Chen
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Despoina Karagianni
- Immune Regulation and Tumor Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Sonia Cinque
- Laboratory for RNA Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sam Kint
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Katy Vandereyken
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Benjamin Rombaut
- Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | | | - Wim Annaert
- Laboratory for Membrane Trafficking, Center for Brain and Disease Research, VIB, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium; Center for Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Yvan Saeys
- Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Joost van den Oord
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, UZ Leuven, Leuven, Belgium
| | - Francesca Bosisio
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, UZ Leuven, Leuven, Belgium
| | - Panagiotis Karras
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium
| | - A Hunter Shain
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Marcus Bosenberg
- Departments of Dermatology, Pathology and Immunobiology, Yale University, New Haven, CT 05610, USA
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Annette Paschen
- Laboratory of Molecular Tumor Immunology, Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany; German Cancer Consortium (DKTK), Partner Site Essen, Essen, Germany
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium; Department of Applied Computational Cancer Research, Institute for AI in Medicine (IKIM), University Hospital Essen, Essen, Germany; University Duisburg-Essen, Essen, Germany.
| | - Oliver Bechter
- Department of General Medical Oncology, UZ Leuven, Leuven, Belgium.
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium.
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3
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Lamarthée B, Callemeyn J, Van Herck Y, Antoranz A, Anglicheau D, Boada P, Becker JU, Debyser T, De Smet F, De Vusser K, Eloudzeri M, Franken A, Gwinner W, Koshy P, Kuypers D, Lambrechts D, Marquet P, Mathias V, Rabant M, Sarwal MM, Senev A, Sigdel TK, Sprangers B, Thaunat O, Tinel C, Van Brussel T, Van Craenenbroeck A, Van Loon E, Vaulet T, Bosisio F, Naesens M. Transcriptional and spatial profiling of the kidney allograft unravels a central role for FcyRIII+ innate immune cells in rejection. Nat Commun 2023; 14:4359. [PMID: 37468466 DOI: 10.1038/s41467-023-39859-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 06/28/2023] [Indexed: 07/21/2023] Open
Abstract
Rejection remains the main cause of premature graft loss after kidney transplantation, despite the use of potent immunosuppression. This highlights the need to better understand the composition and the cell-to-cell interactions of the alloreactive inflammatory infiltrate. Here, we performed droplet-based single-cell RNA sequencing of 35,152 transcriptomes from 16 kidney transplant biopsies with varying phenotypes and severities of rejection and without rejection, and identified cell-type specific gene expression signatures for deconvolution of bulk tissue. A specific association was identified between recipient-derived FCGR3A+ monocytes, FCGR3A+ NK cells and the severity of intragraft inflammation. Activated FCGR3A+ monocytes overexpressed CD47 and LILR genes and increased paracrine signaling pathways promoting T cell infiltration. FCGR3A+ NK cells overexpressed FCRL3, suggesting that antibody-dependent cytotoxicity is a central mechanism of NK-cell mediated graft injury. Multiplexed immunofluorescence using 38 markers on 18 independent biopsy slides confirmed this role of FcγRIII+ NK and FcγRIII+ nonclassical monocytes in antibody-mediated rejection, with specificity to the glomerular area. These results highlight the central involvement of innate immune cells in the pathogenesis of allograft rejection and identify several potential therapeutic targets that might improve allograft longevity.
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Affiliation(s)
- Baptiste Lamarthée
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Université de Franche-Comté, UBFC, EFS, Inserm UMR RIGHT, Besançon, France
| | - Jasper Callemeyn
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Yannick Van Herck
- Department of Oncology, Laboratory for Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Asier Antoranz
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Dany Anglicheau
- Department of Nephrology and Kidney Transplantation, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université Paris Cité, Inserm U1151, Necker Enfants-Malades Institute, Paris, France
| | - Patrick Boada
- Division of Multi-Organ Transplantation, Department of Surgery, UCSF, 513 Parnassus, San Francisco, CA, USA
| | - Jan Ulrich Becker
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Tim Debyser
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Frederik De Smet
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Katrien De Vusser
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Maëva Eloudzeri
- Université Paris Cité, Inserm U1151, Necker Enfants-Malades Institute, Paris, France
| | - Amelie Franken
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Human Genetics, Laboratory of Translational Genetics, KU Leuven, Leuven, Belgium
| | - Wilfried Gwinner
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Priyanka Koshy
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Dirk Kuypers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Human Genetics, Laboratory of Translational Genetics, KU Leuven, Leuven, Belgium
| | - Pierre Marquet
- Department of Pharmacology and Transplantation, University of Limoges, Inserm U1248, Limoges University Hospital, Limoges, France
| | - Virginie Mathias
- EFS, HLA Laboratory, Décines, France
- Université Claude Bernard Lyon I, Inserm U1111, CNRS UMR5308, CIRI, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Marion Rabant
- Université Paris Cité, Inserm U1151, Necker Enfants-Malades Institute, Paris, France
- Department of Pathology, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Minnie M Sarwal
- Division of Multi-Organ Transplantation, Department of Surgery, UCSF, 513 Parnassus, San Francisco, CA, USA
| | - Aleksandar Senev
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Histocompatibility and Immunogenetics Laboratory, Red Cross-Flanders, Mechelen, Belgium
| | - Tara K Sigdel
- Division of Multi-Organ Transplantation, Department of Surgery, UCSF, 513 Parnassus, San Francisco, CA, USA
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Olivier Thaunat
- Université Claude Bernard Lyon I, Inserm U1111, CNRS UMR5308, CIRI, Ecole Normale Supérieure de Lyon, Lyon, France
- Hospices Civils de Lyon, Edouard Herriot Hospital, Department of Transplantation, Nephrology and Clinical Immunology, Lyon, France
| | - Claire Tinel
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Université de Franche-Comté, UBFC, EFS, Inserm UMR RIGHT, Besançon, France
- Department of Nephrology and Kidney Transplantation, Dijon Hospital, Dijon, France
| | - Thomas Van Brussel
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Human Genetics, Laboratory of Translational Genetics, KU Leuven, Leuven, Belgium
| | - Amaryllis Van Craenenbroeck
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Elisabet Van Loon
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium
| | - Thibaut Vaulet
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Francesca Bosisio
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Maarten Naesens
- Department of Microbiology, Immunology and Transplantation, Nephrology and Kidney Transplantation Research Group, KU Leuven, Leuven, Belgium.
- Department of Nephrology and Kidney Transplantation, University Hospitals Leuven, Leuven, Belgium.
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4
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Kruse B, Buzzai AC, Shridhar N, Braun AD, Gellert S, Knauth K, Pozniak J, Peters J, Dittmann P, Mengoni M, van der Sluis TC, Höhn S, Antoranz A, Krone A, Fu Y, Yu D, Essand M, Geffers R, Mougiakakos D, Kahlfuß S, Kashkar H, Gaffal E, Bosisio FM, Bechter O, Rambow F, Marine JC, Kastenmüller W, Müller AJ, Tüting T. CD4 + T cell-induced inflammatory cell death controls immune-evasive tumours. Nature 2023:10.1038/s41586-023-06199-x. [PMID: 37316667 DOI: 10.1038/s41586-023-06199-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 05/11/2023] [Indexed: 06/16/2023]
Abstract
Most clinically applied cancer immunotherapies rely on the ability of CD8+ cytolytic T cells to directly recognize and kill tumour cells1-3. These strategies are limited by the emergence of major histocompatibility complex (MHC)-deficient tumour cells and the formation of an immunosuppressive tumour microenvironment4-6. The ability of CD4+ effector cells to contribute to antitumour immunity independently of CD8+ T cells is increasingly recognized, but strategies to unleash their full potential remain to be identified7-10. Here, we describe a mechanism whereby a small number of CD4+ T cells is sufficient to eradicate MHC-deficient tumours that escape direct CD8+ T cell targeting. The CD4+ effector T cells preferentially cluster at tumour invasive margins where they interact with MHC-II+CD11c+ antigen-presenting cells. We show that T helper type 1 cell-directed CD4+ T cells and innate immune stimulation reprogramme the tumour-associated myeloid cell network towards interferon-activated antigen-presenting and iNOS-expressing tumouricidal effector phenotypes. Together, CD4+ T cells and tumouricidal myeloid cells orchestrate the induction of remote inflammatory cell death that indirectly eradicates interferon-unresponsive and MHC-deficient tumours. These results warrant the clinical exploitation of this ability of CD4+ T cells and innate immune stimulators in a strategy to complement the direct cytolytic activity of CD8+ T cells and natural killer cells and advance cancer immunotherapies.
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Affiliation(s)
- Bastian Kruse
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Anthony C Buzzai
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Naveen Shridhar
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Andreas D Braun
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Susan Gellert
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Kristin Knauth
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Joanna Pozniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Johannes Peters
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Paulina Dittmann
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Miriam Mengoni
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Tetje Cornelia van der Sluis
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Simon Höhn
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Asier Antoranz
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Anna Krone
- Institute of Molecular and Clinical Immunology, Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Yan Fu
- Institute of Molecular and Clinical Immunology, Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Di Yu
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Magnus Essand
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Robert Geffers
- Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Dimitrios Mougiakakos
- Department of Hematology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Sascha Kahlfuß
- Institute of Molecular and Clinical Immunology, Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | - Hamid Kashkar
- Institute for Molecular Immunology, Centre for Molecular Medicine Cologne and Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases, University of Cologne, Cologne, Germany
| | - Evelyn Gaffal
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany
| | | | - Oliver Bechter
- Department of General Medical Oncology, UZ Leuven, Leuven, Belgium
| | - Florian Rambow
- Department of Applied Computational Cancer Research, Institute for AI in Medicine (IKIM), University Hospital Essen, Essen, Germany
- University of Duisburg-Essen, Essen, Germany
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | | | - Andreas J Müller
- Institute of Molecular and Clinical Immunology, Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany.
| | - Thomas Tüting
- Laboratory of Experimental Dermatology, Department of Dermatology, University Hospital and Health Campus Immunology Infectiology and Inflammation (GC-I3), Otto-von-Guericke University, Magdeburg, Germany.
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5
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Andhari MD, Antoranz A, De Smet F, Bosisio FM. Recent advancements in tumour microenvironment landscaping for target selection and response prediction in immune checkpoint therapies achieved through spatial protein multiplexing analysis. Int Rev Cell Mol Biol 2023; 382:207-237. [PMID: 38225104 DOI: 10.1016/bs.ircmb.2023.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Immune checkpoint therapies have significantly advanced cancer treatment. Nevertheless, the high costs and potential adverse effects associated with these therapies highlight the need for better predictive biomarkers to identify patients who are most likely to benefit from treatment. Unfortunately, the existing biomarkers are insufficient to identify such patients. New high-dimensional spatial technologies have emerged as a valuable tool for discovering novel biomarkers by analysing multiple protein markers at a single-cell resolution in tissue samples. These technologies provide a more comprehensive map of tissue composition, cell functionality, and interactions between different cell types in the tumour microenvironment. In this review, we provide an overview of how spatial protein-based multiplexing technologies have fuelled biomarker discovery and advanced the field of immunotherapy. In particular, we will focus on how these technologies contributed to (i) characterise the tumour microenvironment, (ii) understand the role of tumour heterogeneity, (iii) study the interplay of the immune microenvironment and tumour progression, (iv) discover biomarkers for immune checkpoint therapies (v) suggest novel therapeutic strategies.
