1
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Verhoeft K, Cools J. The unexpected and unresolved roles of PDGFRA and PDGFRB in T-cell acute lymphoblastic leukemia. Haematologica 2024. [PMID: 38385300 DOI: 10.3324/haematol.2023.284524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Not available.
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Affiliation(s)
- Krista Verhoeft
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, Leuven
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, Leuven.
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2
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Pollenus E, Possemiers H, Knoops S, Prenen F, Vandermosten L, Thienpont C, Abdurahiman S, Demeyer S, Cools J, Matteoli G, Vanoirbeek JAJ, Vande Velde G, Van den Steen PE. Single cell RNA sequencing reveals endothelial cell killing and resolution pathways in experimental malaria-associated acute respiratory distress syndrome. PLoS Pathog 2024; 20:e1011929. [PMID: 38236930 PMCID: PMC10826972 DOI: 10.1371/journal.ppat.1011929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/30/2024] [Accepted: 12/29/2023] [Indexed: 01/31/2024] Open
Abstract
Plasmodium parasites cause malaria, a global health disease that is responsible for more than 200 million clinical cases and 600 000 deaths each year. Most deaths are caused by various complications, including malaria-associated acute respiratory distress syndrome (MA-ARDS). Despite the very rapid and efficient killing of parasites with antimalarial drugs, 15% of patients with complicated malaria succumb. This stresses the importance of investigating resolution mechanisms that are involved in the recovery from these complications once the parasite is killed. To study the resolution of MA-ARDS, P. berghei NK65-infected C57BL/6 mice were treated with antimalarial drugs after onset of symptoms, resulting in 80% survival. Micro-computed tomography revealed alterations of the lungs upon infection, with an increase in total and non-aerated lung volume due to edema. Whole body plethysmography confirmed a drastically altered lung ventilation, which was restored during resolution. Single-cell RNA sequencing indicated an increased inflammatory state in the lungs upon infection, which was accompanied by a drastic decrease in endothelial cells, consistent with CD8+ T cell-mediated killing. During resolution, anti-inflammatory pathways were upregulated and proliferation of endothelial cells was observed. MultiNicheNet interactome analysis identified important changes in the ligand-receptor interactions during disease resolution that warrant further exploration in order to develop new therapeutic strategies. In conclusion, our study provides insights in pro-resolving pathways that limit inflammation and promote endothelial cell proliferation in experimental MA-ARDS. This information may be useful for the design of adjunctive treatments to enhance resolution after Plasmodium parasite killing by antimalarial drugs.
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Affiliation(s)
- Emilie Pollenus
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Hendrik Possemiers
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Sofie Knoops
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Fran Prenen
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Leen Vandermosten
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Chloë Thienpont
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Saeed Abdurahiman
- Laboratory of Mucosal Immunology, Translational Research in Gastro-Intestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Laboratory of Molecular Biology of Leukemia, Department of Human Genetics, VIB—KU Leuven, Leuven, Belgium
| | - Jan Cools
- Laboratory of Molecular Biology of Leukemia, Department of Human Genetics, VIB—KU Leuven, Leuven, Belgium
| | - Gianluca Matteoli
- Laboratory of Mucosal Immunology, Translational Research in Gastro-Intestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Jeroen A. J. Vanoirbeek
- Centre for Environment and Health, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Greetje Vande Velde
- Biomedical MRI, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Philippe E. Van den Steen
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology & Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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3
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Vermeulen S, Cools J, Staes J, Van Passel S. A review of economic assessments of drought risk reduction approaches in agriculture. J Environ Manage 2023; 345:118909. [PMID: 37657290 DOI: 10.1016/j.jenvman.2023.118909] [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] [Received: 03/17/2023] [Revised: 08/21/2023] [Accepted: 08/27/2023] [Indexed: 09/03/2023]
Abstract
Due to climate change, the frequency and intensity of droughts are expected to increase. To improve resilience to droughts, proactive drought management is essential. Economic assessments are typically included to decide on the drought risk-reducing investments to make. The choice of both methods and scope of economic assessments influences the outcome, and thus the investment choice. This paper aims to identify how comprehensively economic assessments are applied in practice. Through a systematic literature review, 14 actual economic assessments are identified and their methods are evaluated based on seven criteria for economic assessments as derived from the United Nations Framework Convention on Climate Change (UNFCCC). The results show that in practice, economic assessments rarely address all criteria. Applying a limited number of criteria reduces the scope and narrows the approach, possibly leading to the underestimation of drought risk reduction approaches' related benefits. Applying the seven criteria in practice will improve the results of economic assessments of drought risk reduction measures, allowing for optimal investment selection. Based on the different criteria, a Framework for Economic Assessments of Drought Risk-Reducing Applications (FEADRRA) is proposed. Applying the criteria of the framework can support decision-makers in drought risk management and in carrying out the most fitting drought interventions.
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Affiliation(s)
- Sam Vermeulen
- University of Antwerp, Department of Engineering Management, Prinsstraat 13, 2000 Antwerp, Belgium.
| | - Jan Cools
- University of Antwerp, Institute of Environment and Sustainable Development, Prinsstraat 13, 2000 Antwerp, Belgium
| | - Jan Staes
- University of Antwerp, Ecosystem Management Research Group, Universiteitsplein 1C, 2610 Wilrijk, Belgium
| | - Steven Van Passel
- University of Antwerp, Department of Engineering Management, Prinsstraat 13, 2000 Antwerp, Belgium; VCCM, Flanders Make | Nanolab Centre of Excellence, Prinsstraat 13, 2000, Antwerp, Belgium
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4
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Abstract
The CRISPR genome editing technology has revolutionized the way gene function is studied. Genome editing can be achieved in single genes or for thousands of genes simultaneously in sensitive genetic screens. While conventional genetic screens are limited to bulk measurements of cell behavior, recent developments in single-cell technologies make it possible to combine CRISPR screening with single-cell profiling. In this way, cell behavior and gene expression can be monitored simultaneously, with the additional possibility of including data on chromatin accessibility and protein levels. Moreover, the availability of various Cas proteins leading to inactivation, activation, or other effects on gene function further broadens the scope of such screens. The integration of single-cell multi-omics approaches with CRISPR screening open the path to high-content information on the impact of genetic perturbations at single-cell resolution. Current limitations in cell throughput and data density need to be taken into consideration, but new technologies are rapidly evolving and are likely to easily overcome these limitations. In this review, we discuss the use of bulk CRISPR screening in hematology research, as well as the emergence of single-cell CRISPR screening and its added value to the field.
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Affiliation(s)
- Sarah Meyers
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium.
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5
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Vandersmissen C, Prieto C, Gielen O, Jacobs K, Nittner D, Maertens J, Segers H, Cools J. Combination therapy of a PSEN1-selective γ-secretase inhibitor with dexamethasone and an XPO1 inhibitor to target T-cell acute lymphoblastic leukemia. Haematologica 2023; 108:2507-2512. [PMID: 36700404 PMCID: PMC10483366 DOI: 10.3324/haematol.2022.282144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
Not available.
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Affiliation(s)
- Charlien Vandersmissen
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer biology, VIB, Leuven, Belgium; Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven
| | - Cristina Prieto
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer biology, VIB, Leuven, Belgium; Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven
| | - Olga Gielen
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer biology, VIB, Leuven, Belgium; Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven
| | - Kris Jacobs
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer biology, VIB, Leuven, Belgium; Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven
| | | | - Johan Maertens
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium; Department of Hematology, UZ Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven
| | - Heidi Segers
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium; Department of Pediatric Oncology, UZ Leuven, Leuven
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer biology, VIB, Leuven, Belgium; Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven.
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6
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Veloso A, Cools J. Targeting STAT5B in T-cell acute lymphoblastic leukemia. Blood 2023; 142:215-217. [PMID: 37471110 DOI: 10.1182/blood.2023020639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
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7
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Altea-Manzano P, Doglioni G, Liu Y, Cuadros AM, Nolan E, Fernández-García J, Wu Q, Planque M, Laue KJ, Cidre-Aranaz F, Liu XZ, Marin-Bejar O, Van Elsen J, Vermeire I, Broekaert D, Demeyer S, Spotbeen X, Idkowiak J, Montagne A, Demicco M, Alkan HF, Rabas N, Riera-Domingo C, Richard F, Geukens T, De Schepper M, Leduc S, Hatse S, Lambrechts Y, Kay EJ, Lilla S, Alekseenko A, Geldhof V, Boeckx B, de la Calle Arregui C, Floris G, Swinnen JV, Marine JC, Lambrechts D, Pelechano V, Mazzone M, Zanivan S, Cools J, Wildiers H, Baud V, Grünewald TGP, Ben-David U, Desmedt C, Malanchi I, Fendt SM. A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation resulting in pro-metastatic NF-κB signaling. Nat Cancer 2023; 4:344-364. [PMID: 36732635 PMCID: PMC7615234 DOI: 10.1038/s43018-023-00513-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023]
Abstract
Metabolic rewiring is often considered an adaptive pressure limiting metastasis formation; however, some nutrients available at distant organs may inherently promote metastatic growth. We find that the lung and liver are lipid-rich environments. Moreover, we observe that pre-metastatic niche formation increases palmitate availability only in the lung, whereas a high-fat diet increases it in both organs. In line with this, targeting palmitate processing inhibits breast cancer-derived lung metastasis formation. Mechanistically, breast cancer cells use palmitate to synthesize acetyl-CoA in a carnitine palmitoyltransferase 1a-dependent manner. Concomitantly, lysine acetyltransferase 2a expression is promoted by palmitate, linking the available acetyl-CoA to the acetylation of the nuclear factor-kappaB subunit p65. Deletion of lysine acetyltransferase 2a or carnitine palmitoyltransferase 1a reduces metastasis formation in lean and high-fat diet mice, and lung and liver metastases from patients with breast cancer show coexpression of both proteins. In conclusion, palmitate-rich environments foster metastases growth by increasing p65 acetylation, resulting in a pro-metastatic nuclear factor-kappaB signaling.
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Affiliation(s)
- Patricia Altea-Manzano
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Ginevra Doglioni
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Yawen Liu
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Alejandro M Cuadros
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | | | - Juan Fernández-García
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Qi Wu
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Mélanie Planque
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Kathrin Julia Laue
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Florencia Cidre-Aranaz
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Xiao-Zheng Liu
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Oskar Marin-Bejar
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Joke Van Elsen
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Ines Vermeire
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Dorien Broekaert
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Sofie Demeyer
- Laboratory for Molecular Biology of Leukemia, VIB-KU Leuven, Leuven, Belgium
| | - Xander Spotbeen
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jakub Idkowiak
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Aurélie Montagne
- Université Paris Cité, NF-kappaB, Différenciation et Cancer, Paris, France
| | - Margherita Demicco
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - H Furkan Alkan
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | | | - Carla Riera-Domingo
- Laboratory of Tumor Inflammation and Angiogenesis, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - François Richard
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Tatjana Geukens
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Maxim De Schepper
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sophia Leduc
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sigrid Hatse
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Yentl Lambrechts
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | | | - Sergio Lilla
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Alisa Alekseenko
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Vincent Geldhof
- Laboratory for Angiogenesis and Vascular Metabolism, VIB-KU Leuven, Leuven, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Celia de la Calle Arregui
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Giuseppe Floris
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Johannes V Swinnen
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sara Zanivan
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Jan Cools
- Laboratory for Molecular Biology of Leukemia, VIB-KU Leuven, Leuven, Belgium
| | - Hans Wildiers
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Véronique Baud
- Université Paris Cité, NF-kappaB, Différenciation et Cancer, Paris, France
| | - Thomas G P Grünewald
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Uri Ben-David
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, Department of Oncology, KU Leuven, Leuven, Belgium
| | | | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium.
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium.
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8
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Vanden Bempt M, Debackere K, Demeyer S, Van Thillo Q, Meeuws N, Prieto C, Provost S, Mentens N, Jacobs K, Gielen O, Nittner D, Ogawa S, Kataoka K, Graux C, Tousseyn T, Cools J, Dierickx D. Aberrant MYCN expression drives oncogenic hijacking of EZH2 as a transcriptional activator in peripheral T-cell lymphoma. Blood 2022; 140:2463-2476. [PMID: 35960849 PMCID: PMC10653048 DOI: 10.1182/blood.2022016428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 12/13/2022] Open
Abstract
Peripheral T-cell lymphoma (PTCL) is a heterogeneous group of hematological cancers arising from the malignant transformation of mature T cells. In a cohort of 28 PTCL cases, we identified recurrent overexpression of MYCN, a member of the MYC family of oncogenic transcription factors. Approximately half of all PTCL cases was characterized by a MYC expression signature. Inducible expression of MYCN in lymphoid cells in a mouse model caused T-cell lymphoma that recapitulated human PTCL with an MYC expression signature. Integration of mouse and human expression data identified EZH2 as a key downstream target of MYCN. Remarkably, EZH2 was found to be an essential cofactor for the transcriptional activation of the MYCN-driven gene expression program, which was independent of methyltransferase activity but dependent on phosphorylation by CDK1. MYCN-driven T-cell lymphoma was sensitive to EZH2 degradation or CDK1 inhibition, which displayed synergy with US Food and Drug Administration-approved histone deacetylase (HDAC) inhibitors.