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Affiliation(s)
- Madhavi Dipak Andhari
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium; The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Asier Antoranz
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium; The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Frederik De Smet
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium; The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Francesca Maria Bosisio
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium.
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6
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Bolognesi MM, Antoranz A, Bosisio FM, Cattoretti G. Quantitative multiplex immunohistochemistry with colorimetric staining (QUIVER) may still benefit from MILAN. Acta Neuropathol Commun 2023; 11:91. [PMID: 37287032 DOI: 10.1186/s40478-023-01585-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Affiliation(s)
- Maddalena M Bolognesi
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Via Cadore 48, Monza, MI, Italy
| | - Asier Antoranz
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Francesca Maria Bosisio
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Giorgio Cattoretti
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Via Cadore 48, Monza, MI, Italy.
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7
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Panovska D, Nazari P, Cole B, Creemers PJ, Derweduwe M, Solie L, Van Gassen S, Claeys A, Verbeke T, Cohen EF, Tolstorukov MY, Saeys Y, Van der Planken D, Bosisio FM, Put E, Bamps S, Clement PM, Verfaillie M, Sciot R, Ligon KL, De Vleeschouwer S, Antoranz A, De Smet F. Single-cell molecular profiling using ex vivo functional readouts fuels precision oncology in glioblastoma. Cell Mol Life Sci 2023; 80:147. [PMID: 37171617 DOI: 10.1007/s00018-023-04772-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/06/2023] [Accepted: 03/29/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Functional profiling of freshly isolated glioblastoma (GBM) cells is being evaluated as a next-generation method for precision oncology. While promising, its success largely depends on the method to evaluate treatment activity which requires sufficient resolution and specificity. METHODS Here, we describe the 'precision oncology by single-cell profiling using ex vivo readouts of functionality' (PROSPERO) assay to evaluate the intrinsic susceptibility of high-grade brain tumor cells to respond to therapy. Different from other assays, PROSPERO extends beyond life/death screening by rapidly evaluating acute molecular drug responses at single-cell resolution. RESULTS The PROSPERO assay was developed by correlating short-term single-cell molecular signatures using mass cytometry by time-of-flight (CyTOF) to long-term cytotoxicity readouts in representative patient-derived glioblastoma cell cultures (n = 14) that were exposed to radiotherapy and the small-molecule p53/MDM2 inhibitor AMG232. The predictive model was subsequently projected to evaluate drug activity in freshly resected GBM samples from patients (n = 34). Here, PROSPERO revealed an overall limited capacity of tumor cells to respond to therapy, as reflected by the inability to induce key molecular markers upon ex vivo treatment exposure, while retaining proliferative capacity, insights that were validated in patient-derived xenograft (PDX) models. This approach also allowed the investigation of cellular plasticity, which in PDCLs highlighted therapy-induced proneural-to-mesenchymal (PMT) transitions, while in patients' samples this was more heterogeneous. CONCLUSION PROSPERO provides a precise way to evaluate therapy efficacy by measuring molecular drug responses using specific biomarker changes in freshly resected brain tumor samples, in addition to providing key functional insights in cellular behavior, which may ultimately complement standard, clinical biomarker evaluations.
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Affiliation(s)
- Dena Panovska
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium
| | - Pouya Nazari
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium
| | - Basiel Cole
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium
| | - Pieter-Jan Creemers
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium
| | - Marleen Derweduwe
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium
| | - Lien Solie
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium
- Department of Neurosurgery, University Hospitals (UZ) Leuven, Leuven, Belgium
- Laboratory of Experimental Neurosurgery and Neuroanatomy, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Sofie Van Gassen
- Data Mining and Modeling for Biomedicine Group, VIB Inflammation Research Center, Ghent University, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Annelies Claeys
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium
| | - Tatjana Verbeke
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium
| | - Elizabeth F Cohen
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine Group, VIB Inflammation Research Center, Ghent University, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | | | - Francesca M Bosisio
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium
| | - Eric Put
- Neurosurgery Department, Faculty of Medicine and Life Sciences UHasselt, Hasselt, Belgium
| | - Sven Bamps
- Neurosurgery Department, Faculty of Medicine and Life Sciences UHasselt, Hasselt, Belgium
| | - Paul M Clement
- Department of Oncology, KU Leuven/UZ Leuven, Leuven, Belgium
| | - Michiel Verfaillie
- Europaziekenhuizen, Cliniques de l'Europe, Sint-Elisabeth, Brussels, Belgium
| | - Raf Sciot
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium
| | - Keith L Ligon
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Steven De Vleeschouwer
- Department of Neurosurgery, University Hospitals (UZ) Leuven, Leuven, Belgium
- Laboratory of Experimental Neurosurgery and Neuroanatomy, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Asier Antoranz
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium
| | - Frederik De Smet
- Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 1032, Leuven, Belgium.
- Leuven Institute for single-cell omics (LISCO), Leuven, Belgium.
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8
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De Schepper M, Antoranz A, Dubroja N, Floris G, De Smet F, Bosisio F. Abstract 6773: Spatial dynamics of cytotoxic T lymphocyte exhaustion in reactive and tumoral tissue. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6773] [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: 04/07/2023]
Abstract
Abstract
Background The study of cytotoxic T-lymphocytes (Tcy) has shown increased attention from the scientific community in the last years because of their predictive role in anti-cancer therapy with specific interest in immune check point blocking therapy. However, most of these studies have used bulk or dissociation-based single-cell technologies to draw their biological insights. Lately, new spatial -omics technologies are increasing our knowledge on this population by adding the spatial location of these cells in-situ in the native structure of the tissue. In this study, we have compared the activation of Tcy in reactive and cancerous conditions at single cell level and in the micro-anatomical context of the tissue.
Experimental procedures One tissue micro array slide containing: reactive tonsil, inflammatory liver disease, breast cancer, glioblastoma and melanoma was stained using the COMET™ instrument (Lunaphore Technologies SA) for a multiplex panel of 20 markers. The derived multiplexed images were analyzed using the DISSCOVERY software platform developed by the MILAN Unit at KU Leuven (Belgium). 12/20 markers were specifically aimed at identifying the main cell populations in the tissue (CD11b, CD163, CD20, CD3, CD31, CD4, CD56, CD68, CD8, CK, FOXP3, S100) while the remaining 8 markers were aimed at adding functional information on immune cell types of interest (CD69, HLA-DR, Ki67, LAG3, OX40, PD-1, PD-L1, TIM3).
Results The general activation levels of the Tcy in the reactive conditions were higher than in the three cancer subtypes. When looking at Tcy activation as a function of the distance from the vascular structures (identified via CD31+ endothelial cells), we observed an orderly distribution of activated Tcy around CD31+ endothelial cells with a gradient of increasing exhaustion levels with increasing distance from the vessel in the reactive conditions. In the cancer samples, on the contrary, a patchy disorderly organized pattern of exhausted and activated Tcy was observed around the vessels.
Conclusion The spatial location of inflammatory cells plays a critical role to understand their functional behavior and thanks to technological progress it is now possible to start doing this at scale. The study of the dynamics of exhaustion of Tcy in the tissue will help clarify the interplay between cancer cells and immune environment. These results will be crucial to better select patients who may benefit the most of immune check point blockade.
Citation Format: Maxim De Schepper, Asier Antoranz, Nikolina Dubroja, Giuseppe Floris, Frederik De Smet, Francesca Bosisio. Spatial dynamics of cytotoxic T lymphocyte exhaustion in reactive and tumoral tissue. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6773.
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9
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De Wispelaere W, Annibali D, Tuyaerts S, Messiaen J, Antoranz A, Baiden-Amissah R, Van Brussel T, Schepers R, Philips G, Boeckx B, Baietti M, Ho Wang Yin K, Bayon E, Van Rompuy AS, Leucci E, Tabruyn S, Bosisio F, Lambrechts D, Amant F. 17P Exploiting the immune-modulatory effects of PI3K/mTOR inhibitors to enhance response to immune-checkpoint blockade in uterine leiomyosarcoma. ESMO Open 2023. [DOI: 10.1016/j.esmoop.2023.101038] [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: 04/05/2023] Open
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10
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Frias A, Di Leo L, Antoranz A, Nazerai L, Carretta M, Bodemeyer V, Pagliuca C, Dahl C, Claps G, Mandelli GE, Andhari MD, Pacheco MP, Sauter T, Robert C, Guldberg P, Madsen DH, Cecconi F, Bosisio FM, De Zio D. Ambra1 modulates the tumor immune microenvironment and response to PD-1 blockade in melanoma. J Immunother Cancer 2023; 11:jitc-2022-006389. [PMID: 36868570 PMCID: PMC9990656 DOI: 10.1136/jitc-2022-006389] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Loss of Ambra1 (autophagy and beclin 1 regulator 1), a multifunctional scaffold protein, promotes the formation of nevi and contributes to several phases of melanoma development. The suppressive functions of Ambra1 in melanoma are mediated by negative regulation of cell proliferation and invasion; however, evidence suggests that loss of Ambra1 may also affect the melanoma microenvironment. Here, we investigate the possible impact of Ambra1 on antitumor immunity and response to immunotherapy. METHODS This study was performed using an Ambra1-depleted BrafV600E /Pten-/ - genetically engineered mouse (GEM) model of melanoma, as well as GEM-derived allografts of BrafV600E /Pten-/ - and BrafV600E /Pten-/ -/Cdkn2a-/ - tumors with Ambra1 knockdown. The effects of Ambra1 loss on the tumor immune microenvironment (TIME) were analyzed using NanoString technology, multiplex immunohistochemistry, and flow cytometry. Transcriptome and CIBERSORT digital cytometry analyses of murine melanoma samples and human melanoma patients (The Cancer Genome Atlas) were applied to determine the immune cell populations in null or low-expressing AMBRA1 melanoma. The contribution of Ambra1 on T-cell migration was evaluated using a cytokine array and flow cytometry. Tumor growth kinetics and overall survival analysis in BrafV600E /Pten-/ -/Cdkn2a-/ - mice with Ambra1 knockdown were evaluated prior to and after administration of a programmed cell death protein-1 (PD-1) inhibitor. RESULTS Loss of Ambra1 was associated with altered expression of a wide range of cytokines and chemokines as well as decreased infiltration of tumors by regulatory T cells, a subpopulation of T cells with potent immune-suppressive properties. These changes in TIME composition were associated with the autophagic function of Ambra1. In the BrafV600E /Pten-/ -/Cdkn2a-/ - model inherently resistant to immune checkpoint blockade, knockdown of Ambra1 led to accelerated tumor growth and reduced overall survival, but at the same time conferred sensitivity to anti-PD-1 treatment. CONCLUSIONS This study shows that loss of Ambra1 affects the TIME and the antitumor immune response in melanoma, highlighting new functions of Ambra1 in the regulation of melanoma biology.
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Affiliation(s)
- Alex Frias
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Luca Di Leo
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Asier Antoranz
- Lab of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Loulieta Nazerai
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Marco Carretta
- National Center for Cancer Immunotherapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Valérie Bodemeyer
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Chiara Pagliuca
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Christina Dahl
- Molecular Diagnostics Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Giuseppina Claps
- INSERM U981 and Department of Oncologic Medicine, Gustave Roussy Institute and Paris Saclay University, Villejuif, France
| | | | | | - Maria Pires Pacheco
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Thomas Sauter
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Caroline Robert
- INSERM U981 and Department of Oncologic Medicine, Gustave Roussy Institute and Paris Saclay University, Villejuif, France
| | - Per Guldberg
- Molecular Diagnostics Group, Danish Cancer Society Research Center, Copenhagen, Denmark.,Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Daniel Hargbøl Madsen
- National Center for Cancer Immunotherapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Francesco Cecconi
- Cell Stress and Survival, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | | | - Daniela De Zio
- Melanoma Research Team, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, Copenhagen, Denmark .,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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11
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Decraene B, Antoranz A, Verbeke T, Vanmechelen M, Nazari P, Solie L, Dubroja N, Derweduwe M, Spans L, Bempt IV, Sciot R, De Smet F, De Vleeschouwer S. TMIC-37. SINGLE-CELL CHARACTERIZATION OF THE IMMUNE LANDSCAPE OF EXTREME LONG-TERM SURVIVORS WITH MALIGNANT GLIOMA. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.1081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Glioblastoma Multiforme (GBM) remains the most common malignant primary brain tumor with a dismal prognosis that rarely exceeds beyond two years despite extensive therapy, which consists of maximal safe surgical resection, radiotherapy and/or chemotherapy. Recently, it has become clear that GBM is not one homogeneous entity and that both intra-and intertumoral heterogeneity contribute significantly to differences in tumoral behavior which may consequently be responsible for differences in survival. Strikingly and despite its dismal prognosis, small fractions of GBM patients seem to display extreme extended survival compared to the large majority of patients. The underlying mechanisms for this peculiarity remain largely unknown however, even though emerging data suggest that both cancer cell-autonomous and microenvironmental factors and their interplay probably play an important role. We used high-dimensional, multiplexed immunohistochemistry to spatially, and cytometry by time-of-flight to quantitively, characterize the cell constitution and interactions within the tumor microenvironment (TME) in 21 extreme long-term survivors (living over 10 year) and 42 deeply matched controls and therefore short-term survivors (living under 1.5 year) on a single cell level. For all tumors (epi)genetic data was also collected. We identified a high level of both inter-and intrapatient heterogeneity defined by several distinct tumoral niches, as well as described interactions within these niches and with the surrounding infiltrating immune cells of the TME in GBM. Finally, by linking patient characteristics with the heterogeneous immune composition we are able to create an immune stratification that can be linked to patient survival in GBM. Therefore, this study is an essential initial step towards strategies to alter the TME in a favorable way with a personalized modulation strategy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Raf Sciot
- University Hospitals Leuven & KU Leuven , Leuven , USA
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12
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Antoranz A, Van Herck Y, Bolognesi MM, Lynch SM, Rahman A, Gallagher WM, Boecxstaens V, Marine JC, Cattoretti G, van den Oord JJ, De Smet F, Bechter O, Bosisio FM. Mapping the Immune Landscape in Metastatic Melanoma Reveals Localized Cell-Cell Interactions That Predict Immunotherapy Response. Cancer Res 2022; 82:3275-3290. [PMID: 35834277 PMCID: PMC9478533 DOI: 10.1158/0008-5472.can-22-0363] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/30/2022] [Accepted: 07/07/2022] [Indexed: 01/07/2023]
Abstract
While immune checkpoint-based immunotherapy (ICI) shows promising clinical results in patients with cancer, only a subset of patients responds favorably. Response to ICI is dictated by complex networks of cellular interactions between malignant and nonmalignant cells. Although insights into the mechanisms that modulate the pivotal antitumoral activity of cytotoxic T cells (Tcy) have recently been gained, much of what has been learned is based on single-cell analyses of dissociated tumor samples, resulting in a lack of critical information about the spatial distribution of relevant cell types. Here, we used multiplexed IHC to spatially characterize the immune landscape of metastatic melanoma from responders and nonresponders to ICI. Such high-dimensional pathology maps showed that Tcy gradually evolve toward an exhausted phenotype as they approach and infiltrate the tumor. Moreover, a key cellular interaction network functionally linked Tcy and PD-L1+ macrophages. Mapping the respective spatial distributions of these two cell populations predicted response to anti-PD-1 immunotherapy with high confidence. These results suggest that baseline measurements of the spatial context should be integrated in the design of predictive biomarkers to identify patients likely to benefit from ICI. SIGNIFICANCE This study shows that spatial characterization can address the challenge of finding efficient biomarkers, revealing that localization of macrophages and T cells in melanoma predicts patient response to ICI. See related commentary by Smalley and Smalley, p. 3198.
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Affiliation(s)
- Asier Antoranz
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Belgium, Leuven
| | - Yannick Van Herck
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Belgium, Leuven
| | - Maddalena M. Bolognesi
- Pathology, Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Seodhna M. Lynch
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Arman Rahman
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - William M. Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Veerle Boecxstaens
- Department of Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB/KU Leuven Center for Cancer Biology, Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, Leuven, Belgium
| | - Giorgio Cattoretti
- Pathology, Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Joost J. van den Oord
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Belgium, Leuven
| | - Frederik De Smet
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Belgium, Leuven
| | - Oliver Bechter
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Belgium, Leuven
| | - Francesca M. Bosisio
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Belgium, Leuven.,Corresponding Author: Francesca M Bosisio, Laboratory of Translational Cell and Tissue Research, KU Leuven, Herestraat 49, Leuven 3000, Belgium. Phone: 321-632-9965; E-mail:
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13
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Decraene B, Antoranz A, Verbeke T, Nazari P, Solie L, Dubroja N, Derweduwe M, De Smet F, De Vleeschouwer S. KS05.7.A Characterization of the immune composition of extreme long-term survivors with malignant glioma at single-cell level. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac174.017] [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: 11/12/2022] Open
Abstract
Abstract
Background
Glioblastoma Multiforme (GBM) remains the most common malignant primary brain tumor with a dismal prognosis that rarely exceeds beyond two years despite extensive therapy, which consists of maximal safe surgical resection, radiotherapy and/or chemotherapy. Recently, it has become clear that GBM is not one homogeneous entity and that both intra-and intertumoral heterogeneity contribute significantly to differences in tumoral behavior which may consequently be responsible for differences in survival. Strikingly and in spite of its dismal prognosis, small fractions of GBM patients seem to display extended survival compared to the large majority of patients. The underlying mechanisms for this peculiarity remain largely unknown however, even though emerging data suggest that both cancer cell-autonomous and microenvironmental factors and their interplay probably play an important role.
Material and Methods
We used high-dimensional, multiplexed immunohistochemistry to spatially, and cytometry by time-of-flight to quantitively characterize the cell constitution and interactions within the tumor microenvironment (TME) in 21 extreme long-term survivors (living over ten years since primary diagnosis or five years after recurrence) and 42 deeply matched short-term controls (living under 1.5 year) on a single cell level. For all tumors (epi-)genetic data was also collected.
Results
We identified a high level of both inter-and intrapatient heterogeneity defined by several distinct tumor niches, as well as described interactions within these niches and with the surrounding infiltrating immune cells of the TME. By linking patient characteristics with the heterogeneous immune composition we are building an immune stratification that can be linked to patient survival in GBM.
Conclusion
Generating an immune stratification for GBM will allow us to identify immune characteristics responsible for longer or even exceptional survival, as well as thoroughly identify tumor components that may serve as a potential target for personalized treatment strategies. Therefore, this study is also an essential initial step towards such clinical trials which alter the TME in a favorable way with a personalized modulation strategy.
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Affiliation(s)
- B Decraene
- KU Leuven , Leuven , Belgium
- University Hospitals Leuven , Leuven , Belgium
| | | | | | | | - L Solie
- KU Leuven , Leuven , Belgium
| | | | | | | | - S De Vleeschouwer
- KU Leuven , Leuven , Belgium
- University Hospitals Leuven , Leuven , Belgium
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14
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Bosisio FM, Van Herck Y, Messiaen J, Bolognesi MM, Marcelis L, Van Haele M, Cattoretti G, Antoranz A, De Smet F. Next-Generation Pathology Using Multiplexed Immunohistochemistry: Mapping Tissue Architecture at Single-Cell Level. Front Oncol 2022; 12:918900. [PMID: 35992810 PMCID: PMC9389457 DOI: 10.3389/fonc.2022.918900] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/20/2022] [Indexed: 01/23/2023] Open
Abstract
Single-cell omics aim at charting the different types and properties of all cells in the human body in health and disease. Over the past years, myriads of cellular phenotypes have been defined by methods that mostly required cells to be dissociated and removed from their original microenvironment, thus destroying valuable information about their location and interactions. Growing insights, however, are showing that such information is crucial to understand complex disease states. For decades, pathologists have interpreted cells in the context of their tissue using low-plex antibody- and morphology-based methods. Novel technologies for multiplexed immunohistochemistry are now rendering it possible to perform extended single-cell expression profiling using dozens of protein markers in the spatial context of a single tissue section. The combination of these novel technologies with extended data analysis tools allows us now to study cell-cell interactions, define cellular sociology, and describe detailed aberrations in tissue architecture, as such gaining much deeper insights in disease states. In this review, we provide a comprehensive overview of the available technologies for multiplexed immunohistochemistry, their advantages and challenges. We also provide the principles on how to interpret high-dimensional data in a spatial context. Similar to the fact that no one can just “read” a genome, pathological assessments are in dire need of extended digital data repositories to bring diagnostics and tissue interpretation to the next level.