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Affiliation(s)
- Marlies Vanden Bempt
- Laboratory for Experimental Hematology, Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Koen Debackere
- Laboratory for Experimental Hematology, Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Quentin Van Thillo
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Nienke Meeuws
- Laboratory for Experimental Hematology, Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Cristina Prieto
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Sarah Provost
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Nicole Mentens
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Kris Jacobs
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Olga Gielen
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - David Nittner
- Histopathology Expertise Center, VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Carlos Graux
- Department of Hematology, Mont-Godinne University Hospital, Yvoir, Belgium
| | - Thomas Tousseyn
- Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospital Leuven, Leuven, Belgium
| | - Jan Cools
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB- Katholieke Universiteit Leuven Center for Cancer Biology, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
| | - Daan Dierickx
- Laboratory for Experimental Hematology, Department of Oncology, KU Leuven, Leuven, Belgium
- Leuvens Kanker Instituut, KU Leuven–UZ Leuven, Leuven, Belgium
- Department of Hematology, University Hospital Leuven, Leuven, Belgium
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9
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van Gils N, Verhagen HJ, Broux M, Martiáñez T, Denkers F, Vermue E, Rutten A, Csikós T, Demeyer S, Çil M, Al M, Cools J, Janssen JJ, Ossenkoppele GJ, Menezes RX, Smit L. Targeting histone methylation to reprogram the transcriptional state that drives survival of drug-tolerant myeloid leukemia persisters. iScience 2022; 25:105013. [PMID: 36097617 PMCID: PMC9463578 DOI: 10.1016/j.isci.2022.105013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Although chemotherapy induces complete remission in the majority of acute myeloid leukemia (AML) patients, many face a relapse. This relapse is caused by survival of chemotherapy-resistant leukemia (stem) cells (measurable residual disease; MRD). Here, we demonstrate that the anthracycline doxorubicin epigenetically reprograms leukemia cells by inducing histone 3 lysine 27 (H3K27) and H3K4 tri-methylation. Within a doxorubicin-sensitive leukemia cell population, we identified a subpopulation of reversible anthracycline-tolerant cells (ATCs) with leukemic stem cell (LSC) features lacking doxorubicin-induced H3K27me3 or H3K4me3 upregulation. These ATCs have a distinct transcriptional landscape than the leukemia bulk and could be eradicated by KDM6 inhibition. In primary AML, reprogramming the transcriptional state by targeting KDM6 reduced MRD load and survival of LSCs residing within MRD, and enhanced chemotherapy response in vivo. Our results reveal plasticity of anthracycline resistance in AML cells and highlight the potential of transcriptional reprogramming by epigenetic-based therapeutics to target chemotherapy-resistant AML cells. Reversible anthracycline-tolerant leukemia cells (ATCs) have low H3K27me3 or H3K4me3 ATCs exhibit stem cell features similar to leukemic stem cells Reprogramming the transcriptional state by inhibition of KDM6 depletes ATCs Inhibiting KDM6 adds to doxorubicin treatment and eradicates AML MRD (stem) cells
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10
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Feyen E, Cools J, Van Fraeyenhove J, Tubeeckx M, De Winter H, Audenaert D, De Keulenaer GW, Segers VF. Identification of small-molecule ERBB4 agonists for the treatment of heart failure. Cardiovasc Res 2022. [DOI: 10.1093/cvr/cvac066.098] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: Public grant(s) – EU funding. Main funding source(s): Dehousse fellowship
Introduction
Although progress has been made in the treatment of heart failure, morbidity and mortality remain high, requiring new therapeutic targets. The neuregulin-1 (NRG1)/ERBB4 axis is cardioprotective and antifibrotic when activated in the myocardium, and therefore a possible target for therapy. Phase 2 and 3 clinical trials with NRG1 are ongoing, but require intravenous administration regimens, limiting applicability and efficacy.
Purpose
To develop small-molecule ERBB4 agonists with cardioprotective and antifibrotic properties.
Methods
A high-throughput screening (HTS) of 10,240 compounds was performed on a ERBB4/ERBB4 dimerization assay. Hit compounds were co-administered with NRG1 or fluorescently labeled NRG1 to determine competitive binding. Selectivity, receptor phosphorylation, cell proliferation and toxicity were determined using Luminex RTK phosphoprotein, ERBB2/ERBB3 dimerization, WST-1 colorimetric, and adenylate kinase assays. Antifibrotic effects were studied in vitro on TGF-β-induced collagen synthesis in human dermal and atrial fibroblasts, and in a mouse model of angiotensin II (AngII, 1000 ng/kg/min)-induced left ventricular (LV) myocardial fibrosis with selected compounds (83 µg/kg/h), administrated with osmotic minipumps (N=4–5/group). mRNA expression was evaluated after 7 days; LV myocardial fibrosis area, cardiomyocyte cross sectional area (CSA), echocardiographic parameters and heart- to bodyweight ratio (HW:BW) were analyzed at 28 days. Antiapoptotic effects were studied on rat atrial cardiomyocytes (AM) after hydrogen peroxide (H2O2)-induced cardiotoxicity.
Results
The HTS (Z’=0.7) resulted in 8 similar pyrimidine derivatives (EF-1–8) inducing ERBB4/ERBB4 dimerization (Emax 9–33% relative to NRG1, EC50 6E-6 to 2E-7 M). Competition assays indicate allosteric binding. The compounds also significantly potentiated NRG1-induced ERBB4 receptor dimerization up to 2.7 fold. Two compounds were excluded because of in vitro toxicity. The other 6 compounds were non-toxic and induced ERBB4, but neither ERBB1, ERBB2 or ERBB3 phosphorylation, nor tumor growth–inducing ERBB2/ERBB3 dimerization. Selected compounds showed significant dose-dependent antiapoptotic properties on H2O2-stimulated AM, and antifibrotic effects on human atrial and dermal fibroblasts. In vivo, compound EF-1 significantly decreased myocardial fibrosis (by 76±26%) and Col1a1, Col3a1 (-70±17%; -61±20%), and Nppa (-78±32%) mRNA expression, and significantly enhanced cardiomyocyte CSA (+24±8%). No differences were observed in cardiac function or HW:BW ratio.
Conclusion
We identified novel pyrimidine derivative small-molecule ERBB4 agonists with cardiomyocyte protective effects and antifibrotic properties in vitro and in AngII-induced myocardial fibrosis in vivo.