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Affiliation(s)
- Francesca Maria Bosisio
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- *Correspondence: Frederik De Smet, ; Francesca Maria Bosisio,
| | | | - Julie Messiaen
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Maddalena Maria Bolognesi
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Monza, Italy
- Department of Pathology, Azienda Socio Sanitaria Territoriale (ASST) Monza, Ospedale San Gerardo, Monza, Italy
| | - Lukas Marcelis
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Matthias Van Haele
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Giorgio Cattoretti
- Pathology, Department of Medicine and Surgery, Università di Milano-Bicocca, Monza, Italy
- Department of Pathology, Azienda Socio Sanitaria Territoriale (ASST) Monza, Ospedale San Gerardo, Monza, Italy
| | - Asier Antoranz
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Frederik De Smet
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- The Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- *Correspondence: Frederik De Smet, ; Francesca Maria Bosisio,
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15
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Messiaen J, Antoranz A, Van Herck Y, Verhaaren B, Nazari P, Sebastian I, Milli G, Bosisio F, Pey J, Bempt IV, Sciot R, Jacobs S, De Smet F. HGG-56. Spatial mapping of the tumor micro-environment in pediatric glioma. Neuro Oncol 2022. [PMCID: PMC9165297 DOI: 10.1093/neuonc/noac079.271] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
High-grade glioma are the main cause of cancer-related death in children. The highly heterogeneous composition of the tumor cells and their interactions with the tumor micro-environment (TME), contribute substantially to the poor response to treatment and the high levels of morbidity and mortality. Here, we used high-dimensional, multiplexed immunohistochemistry to map the single-cell tissue architecture of 26 pediatric glioma samples covering 8 histologic diagnoses, allowing us to determine the spatial distribution of the various tumoral subtypes and how these interact with their local immune-microenvironment. Overall, this analysis showed that tumor grade anti-correlated with the amount of infiltrating cytotoxic T-lymphocytes (CTLs), which were typically more exhausted in the higher grade tumors. In addition, tumor associated macrophages were primarily infiltrating from the blood and presented an M2-like anti-inflammatory phenotype which became more extended with tumor grade. Using the spatial information, possible cell-cell interactions could be determined. In lower grade glioma, we observed an increased activation level of CTLs that were closely located to neighboring T-helper cells. In pediatric glioblastoma, on the other hand, CTLs, even though they were located close to a T-helper cell, could only minimally be activated, and showed more extended exhaustion when residing further away. Additionally, the activation of the CTLs was associated to the distance to the closest PD-L1 positive macrophage in pilocytic astrocytoma and desmoplastic infantile ganglioglioma. In conclusion, with the use of multiplex immunohistochemistry, we are able to study the tumor and TME of pediatric glioma in depth on a single-cell and spatial level, which allows us to further study the heterogeneous landscape of these tumors.
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Affiliation(s)
- Julie Messiaen
- Department of Pediatrics, University Hospitals Leuven , Leuven , Belgium
- Laboratory for Precision Cancer Medicine, Translational cell- and tissue research, Department of Imaging and Pathology, KU Leuven , Leuven , Belgium
| | - Asier Antoranz
- Laboratory for Precision Cancer Medicine, Translational cell- and tissue research, Department of Imaging and Pathology, KU Leuven , Leuven , Belgium
| | - Yannick Van Herck
- Department of Oncology, University Hospitals Leuven , Leuven , Belgium
- Department of Oncology, KU Leuven , Leuven , Belgium
| | - Ben Verhaaren
- Department of Radiology, University Hospitals Leuven , Leuven , Belgium
| | - Pouya Nazari
- Laboratory for Precision Cancer Medicine, Translational cell- and tissue research, Department of Imaging and Pathology, KU Leuven , Leuven , Belgium
| | - Ivey Sebastian
- Laboratory for Precision Cancer Medicine, Translational cell- and tissue research, Department of Imaging and Pathology, KU Leuven , Leuven , Belgium
| | - Giorgia Milli
- Translational cell- and tissue research, Department of Imaging and Pathology, KU Leuven , Leuven , Belgium
| | - Francesca Bosisio
- Translational cell- and tissue research, Department of Imaging and Pathology, KU Leuven , Leuven , Belgium
- Department of Pathology, University Hospitals Leuven , Leuven , Belgium
| | - Jon Pey
- Laboratory for Precision Cancer Medicine, Translational cell- and tissue research, Department of Imaging and Pathology, KU Leuven , Leuven , Belgium
| | - Isabelle Vanden Bempt
- Department of Human Genetics, University Hospitals Leuven , Leuven , Belgium
- Department of Human Genetics, KU Leuven , Leuven , Belgium
| | - Raf Sciot
- Translational cell- and tissue research, Department of Imaging and Pathology, KU Leuven , Leuven , Belgium
- Department of Pathology, University Hospitals Leuven , Leuven , Belgium
| | - Sandra Jacobs
- Department of Pediatric Hematology-Oncology, Department of Pediatrics, University Hospitals Leuven , Leuven , Belgium
- Department of Pediatric Oncology, KU Leuven , Leuven , Belgium
| | - Frederik De Smet
- Laboratory for Precision Cancer Medicine, Translational cell- and tissue research, Department of Imaging and Pathology, KU Leuven , Leuven , Belgium
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16
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Panovska D, Shetty A, Derweduwe M, Claeys A, Van der Voordt M, Smets T, Versele M, Monaco G, De Moor B, Chaltin P, Clement P, Ligon K, De Vleeschouwer S, Sciot R, Pey J, Antoranz A, De Smet F. TMOD-22. DIFFERENTIAL DRUG SENSITIVITY ANALYSIS IN PAIRED PATIENT-DERIVED CELL LINES OF GLIOBLASTOMA. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.883] [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
Glioblastoma (GBM) remains the most aggressive adult brain tumour with dismal prognosis. Even when treated by the most optimal standard-of-care modalities, disease progression remains consistently inevitable. Understanding how tumours evolve from a newly diagnosed to a recurrent setting is therefore critical, but research models to functionally test how therapeutic interventions evolve accordingly remain scarce. Here, we describe our efforts to develop paired models including newly diagnosed and recurrent GBM cell lines derived from the same patients. Overall, we collected 50 tumour samples originating from 24 patients at different time points in their treatment scheme. This resulted in the generation of 27 models overall, from which 18 originated from 9 patients at different timepoints. The latter were subsequently investigated extensively. First, using genomic profiling, we consistently observed an increase in mutational burden and chromosomal aberrations in the recurrent samples, while transcriptomic profiling showed that tumour subtypes evolved in a very patient-specific way. A large fraction of the recurrent models showed resistance to temozolomide (TMZ), which coincided with a downregulation of DNA repair (MMR) pathways or mutations. Half of the tested models also acquired resistance to radiation therapy. Next to standard-of-care therapy, we investigated several small molecule inhibitors that are currently in clinical evaluation, which also showed differential sensitivity. Overall, the developed paired cell lines recapitulate the most important features related to tumour recurrence, and offer the opportunity for more elaborate dependency screening efforts.
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Affiliation(s)
| | | | | | | | | | | | | | - Giovanni Monaco
- Center for Innovation and Stimulation of Drug Discovery, Leuven, Belgium
| | | | | | | | - Keith Ligon
- Dana-Farber Cancer Institute, Boston, MA, USA
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17
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Panovska D, Antoranz A, Creemers PJ, Derweduwe M, Nasari P, Orlando G, Van Gassen S, Claeys A, Verbeke T, Solie L, Sciot R, Clement P, Van der Planken D, Verfaillie M, Rousseau F, Schymkowitz J, Saeys Y, Ligon K, De Vleeschouwer S, De Smet F. EXTH-20. SINGLE-CELL DRUG ACTIVITY MAPPING IN GLIOBLASTOMA IDENTIFIES EXTENDED DRUG RESPONSE HETEROGENEITY AND THERAPY-INDUCED CELLULAR PLASTICITY. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.659] [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
Glioblastoma (GBM) remains a highly malignant and incurable brain tumour. The inability to achieve clinical improvements in GBM treatment can be attributed to the excessive heterogeneity and plasticity of GBM cells, which is reflected by the presence of various cellular states within each tumour. How each of these tumour cell subtypes respond to therapy remains largely unknown. In this work, we developed a functional diagnostic analysis pipeline to measure therapeutic activity in GBM tumour cells at single-cell resolution using mass cytometry by time-of-flight (CyTOF). By applying an optimised GBM-specific and therapy-tailored antibody panel, we measured therapeutic activity upon exposure to ionising radiation (RT) or a small molecule MDM2 inhibitor (AMG232) in a cohort of patient-derived GBM cell lines (n=14). As such, extended heterogeneity in drug responsiveness was reflected by diverse degrees of alterations in cell cycle progression and apoptotic signalling, in addition to shifts in tumoral phenotypic states implying therapy-induced plasticity. A similar approach was used to measure drug activity in freshly resected tumour samples (n=18) harvested from different tumour regions (core or invasive front) within hours following surgery. Accordingly, we identified highly variable fractions of responsive tumour and microenvironmental cell populations in a patient-specific way. The ability to measure drug activity at single-cell resolution in a patient-tailored manner by applying a genotype-agnostic method, paves the way for advanced precision cancer medicine in GBM by offering a novel approach to more precisely select eligible patients for prospective clinical trials.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Keith Ligon
- Dana-Farber Cancer Institute, Boston, MA, USA
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18
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Messiaen J, Nasari P, Van Herck Y, Verhaaren B, Sebastian I, Milli G, Bosisio F, Pey J, De Vleeschouwer S, De Vloo P, Depreitere B, Vanden Bempt I, Sciot R, Antoranz A, Jacobs S, De Smet F. PATH-21. THE SINGLE-CELL PATHOLOGY LANDSCAPE OF PEDIATRIC GLIOMA. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.473] [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: 11/14/2022] Open
Abstract
Abstract
High-grade glioma are the main cause of cancer-related death in children. Despite extensive research, their prognosis remains poor with very few treatment options. This can be attributed to the highly heterogeneous and plastic nature of glioma tumor cells and their interactions with the microenvironment, although quantitative data are still largely missing. Here, we used high-dimensional, multiplexed immunohistochemistry to map the spatial, single-cell tissue architecture of 31 pediatric glioma samples covering 9 histologic diagnoses. This novel approach allowed us to map the spatial distribution of the various tumoral subtypes, which typically occur in specific tumoral niches, and how these interact with their local immune-microenvironment. Finally, by aligning these findings to the clinical data of the patients and comparing these to adult glioblastoma, we are now able to more precisely describe the heterogeneous landscape of pediatric glioma at single-cell resolution.
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19
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Vanmechelen M, Beckervordersandforth J, Pey J, Antoranz A, Nasari P, Pantano D, Bevers S, Leunissen D, Moors W, Messiaen J, Sebastian I, Milli G, Van Herck Y, Geens E, Verduin M, Hoosemans L, Claeys A, Derweduwe M, Zurhausen A, Bosisio F, Eekers D, Weyns F, Daenekindt T, Van Eyken P, Goovers M, Hovinga K, De Vleeschouwer S, Clement P, Broen M, Vooijs M, Sciot R, Hoeben A, Speel EJ, De Smet F. PATH-20. SPATIAL MAPPING OF THERAPY-INDUCED, PATHOLOGICAL CHANGES IN GLIOBLASTOMA AT SINGLE-CELL RESOLUTION. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.472] [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: 11/14/2022] Open
Abstract
Abstract
Glioblastoma (GBM) remains a highly malignant, intrinsically resistant and inevitably recurring brain tumor with dismal prognosis. The aggressiveness and lack of effective GBM treatments can be attributed to the highly heterogeneous and plastic nature of GBM tumor cells, which easily confer resistance to standard-of-care (SOC) therapy. While tumor progression has also been attributed to interactions with the tumor microenvironment, quantitative data describing these interactions are still largely missing. Here, we used high-dimensional, multiplexed immunohistochemistry to map evolutions in the spatial, single-cell tissue architecture of 120 paired adult GBM tumor samples derived from 60 patients at diagnosis (ND) and upon recurrence (REC) following SOC treatment. We mapped the spatial distribution of a multitude of GBM tumoral subtypes across this multicentric cohort, through which we identified a high level of heterogeneity defined by specific tumoral niches within and across patients and which evolved when subjected to SOC therapy. In addition, we describe the relationship of the various tumoral niches with their local immune-infiltrates, highlighting an even more immunosuppressive environment following SOC resistance. Finally, by aligning these findings to the observed genomic aberrations and the clinical data of the patients, we are now able to more precisely describe the heterogeneous landscape of glioblastoma and how it evolves under SOC treatment at spatial, single-cell resolution.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marc Vooijs
- Maastricht University, Maastricht, Netherlands
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20
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Kumar M, Toprakhisar B, Van Haele M, Antoranz A, Boon R, Chesnais F, De Smedt J, Tricot T, Idoype TI, Canella M, Tilliole P, De Boeck J, Bajaj M, Ranga A, Bosisio FM, Roskams T, van Grunsven LA, Verfaillie CM. A fully defined matrix to support a pluripotent stem cell derived multi-cell-liver steatohepatitis and fibrosis model. Biomaterials 2021; 276:121006. [PMID: 34304139 DOI: 10.1016/j.biomaterials.2021.121006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/01/2021] [Indexed: 01/12/2023]
Abstract
Chronic liver injury, as observed in non-alcoholic steatohepatitis (NASH), progressive fibrosis, and cirrhosis, remains poorly treatable. Steatohepatitis causes hepatocyte loss in part by a direct lipotoxic insult, which is amplified by derangements in the non-parenchymal cellular (NPC) interactive network wherein hepatocytes reside, including, hepatic stellate cells, liver sinusoidal endothelial cells and liver macrophages. To create an in vitro culture model encompassing all these cells, that allows studying liver steatosis, inflammation and fibrosis caused by NASH, we here developed a fully defined hydrogel microenvironment, termed hepatocyte maturation (HepMat) gel, that supports maturation and maintenance of pluripotent stem cell (PSC) derived hepatocyte- and NPC-like cells for at least one month. The HepMat-based co-culture system modeled key molecular and functional features of TGFβ-induced liver fibrosis and fatty-acid induced inflammation and fibrosis better than monocultures of its constituent cell populations. The novel co-culture system should open new avenues for studying mechanisms underlying liver steatosis, inflammation and fibrosis as well as for assessing drugs counteracting these effects.
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Affiliation(s)
- Manoj Kumar
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium.
| | - Burak Toprakhisar
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium
| | - Matthias Van Haele
- Translational Cell & Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Asier Antoranz
- Translational Cell & Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Ruben Boon
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium
| | - Francois Chesnais
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium
| | - Jonathan De Smedt
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium
| | - Tine Tricot
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium
| | - Teresa Izuel Idoype
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium
| | - Marco Canella
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium
| | - Pierre Tilliole
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium
| | - Jolan De Boeck
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium
| | - Manmohan Bajaj
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium
| | - Adrian Ranga
- Biomechanics, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Francesca Maria Bosisio
- Translational Cell & Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Tania Roskams
- Translational Cell & Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Leo A van Grunsven
- Liver Cell Biology Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Catherine M Verfaillie
- Stem Cell Institute, Department of Stem Cell and Developmental Biology, KU Leuven, Leuven, Belgium.
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21
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Vanderbeke L, Van Mol P, Van Herck Y, De Smet F, Humblet-Baron S, Martinod K, Antoranz A, Arijs I, Boeckx B, Bosisio FM, Casaer M, Dauwe D, De Wever W, Dooms C, Dreesen E, Emmaneel A, Filtjens J, Gouwy M, Gunst J, Hermans G, Jansen S, Lagrou K, Liston A, Lorent N, Meersseman P, Mercier T, Neyts J, Odent J, Panovska D, Penttila PA, Pollet E, Proost P, Qian J, Quintelier K, Raes J, Rex S, Saeys Y, Sprooten J, Tejpar S, Testelmans D, Thevissen K, Van Buyten T, Vandenhaute J, Van Gassen S, Velásquez Pereira LC, Vos R, Weynand B, Wilmer A, Yserbyt J, Garg AD, Matthys P, Wouters C, Lambrechts D, Wauters E, Wauters J. Monocyte-driven atypical cytokine storm and aberrant neutrophil activation as key mediators of COVID-19 disease severity. Nat Commun 2021; 12:4117. [PMID: 34226537 PMCID: PMC8257697 DOI: 10.1038/s41467-021-24360-w] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [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: 08/16/2020] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Epidemiological and clinical reports indicate that SARS-CoV-2 virulence hinges upon the triggering of an aberrant host immune response, more so than on direct virus-induced cellular damage. To elucidate the immunopathology underlying COVID-19 severity, we perform cytokine and multiplex immune profiling in COVID-19 patients. We show that hypercytokinemia in COVID-19 differs from the interferon-gamma-driven cytokine storm in macrophage activation syndrome, and is more pronounced in critical versus mild-moderate COVID-19. Systems modelling of cytokine levels paired with deep-immune profiling shows that classical monocytes drive this hyper-inflammatory phenotype and that a reduction in T-lymphocytes correlates with disease severity, with CD8+ cells being disproportionately affected. Antigen presenting machinery expression is also reduced in critical disease. Furthermore, we report that neutrophils contribute to disease severity and local tissue damage by amplification of hypercytokinemia and the formation of neutrophil extracellular traps. Together our findings suggest a myeloid-driven immunopathology, in which hyperactivated neutrophils and an ineffective adaptive immune system act as mediators of COVID-19 disease severity.
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Affiliation(s)
- L Vanderbeke
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - P Van Mol
- Laboratory of Translational Genetics, Department of Human Genetics, VIB-KU Leuven, Leuven, Belgium
| | - Y Van Herck
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - F De Smet
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - S Humblet-Baron
- Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - K Martinod
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - A Antoranz
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - I Arijs
- Laboratory of Translational Genetics, Department of Human Genetics, VIB-KU Leuven, Leuven, Belgium
| | - B Boeckx
- Laboratory of Translational Genetics, Department of Human Genetics, VIB-KU Leuven, Leuven, Belgium
| | - F M Bosisio
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - M Casaer
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - D Dauwe
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - W De Wever
- Radiology, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - C Dooms
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - E Dreesen
- Clinical Pharmacology and Pharmacotherapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - A Emmaneel
- Department of Applied Mathematics, Computer Science and Statistics, VIB-UGent Center for Inflammation Research, VIB-UGent, Gent, Belgium
| | - J Filtjens
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - M Gouwy
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - J Gunst
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - G Hermans
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - S Jansen
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, B Leuven, Belgium
| | - K Lagrou
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - A Liston
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - N Lorent
- Department of Pneumology, University Hospitals Leuven, Leuven, Belgium
| | - P Meersseman
- Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - T Mercier
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - J Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, B Leuven, Belgium
| | - J Odent
- Department of Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - D Panovska
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - P A Penttila
- KU Leuven Flow & Mass Cytometry Facility, KU Leuven, Leuven, Belgium
| | - E Pollet
- Department of Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - P Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - J Qian
- Laboratory of Translational Genetics, Department of Human Genetics, VIB-KU Leuven, Leuven, Belgium
| | - K Quintelier
- Department of Applied Mathematics, Computer Science and Statistics, VIB-UGent Center for Inflammation Research, VIB-UGent, Gent, Belgium
| | - J Raes
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, and VIB Center for Microbiology, Leuven, Belgium
| | - S Rex
- Anesthesiology and Algology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Y Saeys
- Department of Applied Mathematics, Computer Science and Statistics, VIB-UGent Center for Inflammation Research, VIB-UGent, Gent, Belgium
| | - J Sprooten
- Laboratory for Cell Stress & Immunity (CSI), Department of Cellular and Molecular Medicine (CMM), KU Leuven, Leuven, Belgium
| | - S Tejpar
- Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - D Testelmans
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - K Thevissen
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - T Van Buyten
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, B Leuven, Belgium
| | - J Vandenhaute
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - S Van Gassen
- Department of Applied Mathematics, Computer Science and Statistics, VIB-UGent Center for Inflammation Research, VIB-UGent, Gent, Belgium
| | - L C Velásquez Pereira
- Centre for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - R Vos
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - B Weynand
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - A Wilmer
- Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - J Yserbyt
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - A D Garg
- Laboratory for Cell Stress & Immunity (CSI), Department of Cellular and Molecular Medicine (CMM), KU Leuven, Leuven, Belgium
| | - P Matthys
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - C Wouters
- Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - D Lambrechts
- Laboratory of Translational Genetics, Department of Human Genetics, VIB-KU Leuven, Leuven, Belgium
| | - E Wauters
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium.
| | - J Wauters
- Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
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22
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Van Herck Y, Antoranz A, Andhari MD, Milli G, Bechter O, De Smet F, Bosisio FM. Multiplexed Immunohistochemistry and Digital Pathology as the Foundation for Next-Generation Pathology in Melanoma: Methodological Comparison and Future Clinical Applications. Front Oncol 2021; 11:636681. [PMID: 33854972 PMCID: PMC8040928 DOI: 10.3389/fonc.2021.636681] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
The state-of-the-art for melanoma treatment has recently witnessed an enormous revolution, evolving from a chemotherapeutic, "one-drug-for-all" approach, to a tailored molecular- and immunological-based approach with the potential to make personalized therapy a reality. Nevertheless, methods still have to improve a lot before these can reliably characterize all the tumoral features that make each patient unique. While the clinical introduction of next-generation sequencing has made it possible to match mutational profiles to specific targeted therapies, improving response rates to immunotherapy will similarly require a deep understanding of the immune microenvironment and the specific contribution of each component in a patient-specific way. Recent advancements in artificial intelligence and single-cell profiling of resected tumor samples are paving the way for this challenging task. In this review, we provide an overview of the state-of-the-art in artificial intelligence and multiplexed immunohistochemistry in pathology, and how these bear the potential to improve diagnostics and therapy matching in melanoma. A major asset of in-situ single-cell profiling methods is that these preserve the spatial distribution of the cells in the tissue, allowing researchers to not only determine the cellular composition of the tumoral microenvironment, but also study tissue sociology, making inferences about specific cell-cell interactions and visualizing distinctive cellular architectures - all features that have an impact on anti-tumoral response rates. Despite the many advantages, the introduction of these approaches requires the digitization of tissue slides and the development of standardized analysis pipelines which pose substantial challenges that need to be addressed before these can enter clinical routine.