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Affiliation(s)
- E Feyen
- University of Antwerp , Wilrijk , Belgium
| | - J Cools
- University of Antwerp , Wilrijk , Belgium
| | | | - M Tubeeckx
- University of Antwerp , Wilrijk , Belgium
| | | | | | | | - VF Segers
- University of Antwerp , Wilrijk , Belgium
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11
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Tuveri S, Debackere K, Marcelis L, Dierckxsens N, Demeulemeester J, Dimitriadou E, Dierickx D, Lefesvre P, Deraedt K, Graux C, Michaux L, Cools J, Tousseyn T, Vermeesch JR, Wlodarska I. Primary mediastinal large B-cell lymphoma is characterized by large-scale copy-neutral loss of heterozygosity. Genes Chromosomes Cancer 2022; 61:603-615. [PMID: 35611992 DOI: 10.1002/gcc.23069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 01/10/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 11/07/2022] Open
Abstract
Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. We discovered a unique copy-neutral loss of heterozygosity (CN-LOH) landscape of PMBL which distinguishes this tumour from other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma. Using single nucleotide polymorphism array analysis we identified large-scale CN-LOH lesions in 91% (30/33) of diagnostic PMBLs and both investigated PMBL-derived cell lines. Altogether, the cohort showed 157 extra-large (25.3-248.4 Mb) CN-LOH lesions affecting up to 14 chromosomes per case (mean of 4.4) and resulting in a reduction of heterozygosity an average of 9.9% (range 1.3-51%) of the genome. Predominant involvement of terminal chromosomal segments suggests the implication of B-cell specific crossover events in the pathogenesis of PMBL. Notably, CN-LOH stretches non-randomly clustered on 6p (60%), 15 (37.2%) and 17q (40%), and frequently co-occurred with homozygous mutations in the MHC I (6p21), B2M (15q15) and GNA13 (17q23) genes, respectively, as shown by preliminary whole-exome/genome sequencing data. Altogether, our findings implicate CN-LOH as a novel and distinct mutational process contributing to the molecular pathogenesis of PMBL. The aberration acting as 'second hit' in the Knudson hypothesis, ranks as the major mechanism converting to homozygosity the PMBL-related driver genes. Screening of the cohort of 199 B cell leukamia/lymphoma whole-genomes revealed significant differences in the CN-LOH landscape of PMBL and other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma.
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Affiliation(s)
| | - Koen Debackere
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lukas Marcelis
- Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | - Jonas Demeulemeester
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | | | - Daan Dierickx
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Pierre Lefesvre
- Department of Pathology, Free University Hospital, Brussels, Belgium
| | - Karen Deraedt
- Anatomo-Pathology, Hospital East Limburg, Genk, Belgium
| | - Carlos Graux
- Department of Hematology, Mont-Godinne University Hospital, Yvoir, Belgium
| | | | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Thomas Tousseyn
- Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
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12
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Rack K, Bie J, Ameye G, Gielen O, Demeyer S, Cools J, Keersmaecker K, Vermeesch JR, Maertens J, Segers H, Michaux L, Dewaele B. Optimizing the diagnostic workflow for acute lymphoblastic leukemia by optical genome mapping. Am J Hematol 2022; 97:548-561. [PMID: 35119131 PMCID: PMC9314940 DOI: 10.1002/ajh.26487] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 10/16/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 12/11/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is a malignancy that can be subdivided into distinct entities based on clinical, immunophenotypic and genomic features, including mutations, structural variants (SVs), and copy number alterations (CNA). Chromosome banding analysis (CBA) and Fluorescent In‐Situ Hybridization (FISH) together with Multiple Ligation‐dependent Probe Amplification (MLPA), array and PCR‐based methods form the backbone of routine diagnostics. This approach is labor‐intensive, time‐consuming and costly. New molecular technologies now exist that can detect SVs and CNAs in one test. Here we apply one such technology, optical genome mapping (OGM), to the diagnostic work‐up of 41 ALL cases. Compared to our standard testing pathway, OGM identified all recurrent CNAs and SVs as well as additional recurrent SVs and the resulting fusion genes. Based on the genomic profile obtained by OGM, 32 patients could be assigned to one of the major cytogenetic risk groups compared to 23 with the standard approach. The latter identified 24/34 recurrent chromosomal abnormalities, while OGM identified 33/34, misinterpreting only 1 case with low hypodiploidy. The results of MLPA were concordant in 100% of cases. Overall, there was excellent concordance between the results. OGM increased the detection rate and cytogenetic resolution, and abrogated the need for cascade testing, resulting in reduced turnaround times. OGM also provided opportunities for better patient stratification and accurate treatment options. However, for comprehensive cytogenomic testing, OGM still needs to be complemented with CBA or SNP‐array to detect ploidy changes and with BCR::ABL1 FISH to assign patients as soon as possible to targeted therapy.
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Affiliation(s)
- Katrina Rack
- Laboratory for the Cytogenetic and Molecular Diagnosis of Hematological Malignancies, Centre for Human Genetics University Hospitals Leuven Leuven Belgium
| | - Jolien Bie
- Laboratory for the Cytogenetic and Molecular Diagnosis of Hematological Malignancies, Centre for Human Genetics University Hospitals Leuven Leuven Belgium
- Laboratory for the Molecular Biology of Leukemia KU Leuven Leuven Belgium
| | - Geneviève Ameye
- Laboratory for the Cytogenetic and Molecular Diagnosis of Hematological Malignancies, Centre for Human Genetics University Hospitals Leuven Leuven Belgium
| | - Olga Gielen
- Laboratory for the Molecular Biology of Leukemia KU Leuven Leuven Belgium
- Centre for Cancer Biology Flemish Institute for Biotechnology (VIB) Leuven Belgium
| | - Sofie Demeyer
- Laboratory for the Molecular Biology of Leukemia KU Leuven Leuven Belgium
- Centre for Cancer Biology Flemish Institute for Biotechnology (VIB) Leuven Belgium
| | - Jan Cools
- Laboratory for the Molecular Biology of Leukemia KU Leuven Leuven Belgium
- Centre for Cancer Biology Flemish Institute for Biotechnology (VIB) Leuven Belgium
- Leuvens Kanker Instituut (LKI) KU Leuven – University Hospitals Leuven Leuven Belgium
| | - Kim Keersmaecker
- Leuvens Kanker Instituut (LKI) KU Leuven – University Hospitals Leuven Leuven Belgium
- Department of Oncology KU Leuven Leuven Belgium
| | - Joris R. Vermeesch
- Department of Human Genetics KU Leuven Leuven Belgium
- Centre for Human Genetics University Hospitals Leuven Leuven Belgium
| | - Johan Maertens
- Department of Hematology University Hospitals Leuven Leuven Belgium
| | - Heidi Segers
- Leuvens Kanker Instituut (LKI) KU Leuven – University Hospitals Leuven Leuven Belgium
- Department of Pediatric Oncology‐Hematology University Hospitals Leuven Leuven Belgium
| | - Lucienne Michaux
- Laboratory for the Cytogenetic and Molecular Diagnosis of Hematological Malignancies, Centre for Human Genetics University Hospitals Leuven Leuven Belgium
| | - Barbara Dewaele
- Laboratory for the Cytogenetic and Molecular Diagnosis of Hematological Malignancies, Centre for Human Genetics University Hospitals Leuven Leuven Belgium
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13
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Rossi M, Altea-Manzano P, Demicco M, Doglioni G, Bornes L, Fukano M, Vandekeere A, Cuadros AM, Fernández-García J, Riera-Domingo C, Jauset C, Planque M, Alkan HF, Nittner D, Zuo D, Broadfield LA, Parik S, Pane AA, Rizzollo F, Rinaldi G, Zhang T, Teoh ST, Aurora AB, Karras P, Vermeire I, Broekaert D, Elsen JV, Knott MML, Orth MF, Demeyer S, Eelen G, Dobrolecki LE, Bassez A, Brussel TV, Sotlar K, Lewis MT, Bartsch H, Wuhrer M, Veelen PV, Carmeliet P, Cools J, Morrison SJ, Marine JC, Lambrechts D, Mazzone M, Hannon GJ, Lunt SY, Grünewald TGP, Park M, Rheenen JV, Fendt SM. PHGDH heterogeneity potentiates cancer cell dissemination and metastasis. Nature 2022; 605:747-753. [PMID: 35585241 PMCID: PMC9888363 DOI: 10.1038/s41586-022-04758-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/12/2022] [Indexed: 02/02/2023]
Abstract
Cancer metastasis requires the transient activation of cellular programs enabling dissemination and seeding in distant organs1. Genetic, transcriptional and translational heterogeneity contributes to this dynamic process2,3. Metabolic heterogeneity has also been observed4, yet its role in cancer progression is less explored. Here we find that the loss of phosphoglycerate dehydrogenase (PHGDH) potentiates metastatic dissemination. Specifically, we find that heterogeneous or low PHGDH expression in primary tumours of patients with breast cancer is associated with decreased metastasis-free survival time. In mice, circulating tumour cells and early metastatic lesions are enriched with Phgdhlow cancer cells, and silencing Phgdh in primary tumours increases metastasis formation. Mechanistically, Phgdh interacts with the glycolytic enzyme phosphofructokinase, and the loss of this interaction activates the hexosamine-sialic acid pathway, which provides precursors for protein glycosylation. As a consequence, aberrant protein glycosylation occurs, including increased sialylation of integrin αvβ3, which potentiates cell migration and invasion. Inhibition of sialylation counteracts the metastatic ability of Phgdhlow cancer cells. In conclusion, although the catalytic activity of PHGDH supports cancer cell proliferation, low PHGDH protein expression non-catalytically potentiates cancer dissemination and metastasis formation. Thus, the presence of PHDGH heterogeneity in primary tumours could be considered a sign of tumour aggressiveness.
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Affiliation(s)
- Matteo Rossi
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Patricia Altea-Manzano
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Margherita Demicco
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Ginevra Doglioni
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Laura Bornes
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marina Fukano
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada
- Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute (GCI), McGill University, Montreal, Quebec, Canada
| | - Anke Vandekeere
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Alejandro M Cuadros
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Juan Fernández-García
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Carla Riera-Domingo
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology (CCB), VIB, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Cristina Jauset
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Mélanie Planque
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - H Furkan Alkan
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - David Nittner
- Histopathology Expertise Center, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Dongmei Zuo
- Rosalind & Morris Goodman Cancer Institute (GCI), McGill University, Montreal, Quebec, Canada
| | - Lindsay A Broadfield
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Sweta Parik
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Antonino Alejandro Pane
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Francesca Rizzollo
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Gianmarco Rinaldi
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Tao Zhang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Shao Thing Teoh
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Arin B Aurora
- Children's Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Panagiotis Karras
- Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory of Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
| | - Ines Vermeire
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Dorien Broekaert
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Joke Van Elsen
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Maximilian M L Knott
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Sofie Demeyer
- Laboratory for Molecular Biology of Leukemia, VIB-KU Leuven, Leuven, Belgium
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Leuven, Belgium
| | | | - Ayse Bassez
- Laboratory for Translational Genetics, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Thomas Van Brussel
- Laboratory for Translational Genetics, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Karl Sotlar
- Institute of Pathology, University Hospital Salzburg, Paracelsus Medical University, Salzburg, Austria
| | | | - Harald Bartsch
- Institute of Pathology, Ludwig Maximilians University, Munich, Germany
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jan Cools
- Laboratory for Molecular Biology of Leukemia, VIB-KU Leuven, Leuven, Belgium
| | - Sean J Morrison
- Children's Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jean-Christophe Marine
- Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory of Molecular Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology (CCB), VIB, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Molecular Biotechnology and Health Science, Molecular Biotechnology Centre, University of Torino, Torino, Italy
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Sophia Y Lunt
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Morag Park
- Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute (GCI), McGill University, Montreal, Quebec, Canada
| | - Jacco van Rheenen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium.
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium.
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Thielemans N, Demeyer S, Mentens N, Gielen O, Provost S, Cools J. TAL1 cooperates with PI3K/AKT pathway activation in T-cell acute lymphoblastic leukemia. Haematologica 2022; 107:2304-2317. [PMID: 35354248 PMCID: PMC9521226 DOI: 10.3324/haematol.2021.279718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
TAL1 is ectopically expressed in about 30% of T-cell acute lymphoblastic leukemia (T-ALL) due to chromosomal rearrangements leading to the STIL-TAL1 fusion genes or due to non-coding mutations leading to a de novo enhancer driving TAL1 expression. Analysis of sequence data from T-ALL cases demonstrates a significant association between TAL1 expression and activating mutations of the PI3K-AKT pathway. We investigated the oncogenic function of TAL1 and the possible cooperation with PI3K-AKT pathway activation using isogenic pro-T-cell cultures ex vivo and in vivo leukemia models. We found that TAL1 on its own suppressed T-cell growth, in part by affecting apoptosis genes, while the combination with AKT pathway activation reduced apoptosis and was strongly driving cell proliferation ex vivo and leukemia development in vivo. As a consequence, we found that TAL1+AKTE17K transformed cells are more sensitive to PI3K-AKT pathway inhibition compared to AKTE17K transformed cells, related to the negative effect of TAL1 in the absence of activated PI3K-AKT signaling. We also found that both TAL1 and PI3K-AKT signaling increased the DNA-repair signature in T cells resulting in synergy between PARP and PI3K-AKT pathway inhibition. In conclusion, we have developed a novel mouse model for TAL1+AKTE17K driven T-ALL development and have identified a vulnerability of these leukemia cells to PI3K-AKT and PARP inhibitors.
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Affiliation(s)
- Naomi Thielemans
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium; Leuven Cancer Institute (LKI), KU Leuven - UZ Leuven, Leuven
| | - Sofie Demeyer
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium; Leuven Cancer Institute (LKI), KU Leuven - UZ Leuven, Leuven
| | - Nicole Mentens
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium; Leuven Cancer Institute (LKI), KU Leuven - UZ Leuven, Leuven
| | - Olga Gielen
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium; Leuven Cancer Institute (LKI), KU Leuven - UZ Leuven, Leuven
| | - Sarah Provost
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium; Leuven Cancer Institute (LKI), KU Leuven - UZ Leuven, Leuven
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium; Center for Cancer Biology, VIB, Leuven, Belgium; Leuven Cancer Institute (LKI), KU Leuven - UZ Leuven, Leuven.