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Affiliation(s)
| | - Asier Antoranz
- Laboratory for Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Madhavi Dipak Andhari
- Laboratory for Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Giorgia Milli
- Laboratory for Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | | | - Frederik De Smet
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Francesca Maria Bosisio
- Laboratory for Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
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23
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Pombo Antunes AR, Scheyltjens I, Lodi F, Messiaen J, Antoranz A, Duerinck J, Kancheva D, Martens L, De Vlaminck K, Van Hove H, Kjølner Hansen SS, Bosisio FM, Van der Borght K, De Vleeschouwer S, Sciot R, Bouwens L, Verfaillie M, Vandamme N, Vandenbroucke RE, De Wever O, Saeys Y, Guilliams M, Gysemans C, Neyns B, De Smet F, Lambrechts D, Van Ginderachter JA, Movahedi K. Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization. Nat Neurosci 2021; 24:595-610. [PMID: 33782623 DOI: 10.1038/s41593-020-00789-y] [Citation(s) in RCA: 254] [Impact Index Per Article: 84.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 12/22/2020] [Indexed: 01/08/2023]
Abstract
Glioblastomas are aggressive primary brain cancers that recur as therapy-resistant tumors. Myeloid cells control glioblastoma malignancy, but their dynamics during disease progression remain poorly understood. Here, we employed single-cell RNA sequencing and CITE-seq to map the glioblastoma immune landscape in mouse tumors and in patients with newly diagnosed disease or recurrence. This revealed a large and diverse myeloid compartment, with dendritic cell and macrophage populations that were conserved across species and dynamic across disease stages. Tumor-associated macrophages (TAMs) consisted of microglia- or monocyte-derived populations, with both exhibiting additional heterogeneity, including subsets with conserved lipid and hypoxic signatures. Microglia- and monocyte-derived TAMs were self-renewing populations that competed for space and could be depleted via CSF1R blockade. Microglia-derived TAMs were predominant in newly diagnosed tumors, but were outnumbered by monocyte-derived TAMs following recurrence, especially in hypoxic tumor environments. Our results unravel the glioblastoma myeloid landscape and provide a framework for future therapeutic interventions.
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Affiliation(s)
- Ana Rita Pombo Antunes
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Isabelle Scheyltjens
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Francesca Lodi
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.,VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
| | - Julie Messiaen
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Asier Antoranz
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | | | | | - Liesbet Martens
- Laboratory of Myeloid Cell Ontogeny and Functional Specialization, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Laboratory of Myeloid Cell Heterogeneity and Function, VIB Center for Inflammation Research, Ghent, Belgium
| | - Karen De Vlaminck
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hannah Van Hove
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Signe Schmidt Kjølner Hansen
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Francesca Maria Bosisio
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | | | - Steven De Vleeschouwer
- Department of Neurosurgery, UZ Leuven, Leuven, Belgium.,Laboratory for Experimental Neurosurgery and Neuroanatomy, Department of Neurosciences and Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Raf Sciot
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Luc Bouwens
- Cell Differentiation Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Michiel Verfaillie
- Department of Neurosurgery, Europe Hospitals Saint Elisabeth, Ukkel, Belgium
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Roosmarijn E Vandenbroucke
- VIB Center for Inflammation Research, Gent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Olivier De Wever
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.,Laboratory for Experimental Cancer Research, Ghent University, Ghent, Belgium
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Martin Guilliams
- Laboratory of Myeloid Cell Ontogeny and Functional Specialization, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Conny Gysemans
- Clinical and Experimental Endocrinology (CEE), KU Leuven, Leuven, Belgium
| | - Bart Neyns
- Department of Medical Oncology, UZ Brussels, Brussels, Belgium
| | - Frederik De Smet
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.,VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
| | - Jo A Van Ginderachter
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kiavash Movahedi
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium. .,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium.
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24
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Gadeyne L, Van Herck Y, Milli G, Atak ZK, Bolognesi MM, Wouters J, Marcelis L, Minia A, Pliaka V, Roznac J, Alexopoulos LG, Cattoretti G, Bechter O, Oord JVD, De Smet F, Antoranz A, Bosisio FM. A Multi-Omics Analysis of Metastatic Melanoma Identifies a Germinal Center-Like Tumor Microenvironment in HLA-DR-Positive Tumor Areas. Front Oncol 2021; 11:636057. [PMID: 33842341 PMCID: PMC8029980 DOI: 10.3389/fonc.2021.636057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/30/2020] [Accepted: 02/26/2021] [Indexed: 12/20/2022] Open
Abstract
The emergence of immune checkpoint inhibitors has dramatically changed the therapeutic landscape for patients with advanced melanoma. However, relatively low response rates and a high incidence of severe immune-related adverse events have prompted the search for predictive biomarkers. A positive predictive value has been attributed to the aberrant expression of Human Leukocyte Antigen-DR (HLA-DR) by melanoma cells, but it remains unknown why this is the case. In this study, we have examined the microenvironment of HLA-DR positive metastatic melanoma samples using a multi-omics approach. First, using spatial, single-cell mapping by multiplexed immunohistochemistry, we found that the microenvironment of HLA-DR positive melanoma regions was enriched by professional antigen presenting cells, including classical dendritic cells and macrophages, while a more general cytotoxic T cell exhaustion phenotype was present in these regions. In parallel, transcriptomic analysis on micro dissected tissue from HLA-DR positive and HLA-DR negative areas showed increased IFNγ signaling, enhanced leukocyte adhesion and mononuclear cell proliferation in HLA-DR positive areas. Finally, multiplexed cytokine profiling identified an increased expression of germinal center cytokines CXCL12, CXCL13 and CCL19 in HLA-DR positive metastatic lesions, which, together with IFNγ and IL4 could serve as biomarkers to discriminate tumor samples containing HLA-DR overexpressing tumor cells from HLA-DR negative samples. Overall, this suggests that HLA-DR positive areas in melanoma attract the anti-tumor immune cell infiltration by creating a dystrophic germinal center-like microenvironment where an enhanced antigen presentation leads to an exhausted microenvironment, nevertheless representing a fertile ground for a better efficacy of anti-PD-1 inhibitors due to simultaneous higher levels of PD-1 in the immune cells and PD-L1 in the HLA-DR positive melanoma cells.
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Affiliation(s)
| | - Yannick Van Herck
- Department of General Medical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Giorgia Milli
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | | | | | - Jasper Wouters
- Laboratory of Computational Biology, KU Leuven, Leuven, Belgium
| | - Lukas Marcelis
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | | | | | - Jan Roznac
- ProtATonce Ltd, Athens, Greece.,Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Leonidas G Alexopoulos
- ProtATonce Ltd, Athens, Greece.,Biomedical Systems Laboratory, Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece
| | - Giorgio Cattoretti
- Pathology, Department of Medicine & Surgery, University of Milano-Bicocca, Milan, Italy
| | - Oliver Bechter
- Department of General Medical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Joost Van Den Oord
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Frederik De Smet
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Asier Antoranz
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Francesca Maria Bosisio
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
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25
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Penttilä PA, Van Gassen S, Panovska D, Vanderbeke L, Van Herck Y, Quintelier K, Emmaneel A, Filtjens J, Malengier-Devlies B, Ahmadzadeh K, Van Mol P, Borràs DM, Antoranz A, Bosisio FM, Wauters E, Martinod K, Matthys P, Saeys Y, Garg AD, Wauters J, De Smet F. High dimensional profiling identifies specific immune types along the recovery trajectories of critically ill COVID19 patients. Cell Mol Life Sci 2021; 78:3987-4002. [PMID: 33715015 PMCID: PMC7955698 DOI: 10.1007/s00018-021-03808-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 10/28/2020] [Revised: 01/27/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022]
Abstract
The COVID-19 pandemic poses a major burden on healthcare and economic systems across the globe. Even though a majority of the population develops only minor symptoms upon SARS-CoV-2 infection, a significant number are hospitalized at intensive care units (ICU) requiring critical care. While insights into the early stages of the disease are rapidly expanding, the dynamic immunological processes occurring in critically ill patients throughout their recovery at ICU are far less understood. Here, we have analysed whole blood samples serially collected from 40 surviving COVID-19 patients throughout their recovery in ICU using high-dimensional cytometry by time-of-flight (CyTOF) and cytokine multiplexing. Based on the neutrophil-to-lymphocyte ratio (NLR), we defined four sequential immunotypes during recovery that correlated to various clinical parameters, including the level of respiratory support at concomitant sampling times. We identified classical monocytes as the first immune cell type to recover by restoration of HLA-DR-positivity and the reduction of immunosuppressive CD163 + monocytes, followed by the recovery of CD8 + and CD4 + T cell and non-classical monocyte populations. The identified immunotypes also correlated to aberrant cytokine and acute-phase reactant levels. Finally, integrative analysis of cytokines and immune cell profiles showed a shift from an initially dysregulated immune response to a more coordinated immunogenic interplay, highlighting the importance of longitudinal sampling to understand the pathophysiology underlying recovery from severe COVID-19.
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Affiliation(s)
- P A Penttilä
- KU Leuven Flow and Mass Cytometry Facility, KU Leuven, Leuven, Belgium
| | - S Van Gassen
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - D Panovska
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - L Vanderbeke
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Y Van Herck
- Laboratory of Experimental Oncology, Department of Oncology,, KU Leuven, Leuven, Belgium
| | - K Quintelier
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - A Emmaneel
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - J Filtjens
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - B Malengier-Devlies
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - K Ahmadzadeh
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - P Van Mol
- Laboratory of Translational Genetics, Department of Human Genetics, VIB-KU Leuven, Leuven, Belgium
| | - D M Borràs
- Laboratory for Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine (CMM), KU Leuven, Leuven, Belgium
| | - A Antoranz
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - F M Bosisio
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - E Wauters
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - K Martinod
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - P Matthys
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Y Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - A D Garg
- Laboratory for Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine (CMM), KU Leuven, Leuven, Belgium
| | - J Wauters
- Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - F De Smet
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium.