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15
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van der Zwet JCG, Buijs-Gladdines JGCAM, Cordo' V, Debets DO, Smits WK, Chen Z, Dylus J, Zaman GJR, Altelaar M, Oshima K, Bornhauser B, Bourquin JP, Cools J, Ferrando AA, Vormoor J, Pieters R, Vormoor B, Meijerink JPP. MAPK-ERK is a central pathway in T-cell acute lymphoblastic leukemia that drives steroid resistance. Leukemia 2021; 35:3394-3405. [PMID: 34007050 DOI: 10.1038/s41375-021-01291-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/17/2021] [Accepted: 05/07/2021] [Indexed: 02/04/2023]
Abstract
(Patho-)physiological activation of the IL7-receptor (IL7R) signaling contributes to steroid resistance in pediatric T-cell acute lymphoblastic leukemia (T-ALL). Here, we show that activating IL7R pathway mutations and physiological IL7R signaling activate MAPK-ERK signaling, which provokes steroid resistance by phosphorylation of BIM. By mass spectrometry, we demonstrate that phosphorylated BIM is impaired in binding to BCL2, BCLXL and MCL1, shifting the apoptotic balance toward survival. Treatment with MEK inhibitors abolishes this inactivating phosphorylation of BIM and restores its interaction with anti-apoptotic BCL2-protein family members. Importantly, the MEK inhibitor selumetinib synergizes with steroids in both IL7-dependent and IL7-independent steroid resistant pediatric T-ALL PDX samples. Despite the anti-MAPK-ERK activity of ruxolitinib in IL7-induced signaling and JAK1 mutant cells, ruxolitinib only synergizes with steroid treatment in IL7-dependent steroid resistant PDX samples but not in IL7-independent steroid resistant PDX samples. Our study highlights the central role for MAPK-ERK signaling in steroid resistance in T-ALL patients, and demonstrates the broader application of MEK inhibitors over ruxolitinib to resensitize steroid-resistant T-ALL cells. These findings strongly support the enrollment of T-ALL patients in the current phase I/II SeluDex trial (NCT03705507) and contributes to the optimization and stratification of newly designed T-ALL treatment regimens.
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Affiliation(s)
| | | | - Valentina Cordo'
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Donna O Debets
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center of Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Willem K Smits
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Zhongli Chen
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jelle Dylus
- Netherlands Translational Research Center B.V., Oss, the Netherlands
| | - Guido J R Zaman
- Netherlands Translational Research Center B.V., Oss, the Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center of Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Koichi Oshima
- Institute of Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Beat Bornhauser
- Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Jean-Pierre Bourquin
- Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Jan Cools
- KU Leuven Center for Human Genetics & VIB Center for Cancer Biology, Leuven, Belgium
| | - Adolfo A Ferrando
- Institute of Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Josef Vormoor
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Newcastle University, Newcastle upon Tyne, UK
| | - Rob Pieters
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Britta Vormoor
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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16
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Van Winckel T, Cools J, Vlaeminck SE, Joos P, Van Meenen E, Borregán-Ochando E, Van Den Steen K, Geerts R, Vandermoere F, Blust R. Towards harmonization of water quality management: A comparison of chemical drinking water and surface water quality standards around the globe. J Environ Manage 2021; 298:113447. [PMID: 34426213 DOI: 10.1016/j.jenvman.2021.113447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Water quality standards (WQS) set the legal definition for safe and desirable water. WQS impose regulatory concentration limits to act as a jurisdiction-specific legislative risk-management tool. Despite its importance in shaping a universal definition of safe, clean water, little information exists with respect to (dis)similarity of chemical WQS worldwide. Therefore, this paper compares chemical WQS for drinking and surface water matrices in eight jurisdictions representing a global geographic distribution: Australia, Brazil, Canada, China, the European Union, the region of Flanders in Belgium, the United States of America, and South Africa. The World Health Organization's list is used as a reference for drinking water standards. Sørensen-Dice indices (SDI) showed little qualitative similarity in the compounds that are regulated in drinking water (median SDI = 40%) and surface water (median SDI = 33%), indicating that the heterogeneity within a matrix is substantial at the level of the standard. Quantitative similarity for matching standards was higher than the qualitative per Kendall correlation (median = 0.73 and 0.58 for drinking water and surface water respectively), yet variance observed within standards remained inexplicably high for organic compounds. Variations in WQS were more pronounced for organic compounds. Most differences cannot be easily explained from a toxicological or risk-based point-of-view. Historical development, ease of measurement, and (toxicological) knowledge gaps on the risk of a vast number of organic compounds are theorized to be the drivers. Therefore, this study argues for a more tailored, risk-based approach in which standards incorporated into water safety plans are dynamically set for compounds that are persistent and could pose a risk for human health and/or aquatic ecosystems. Global variations in WQS should therefore not necessarily be avoided but rather globally harmonized with enough flexibility to ensure a global, up-to-date definition of safe and desirable water everywhere.
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Affiliation(s)
- Tim Van Winckel
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium; Institute of Environment and Sustainable Development, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - Jan Cools
- Institute of Environment and Sustainable Development, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - Siegfried E Vlaeminck
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium.
| | - Pieter Joos
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium; Water-Link, Mechelsesteenweg 111, 2840, Rumst, Belgium
| | | | - Elena Borregán-Ochando
- Institute of Environment and Sustainable Development, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | | | - Robbe Geerts
- Department of Sociology, University of Antwerp, Sint-Jacobstraat 2, 2000, Antwerpen, Belgium
| | - Frédéric Vandermoere
- Department of Sociology, University of Antwerp, Sint-Jacobstraat 2, 2000, Antwerpen, Belgium
| | - Ronny Blust
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
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17
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Anteneh A, Enyew A, Getachew A, Birru Y, Kebebew A, Cools J. Preference and perception of value chain actors to quality parameters and factors affecting the quality of tef ( Eragrostis tef (Zucc. Trotter) in Central and Northwestern Ethiopia. Heliyon 2021; 7:e08090. [PMID: 34660921 PMCID: PMC8503616 DOI: 10.1016/j.heliyon.2021.e08090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 04/14/2021] [Accepted: 09/26/2021] [Indexed: 10/30/2022] Open
Abstract
Tef grain color is considered as the dominant parameter in the trading and price setting on the local markets. However, there are no comprehensive studies conducted so far on the preference and perception of actors on tef grain quality attributes and factors affecting it. Its implicitly assumed that other quality parameters also play a role in the value chain of tef. Using semi-structured questionnaires, this study researched the parameters and factors affecting the quality of tef, perceived by farmers, traders, and consumers in central and northwestern highlands of Ethiopia. Results from this survey indicated that grain color, size, density, shininess, cleanness, purity, and hulledness were the perceived tef grain quality attributes by all respondent groups'. Grain color followed by grain size, cleanness, and purity were the most perceived and directly or indirectly affected the price setting of tef. Farmer and trader respondents' perception for tef color was mainly dependent on their clients' (consumers). However farmer preferred the brown color tef for their consumption. Trader respondents categorized their client's preference of grain color on the income level as high, medium and low-income consumers. The high-income consumers mostly preferred the whitish color; middle-income for the mixed and brown color; and low-income for the brown color tef. The perception between farmer and trader, farmer and consumer, and trader and consumer as well as the same group of respondents living in different areas showed significantly (p < 0.05 to p < 0.0001) different on most of grain quality attributes. Nevertheless, there was no preference variability on grain color and density between farmer and trader respondents. While there were considerable differences in the color of tef between farmer and consumer and trader and consumer respondents. However, between the central and northwestern highland farmers (grain color, density and cleanness, traders, (color and cleanness), and consumer (color, density, purity, and hulledness) did not show considerable differences. From respondents, 100% of farmers, 97.7% of traders, and 93.3% of consumers perceived that grain quality variability comes from the variability of production area. Soil types, topography, and climatic factors were the main perceived causes for the variability of quality. Ninety eight percent of farmer and 100% of trader respondents perceived that black and brown color soils produced tef had highest quality in terms of whiteness or brightness as compared to tef produced on red soils. All respondent groups were also perceived that the quality of injera affected by tef grain quality. To better connect the value chain actors to the needs and preferences of tef grain and the economy in Ethiopia; the quality attributes like grain size, density, and shininess which affect the price of tef needs consideration in Ethiopian tef breeding program. The effects of soil type, agroecology, and crop variety should also be tested experimentally for a better understanding of factors influencing tef grain physical quality.
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Affiliation(s)
- Abewa Anteneh
- Amhara Agricultural Research Institute (ARARI), Bahir Dar, Ethiopia
| | - Adgo Enyew
- Department of Natural Resource Management, Bahir Dar University, Bahir Dar, Ethiopia
| | | | - Yitaferu Birru
- Ethiopian Agricultural Research Council Secretariat, Natural Resource Research Directorate, Addis Ababa, Ethiopia
| | - Assefa Kebebew
- Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, Bisheftu, Ethiopia
| | - Jan Cools
- Institute of Environment and Sustainable Development, University of Antwerp, Antwerp, Belgium
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18
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Segers H, Cools J. Genomics, Transcriptomics, and Minimal Residual Disease Detection: The Winning Team to Guide Treatment of Acute Lymphoblastic Leukemia. Blood Cancer Discov 2021; 2:294-296. [PMID: 34661158 DOI: 10.1158/2643-3230.bcd-21-0068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cytogenetics supported by additional molecular analyses and minimal residual disease detection have been successfully combined to improve the outcome of childhood acute lymphoblastic leukemia (ALL). Results from the St. Jude Total Therapy Study 16 demonstrate that some of the recently identified ALL subtypes can further guide risk stratification. See related article by Jeha et al., p. 326.
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Affiliation(s)
- Heidi Segers
- Department of Oncology, KU Leuven, Leuven, Belgium.,Department of Pediatric Oncology, UZ Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium.,Center for Cancer Biology, VIB, Leuven, Belgium
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19
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Azadi H, Van Passel S, Cools J. Rapid economic valuation of ecosystem services in man and biosphere reserves in Africa: A review. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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20
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Van Thillo Q, De Bie J, Seneviratne JA, Demeyer S, Omari S, Balachandran A, Zhai V, Tam WL, Sweron B, Geerdens E, Gielen O, Provost S, Segers H, Boeckx N, Marshall GM, Cheung BB, Isobe K, Kato I, Takita J, Amos TG, Deveson IW, McCalmont H, Lock RB, Oxley EP, Garwood MM, Dickins RA, Uyttebroeck A, Carter DR, Cools J, de Bock CE. Oncogenic cooperation between TCF7-SPI1 and NRAS(G12D) requires β-catenin activity to drive T-cell acute lymphoblastic leukemia. Nat Commun 2021; 12:4164. [PMID: 34230493 PMCID: PMC8260768 DOI: 10.1038/s41467-021-24442-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Spi-1 Proto-Oncogene (SPI1) fusion genes are recurrently found in T-cell acute lymphoblastic leukemia (T-ALL) cases but are insufficient to drive leukemogenesis. Here we show that SPI1 fusions in combination with activating NRAS mutations drive an immature T-ALL in vivo using a conditional bone marrow transplant mouse model. Addition of the oncogenic fusion to the NRAS mutation also results in a higher leukemic stem cell frequency. Mechanistically, genetic deletion of the β-catenin binding domain within Transcription factor 7 (TCF7)-SPI1 or use of a TCF/β-catenin interaction antagonist abolishes the oncogenic activity of the fusion. Targeting the TCF7-SPI1 fusion in vivo with a doxycycline-inducible knockdown results in increased differentiation. Moreover, both pharmacological and genetic inhibition lead to down-regulation of SPI1 targets. Together, our results reveal an example where TCF7-SPI1 leukemia is vulnerable to pharmacological targeting of the TCF/β-catenin interaction.
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Affiliation(s)
- Quentin Van Thillo
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Jolien De Bie
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, UZ Leuven, Leuven, Belgium
| | - Janith A Seneviratne
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Sofie Demeyer
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Sofia Omari
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Anushree Balachandran
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Vicki Zhai
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Wai L Tam
- Technology Innovation Lab, VIB, Gent, Belgium
| | - Bram Sweron
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Ellen Geerdens
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Olga Gielen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Sarah Provost
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Heidi Segers
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pediatric Hemato-Oncology, UZ Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Laboratory Medicine, UZ Leuven, Leuven, Belgium
| | - Glenn M Marshall
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Belamy B Cheung
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Kiyotaka Isobe
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Timothy G Amos
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Hannah McCalmont
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B Lock
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Ethan P Oxley
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Maximilian M Garwood
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Ross A Dickins
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, Australia
| | - Anne Uyttebroeck
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pediatric Hemato-Oncology, UZ Leuven, Leuven, Belgium
| | - Daniel R Carter
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
- School of Biomedical Engineering, University of Technology, Sydney, NSW, Australia
| | - Jan Cools
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium.
| | - Charles E de Bock
- Children's Cancer Institute, UNSW Sydney, Lowy Cancer Research Centre, Sydney, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia.