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26
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Tzani A, Konstantopoulos P, Doulamis I, Liakea A, Minia A, Antoranz A, Korou LM, Kavantzas N, Alexopoulos L, Stamatelopoulos K, Iliopoulos D, Perrea D. Chios mastic gum inhibits diet-induced non-alcoholic steatohepatitis in mice via activation of PPAR-α. Atherosclerosis 2020. [DOI: 10.1016/j.atherosclerosis.2020.10.148] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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27
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Szumera-Ciećkiewicz A, Bosisio F, Teterycz P, Antoranz A, Delogu F, Koljenović S, van de Wiel BA, Blokx W, van Kempen LC, Rutkowski P, Christopher van Akkooi A, Cook M, Massi D. SOX10 is as specific as S100 protein in detecting metastases of melanoma in lymph nodes and is recommended for sentinel lymph node assessment. Eur J Cancer 2020; 137:175-182. [PMID: 32781392 DOI: 10.1016/j.ejca.2020.06.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/22/2020] [Accepted: 06/29/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Sentinel lymph node (SLN) biopsy remains crucial for melanoma staging. The European Organisation for Research and Treatment of Cancer Melanoma Group recommends performing immunohistochemical stainings for reproducible identification of melanoma metastases. S100 protein (pS100) is a commonly used melanocytic antigen because of its high sensitivity in spite of relatively low specificity. SRY-related HMG-box 10 protein (SOX10) is a transcription factor characterising neural crest-derived cells. It is uniformly expressed mostly in the nuclei of melanocytes, neural, and myoepithelial cells. Pathologists sometimes prefer SOX10 as a melanoma marker, but it has not yet been investigated on a large-scale to confirm that it is reliable and recommendable for routine SLN evaluation. METHODS Four hundred one treatment-naïve lymph node (LN) metastatic melanomas were included in high-density tissue microarrays and were assessed for the presence of SOX10 and pS100 by immunohistochemistry. The slides were digitalised, shared and evaluated by a panel of experienced melanoma pathologists. RESULTS The vast majority of melanomas were double-positive for pS100 and SOX10 (93.2%); a small percentage of the cases (3.9%) were double-negative melanomas. Discordance between the two markers was observed: 1.9% pS100(-)/SOX10(+) and 0.75% pS100(+)/SOX10(-). SOX10 was not expressed by immune cell types in the LN, resulting in a less controversial interpretation of the staining. CONCLUSIONS SOX10 is as equally specific as pS100 for the detection of melanoma metastases in LNs. The interpretation of SOX10 staining is highly reproducible among different centres and different pathologists because of the absence of staining of immune cells.
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Affiliation(s)
- Anna Szumera-Ciećkiewicz
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland; Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine Warsaw, Poland.
| | - Francesca Bosisio
- Laboratory of Translational Cell and Tissue Research and Pathology Department, KU Leuven and UZ Leuven, Leuven, Belgium
| | - Paweł Teterycz
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Asier Antoranz
- Laboratory of Translational Cell and Tissue Research and Pathology Department, KU Leuven and UZ Leuven, Leuven, Belgium
| | - Francesco Delogu
- Department of Health Sciences, Clinical Pharmacology and Oncology Unit, University of Florence, Florence, Italy
| | - Senada Koljenović
- Department of Pathology, Erasmus MC, University Medical Centre Rotterdam, the Netherlands
| | - Bart A van de Wiel
- Department of Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Willeke Blokx
- Department of Pathology, Division of Laboratories, Pharmacy and Biomedical Genetics, University Medical Center, Utrecht, the Netherlands
| | - Léon C van Kempen
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | | | - Martin Cook
- Histopathology, Royal Surrey County Hospital, Guildford, UK
| | - Daniela Massi
- Section of Pathological Anatomy, Department of Health Sciences, University of Florence, Florence, Italy
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28
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Qian J, Olbrecht S, Boeckx B, Vos H, Laoui D, Etlioglu E, Wauters E, Pomella V, Verbandt S, Busschaert P, Bassez A, Franken A, Bempt MV, Xiong J, Weynand B, van Herck Y, Antoranz A, Bosisio FM, Thienpont B, Floris G, Vergote I, Smeets A, Tejpar S, Lambrechts D. A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling. Cell Res 2020; 30:745-762. [PMID: 32561858 PMCID: PMC7608385 DOI: 10.1038/s41422-020-0355-0] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
The stromal compartment of the tumor microenvironment consists of a heterogeneous set of tissue-resident and tumor-infiltrating cells, which are profoundly moulded by cancer cells. An outstanding question is to what extent this heterogeneity is similar between cancers affecting different organs. Here, we profile 233,591 single cells from patients with lung, colorectal, ovary and breast cancer (n = 36) and construct a pan-cancer blueprint of stromal cell heterogeneity using different single-cell RNA and protein-based technologies. We identify 68 stromal cell populations, of which 46 are shared between cancer types and 22 are unique. We also characterise each population phenotypically by highlighting its marker genes, transcription factors, metabolic activities and tissue-specific expression differences. Resident cell types are characterised by substantial tissue specificity, while tumor-infiltrating cell types are largely shared across cancer types. Finally, by applying the blueprint to melanoma tumors treated with checkpoint immunotherapy and identifying a naïve CD4+ T-cell phenotype predictive of response to checkpoint immunotherapy, we illustrate how it can serve as a guide to interpret scRNA-seq data. In conclusion, by providing a comprehensive blueprint through an interactive web server, we generate the first panoramic view on the shared complexity of stromal cells in different cancers.
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Affiliation(s)
- Junbin Qian
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Siel Olbrecht
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Bram Boeckx
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Hanne Vos
- Department of Oncology, KU Leuven, Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Damya Laoui
- Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium.,Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
| | - Emre Etlioglu
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Els Wauters
- Respiratory Oncology Unit (Pneumology) and Leuven Lung Cancer Group, University Hospital KU Leuven, Leuven, Belgium.,Laboratory of Pneumology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Valentina Pomella
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sara Verbandt
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Pieter Busschaert
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Ayse Bassez
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Amelie Franken
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marlies Vanden Bempt
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jieyi Xiong
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | | | - Asier Antoranz
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | - Francesca Maria Bosisio
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Giuseppe Floris
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | - Ignace Vergote
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Ann Smeets
- Department of Oncology, KU Leuven, Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Sabine Tejpar
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium. .,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
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Berben L, Wildiers H, Marcelis L, Antoranz A, Bosisio F, Hatse S, Floris G. Computerised scoring protocol for identification and quantification of different immune cell populations in breast tumour regions by the use of QuPath software. Histopathology 2020; 77:79-91. [PMID: 32281132 DOI: 10.1111/his.14108] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/18/2020] [Indexed: 01/06/2023]
Abstract
AIMS As important prognostic and predictive information can be obtained from the composition, functionality and spatial arrangement of different immune cell subtypes, this study aims at characterizing the immune infiltrate in breast tumours. METHODS AND RESULTS Tumour-infiltrating lymphocytes (TILs) in 62 patients with luminal B-like breast cancer were characterised by immunohistochemical staining with standard markers, and were subsequently classified and quantified by the use of QuPath software. In different delineated tumour regions, the proportion and density of CD3+ , CD4+ , CD5+ , CD8+ , CD20+ and FOXP3+ cells were assessed. The results of the software analysis were compared with those of manual counting for CD8 and CD20 staining. The QuPath scoring protocol slightly overestimated positive, negative and total lymphocyte counts and density, while minimally underestimating the proportion of positively stained lymphocytes. However, for density and proportion, no real differences from manual counting were observed. For all markers, the density of positively stained immune cells was higher in the invasive front than in the tumour centre, pointing to an accumulation of immune cells near the tumour boundaries. When we looked at the proportion of immunohistochemically positive immune cells, we observed enrichment of CD5 (P = 0.025) and CD20 (P < 0.001) at the periphery, and FOXP3 enrichment in the centre (P < 0.001). CONCLUSION The QuPath scoring protocol can adequately identify positively stained immune cells in breast tumours, and allows the evaluation of differences in immune cell proportion and density within different tumour regions. The entire tumour section can be quantitatively assessed quite rapidly, which is a major advantage over manual counting.
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Affiliation(s)
- Lieze Berben
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Hans Wildiers
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium.,Department of General Medical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Lukas Marcelis
- Department of Pathology, Laboratory of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Asier Antoranz
- Department of Pathology, Laboratory of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Francesca Bosisio
- Department of Pathology, Laboratory of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium.,Department of Pathology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Sigrid Hatse
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Giuseppe Floris
- Department of Pathology, Laboratory of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium.,Department of Pathology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
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30
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Bosisio FM, Antoranz A, van Herck Y, Bolognesi MM, Marcelis L, Chinello C, Wouters J, Magni F, Alexopoulos L, Stas M, Boecxstaens V, Bechter O, Cattoretti G, van den Oord J. Functional heterogeneity of lymphocytic patterns in primary melanoma dissected through single-cell multiplexing. eLife 2020; 9:53008. [PMID: 32057296 PMCID: PMC7053517 DOI: 10.7554/elife.53008] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/14/2020] [Indexed: 01/08/2023] Open
Abstract
In melanoma, the lymphocytic infiltrate is a prognostic parameter classified morphologically into 'brisk', 'non-brisk' and 'absent' entailing a functional association that has never been proved. Recently, it has been shown that lymphocytic populations can be very heterogeneous, and that anti-PD-1 immunotherapy supports activated T cells. Here, we characterize the immune landscape in primary melanoma by high-dimensional single-cell multiplex analysis in tissue sections (MILAN technique) followed by image analysis, RT-PCR and shotgun proteomics. We observed that the brisk and non-brisk patterns are heterogeneous functional categories that can be further sub-classified into active, transitional or exhausted. The classification of primary melanomas based on the functional paradigm also shows correlation with spontaneous regression, and an improved prognostic value when compared to that of the brisk classification. Finally, the main inflammatory cell subpopulations that are present in the microenvironment associated with activation and exhaustion and their spatial relationships are described using neighbourhood analysis.
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Affiliation(s)
- Francesca Maria Bosisio
- Laboratory of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium.,Pathology, Department of Medicine & Surgery, Università degli studi di Milano-Bicocca, Milan, Italy
| | - Asier Antoranz
- ProtATonce Ltd, Athens, Greece.,National Technical University of Athens, Athens, Greece
| | | | | | - Lukas Marcelis
- Laboratory of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Clizia Chinello
- Pathology, Department of Medicine & Surgery, Università degli studi di Milano-Bicocca, Milan, Italy
| | - Jasper Wouters
- Laboratory of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Fulvio Magni
- Pathology, Department of Medicine & Surgery, Università degli studi di Milano-Bicocca, Milan, Italy
| | - Leonidas Alexopoulos
- ProtATonce Ltd, Athens, Greece.,National Technical University of Athens, Athens, Greece
| | | | | | - Oliver Bechter
- Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Giorgio Cattoretti
- Pathology, Department of Medicine & Surgery, Università degli studi di Milano-Bicocca, Milan, Italy
| | - Joost van den Oord
- Laboratory of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
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31
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Tajti F, Kuppe C, Antoranz A, Ibrahim MM, Kim H, Ceccarelli F, Holland CH, Olauson H, Floege J, Alexopoulos LG, Kramann R, Saez-Rodriguez J. A Functional Landscape of CKD Entities From Public Transcriptomic Data. Kidney Int Rep 2019; 5:211-224. [PMID: 32043035 PMCID: PMC7000845 DOI: 10.1016/j.ekir.2019.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 06/07/2019] [Revised: 10/09/2019] [Accepted: 11/04/2019] [Indexed: 12/18/2022] Open
Abstract
Introduction To develop effective therapies and identify novel early biomarkers for chronic kidney disease, an understanding of the molecular mechanisms orchestrating it is essential. We here set out to understand how differences in chronic kidney disease (CKD) origin are reflected in gene expression. To this end, we integrated publicly available human glomerular microarray gene expression data for 9 kidney disease entities that account for most of CKD worldwide. Our primary goal was to demonstrate the possibilities and potential on data analysis and integration to the nephrology community. Methods We integrated data from 5 publicly available studies and compared glomerular gene expression profiles of disease with that of controls from nontumor parts of kidney cancer nephrectomy tissues. A major challenge was the integration of the data from different sources, platforms, and conditions that we mitigated with a bespoke stringent procedure. Results We performed a global transcriptome-based delineation of different kidney disease entities, obtaining a transcriptomic diffusion map of their similarities and differences based on the genes that acquire a consistent differential expression between each kidney disease entity and nephrectomy tissue. We derived functional insights by inferring the activity of signaling pathways and transcription factors from the collected gene expression data and identified potential drug candidates based on expression signature matching. We validated representative findings by immunostaining in human kidney biopsies indicating, for example, that the transcription factor FOXM1 is significantly and specifically expressed in parietal epithelial cells in rapidly progressive glomerulonephritis (RPGN) whereas not expressed in control kidney tissue. Furthermore, we found drug candidates by matching the signature on expression of drugs to that of the CKD entities, in particular, the Food and Drug Administration-approved drug nilotinib. Conclusion These results provide a foundation to comprehend the specific molecular mechanisms underlying different kidney disease entities that can pave the way to identify biomarkers and potential therapeutic targets. To facilitate further use, we provide our results as a free interactive Web application: https://saezlab.shinyapps.io/ckd_landscape/. However, because of the limitations of the data and the difficulties in its integration, any specific result should be considered with caution. Indeed, we consider this study rather an illustration of the value of functional genomics and integration of existing data.
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Affiliation(s)
- Ferenc Tajti
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Christoph Kuppe
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Asier Antoranz
- Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece.,Department of Testing Services, ProtATonce Ltd., Athens, Greece
| | - Mahmoud M Ibrahim
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Hyojin Kim
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany
| | - Francesco Ceccarelli
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany
| | - Christian H Holland
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Institute for Computational Biomedicine, Heidelberg University, Bioquant, Heidelberg, Germany
| | - Hannes Olauson
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Jürgen Floege
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Leonidas G Alexopoulos
- Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece.,Department of Testing Services, ProtATonce Ltd., Athens, Greece
| | - Rafael Kramann
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Institute for Computational Biomedicine, Heidelberg University, Bioquant, Heidelberg, Germany
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32
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Tajti F, Kuppe C, Antoranz A, Ibrahim M, Kim H, Ceccarelli F, Holland C, Olauson H, Floege J, Alexopoulos LG, Kramann R, Saez-Rodriguez J. SP321DISSECTING THE MOLECULAR DIFFERENCES BETWEEN CHRONIC KIDNEY DISEASE SUBTYPES FROM TRANSCRIPTOMICS DATA. Nephrol Dial Transplant 2019. [DOI: 10.1093/ndt/gfz103.sp321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | | | | | - Hyojin Kim
- Heidelberg University, Heidelberg, Germany
| | | | | | | | | | | | - Rafael Kramann
- Erasmus University Medical Center, Rotterdam, Netherlands
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Rožanc J, Sakellaropoulos T, Antoranz A, Guttà C, Podder B, Vetma V, Rufo N, Agostinis P, Pliaka V, Sauter T, Kulms D, Rehm M, Alexopoulos LG. Phosphoprotein patterns predict trametinib responsiveness and optimal trametinib sensitisation strategies in melanoma. Cell Death Differ 2018; 26:1365-1378. [PMID: 30323272 DOI: 10.1038/s41418-018-0210-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/19/2018] [Accepted: 09/10/2018] [Indexed: 01/02/2023] Open
Abstract
Malignant melanoma is a highly aggressive form of skin cancer responsible for the majority of skin cancer-related deaths. Recent insight into the heterogeneous nature of melanoma suggests more personalised treatments may be necessary to overcome drug resistance and improve patient care. To this end, reliable molecular signatures that can accurately predict treatment responsiveness need to be identified. In this study, we applied multiplex phosphoproteomic profiling across a panel of 24 melanoma cell lines with different disease-relevant mutations, to predict responsiveness to MEK inhibitor trametinib. Supported by multivariate statistical analysis and multidimensional pattern recognition algorithms, the responsiveness of individual cell lines to trametinib could be predicted with high accuracy (83% correct predictions), independent of mutation status. We also successfully employed this approach to case specifically predict whether individual melanoma cell lines could be sensitised to trametinib. Our predictions identified that combining MEK inhibition with selective targeting of c-JUN and/or FAK, using siRNA-based depletion or pharmacological inhibitors, sensitised resistant cell lines and significantly enhanced treatment efficacy. Our study indicates that multiplex proteomic analyses coupled with pattern recognition approaches could assist in personalising trametinib-based treatment decisions in the future.
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Affiliation(s)
- Jan Rožanc
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg.,ProtATonce Ltd, Science Park Demokritos, Athens, Greece
| | | | - Asier Antoranz
- ProtATonce Ltd, Science Park Demokritos, Athens, Greece.,Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece
| | - Cristiano Guttà
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Biswajit Podder
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Vesna Vetma
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Nicole Rufo
- Laboratory for Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Laboratory for Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Vaia Pliaka
- ProtATonce Ltd, Science Park Demokritos, Athens, Greece
| | - Thomas Sauter
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Dagmar Kulms
- Experimental Dermatology, Department of Dermatology, Technical University Dresden, Dresden, Germany.,Center for Regenerative Therapies, Technical University Dresden, Dresden, Germany
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany.,Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.,Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leonidas G Alexopoulos
- ProtATonce Ltd, Science Park Demokritos, Athens, Greece. .,Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece.
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Doulamis I, Konstantopoulos P, Tzani A, Antoranz A, Daskalopoulou A, Minia A, Charalampopoulos A, Perrea D, Alexopoulos L, Menenakos E. Tumor necrosis factor (TNF) superfamily members 10 and 12 are associated with the metabolic health status of morbid obese patients. Atherosclerosis 2018. [DOI: 10.1016/j.atherosclerosis.2018.06.210] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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35
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Tzani A, Daskalopoulou A, Doulamis I, Konstantopoulos P, Antoranz A, Minia A, Marinos G, Alexopoulos L, Perrea D. PPAR-alpha independent anti-inflammatory effects of fenofibrate in a transgenic model of atherosclerosis. Atherosclerosis 2018. [DOI: 10.1016/j.atherosclerosis.2018.06.333] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Doulamis I, Konstantopoulos P, Tzani A, Antoranz A, Daskalopoulou A, Minia A, Charalampopoulos A, Perrea D, Alexopoulos L, Menenakos E. Proteomic discovery of biomarkers associated with morbid obesity in patients undergoing bariatric surgery. Atherosclerosis 2018. [DOI: 10.1016/j.atherosclerosis.2018.06.613] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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Doulamis IP, Samanidis G, Tzani A, Antoranz A, Gkogkos A, Konstantopoulos P, Pliaka V, Minia A, Alexopoulos LG, Perrea DN, Perreas K. Proteomic profile of patients with atrial fibrillation undergoing cardiac surgery†. Interact Cardiovasc Thorac Surg 2018; 28:94-101. [PMID: 29992263 DOI: 10.1093/icvts/ivy210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 06/01/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Ilias P Doulamis
- Laboratory for Experimental Surgery and Surgical Research “N.S Christeas”, Athens Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - George Samanidis
- First Department of Adult Cardiac Surgery, Onassis Cardiac Surgery Center, Athens, Greece
| | - Aspasia Tzani
- Laboratory for Experimental Surgery and Surgical Research “N.S Christeas”, Athens Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Anastasios Gkogkos
- Laboratory for Experimental Surgery and Surgical Research “N.S Christeas”, Athens Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Konstantopoulos
- Laboratory for Experimental Surgery and Surgical Research “N.S Christeas”, Athens Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | | | - Leonidas G Alexopoulos
- Protatonce Ltd, Athens, Greece
- Department of Mechanical Engineering, Laboratory for Experimental Surgery and Surgical Research “N.S Christeas”,National Technical University of Athens, Athens, Greece
| | - Despina N Perrea
- Laboratory for Experimental Surgery and Surgical Research “N.S Christeas”, Athens Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Perreas
- First Department of Adult Cardiac Surgery, Onassis Cardiac Surgery Center, Athens, Greece
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38
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Fotis C, Antoranz A, Hatziavramidis D, Sakellaropoulos T, Alexopoulos LG. Network-based technologies for early drug discovery. Drug Discov Today 2017; 23:626-635. [PMID: 29294361 DOI: 10.1016/j.drudis.2017.12.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [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: 06/09/2017] [Revised: 11/22/2017] [Accepted: 12/20/2017] [Indexed: 02/07/2023]
Abstract
Although the traditional drug discovery approach has led to the development of many successful drugs, the attrition rates remain high. Recent advances in systems-oriented approaches (systems-biology and/or pharmacology) and 'omics technologies has led to a plethora of new computational tools that promise to enable a more-informed and successful implementation of the reductionist, one drug for one target for one disease, approach. These tools, based on biomolecular pathways and interaction networks, offer a systematic approach to unravel the mechanism(s) of a disease and link them to the chemical space and network footprint of a drug. Drug discovery can draw upon this holistic approach to identify the most-promising targets and compounds during the early phases of development.
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Affiliation(s)
- Chris Fotis
- National Technical University of Athens, Athens, Greece
| | - Asier Antoranz
- National Technical University of Athens, Athens, Greece; Protavio Ltd, Cambridge, UK
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39
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Tzani A, Doulamis IP, Antoranz A, Samanidis G, Pliaka V, Gkogkos A, Konstantopoulos P, Sakellaropoulos T, Alexopoulos L, Perreas KG, Perrea DN. PROTEOMICS DISCOVERY OF BIOMARKERS FOR ATRIAL FIBRILLATION IN PATIENTS WITH CARDIOVASCULAR DISEASE. J Am Coll Cardiol 2017. [DOI: 10.1016/s0735-1097(17)33858-5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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