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21
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Govaerts I, Prieto C, Vandersmissen C, Gielen O, Jacobs K, Provost S, Nittner D, Maertens J, Boeckx N, De Keersmaecker K, Segers H, Cools J. PSEN1-selective gamma-secretase inhibition in combination with kinase or XPO-1 inhibitors effectively targets T cell acute lymphoblastic leukemia. J Hematol Oncol 2021; 14:97. [PMID: 34167562 PMCID: PMC8223323 DOI: 10.1186/s13045-021-01114-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/15/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND T cell acute lymphoblastic leukemia (T-ALL) is a high-risk subtype that comprises 10-15% of childhood and 20-25% of adult ALL cases. Over 70% of T-ALL patients harbor activating mutations in the NOTCH1 signaling pathway and are predicted to be sensitive to gamma-secretase inhibitors. We have recently demonstrated that selective inhibition of PSEN1-containing gamma-secretase complexes can overcome the dose-limiting toxicity associated with broad gamma-secretase inhibitors. In this study, we developed combination treatment strategies with the PSEN1-selective gamma-secretase inhibitor MRK-560 and other targeted agents (kinase inhibitors ruxolitinib and imatinib; XPO-1 inhibitor KPT-8602/eltanexor) for the treatment of T-ALL. METHODS We treated T-ALL cell lines in vitro and T-ALL patient-derived xenograft (PDX) models in vivo with MRK-560 alone or in combination with other targeted inhibitors (ruxolitinib, imatinib or KPT-8602/eltanexor). We determined effects on proliferation of the cell lines and leukemia development and survival in the PDX models. RESULTS All NOTCH1-signaling-dependent T-ALL cell lines were sensitive to MRK-560 and its combination with ruxolitinib or imatinib in JAK1- or ABL1-dependent cell lines synergistically inhibited leukemia proliferation. We also observed strong synergy between MRK-560 and KPT-8602 (eltanexor) in all NOTCH1-dependent T-ALL cell lines. Such synergy was also observed in vivo in a variety of T-ALL PDX models with NOTCH1 or FBXW7 mutations. Combination treatment significantly reduced leukemic infiltration in vivo and resulted in a survival benefit when compared to single treatment groups. We did not observe weight loss or goblet cell hyperplasia in single drug or combination treated mice when compared to control. CONCLUSIONS These data demonstrate that the antileukemic effect of PSEN1-selective gamma-secretase inhibition can be synergistically enhanced by the addition of other targeted inhibitors. The combination of MRK-560 with KPT-8602 is a highly effective treatment combination, which circumvents the need for the identification of additional mutations and provides a clear survival benefit in vivo. These promising preclinical data warrant further development of combination treatment strategies for T-ALL based on PSEN1-selective gamma-secretase inhibition.
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Affiliation(s)
- Inge Govaerts
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Cristina Prieto
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Charlien Vandersmissen
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Olga Gielen
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Kris Jacobs
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Sarah Provost
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | | | - Johan Maertens
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Hematology, UZ Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Department of Laboratory Medicine, UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Kim De Keersmaecker
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Heidi Segers
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- Department of Pediatric Oncology, UZ Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium.
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22
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Debackere K, Marcelis L, Demeyer S, Vanden Bempt M, Mentens N, Gielen O, Jacobs K, Broux M, Verhoef G, Michaux L, Graux C, Wlodarska I, Gaulard P, de Leval L, Tousseyn T, Cools J, Dierickx D. Fusion transcripts FYN-TRAF3IP2 and KHDRBS1-LCK hijack T cell receptor signaling in peripheral T-cell lymphoma, not otherwise specified. Nat Commun 2021; 12:3705. [PMID: 34140493 PMCID: PMC8211700 DOI: 10.1038/s41467-021-24037-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Peripheral T-cell lymphoma (PTCL) is a heterogeneous group of non-Hodgkin lymphomas with poor prognosis. Up to 30% of PTCL lack distinctive features and are classified as PTCL, not otherwise specified (PTCL-NOS). To further improve our understanding of the genetic landscape and biology of PTCL-NOS, we perform RNA-sequencing of 18 cases and validate results in an independent cohort of 37 PTCL cases. We identify FYN-TRAF3IP2, KHDRBS1-LCK and SIN3A-FOXO1 as new in-frame fusion transcripts, with FYN-TRAF3IP2 as a recurrent fusion detected in 8 of 55 cases. Using ex vivo and in vivo experiments, we demonstrate that FYN-TRAF3IP2 and KHDRBS1-LCK activate signaling pathways downstream of the T cell receptor (TCR) complex and confer therapeutic vulnerability to clinically available drugs.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Cell Line, Tumor
- Cell Membrane/metabolism
- Cohort Studies
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Forkhead Box Protein O1/genetics
- Forkhead Box Protein O1/metabolism
- Gene Expression Regulation, Neoplastic/genetics
- Humans
- Intracellular Signaling Peptides and Proteins/metabolism
- Kaplan-Meier Estimate
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/genetics
- Lymphocyte Specific Protein Tyrosine Kinase p56(lck)/metabolism
- Lymphoma, T-Cell, Peripheral/genetics
- Lymphoma, T-Cell, Peripheral/metabolism
- Lymphoma, T-Cell, Peripheral/pathology
- Mice
- Mice, Inbred C57BL
- NF-kappa B/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Proto-Oncogene Proteins c-fyn/genetics
- Proto-Oncogene Proteins c-fyn/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- RNA-Seq
- Receptors, Antigen, T-Cell/metabolism
- Signal Transduction/genetics
- Sin3 Histone Deacetylase and Corepressor Complex/genetics
- Sin3 Histone Deacetylase and Corepressor Complex/metabolism
- bcl-X Protein/antagonists & inhibitors
- bcl-X Protein/metabolism
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Affiliation(s)
- Koen Debackere
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lukas Marcelis
- Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Marlies Vanden Bempt
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Nicole Mentens
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Olga Gielen
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Kris Jacobs
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Michael Broux
- Center for Cancer Biology, VIB, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Gregor Verhoef
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Lucienne Michaux
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Carlos Graux
- Mont-Godinne University Hospital, Yvoir, Belgium
| | - Iwona Wlodarska
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Philippe Gaulard
- Département de Pathologie, Groupe Hospitalier Henri Mondor, AP-HP, Créteil, France
- INSERM U955 and Université Paris-Est, Créteil, France
| | - Laurence de Leval
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Thomas Tousseyn
- Translational Cell & Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Cancer Biology, VIB, Leuven, Belgium.
- Center for Human Genetics, KU Leuven, Leuven, Belgium.
| | - Daan Dierickx
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium.
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium.
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23
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Verbeke D, Demeyer S, Prieto C, de Bock CE, De Bie J, Gielen O, Jacobs K, Mentens N, Verhoeven BM, Uyttebroeck A, Boeckx N, De Keersmaecker K, Maertens J, Segers H, Cools J. The XPO1 Inhibitor KPT-8602 Synergizes with Dexamethasone in Acute Lymphoblastic Leukemia. Clin Cancer Res 2020; 26:5747-5758. [PMID: 32826328 DOI: 10.1158/1078-0432.ccr-20-1315] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/20/2020] [Accepted: 08/18/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE KPT-8602 (Eltanexor) is a second-generation exportin-1 (XPO1) inhibitor with potent activity against acute lymphoblastic leukemia (ALL) in preclinical models and with minimal effects on normal cells. In this study, we evaluated whether KPT-8602 would synergize with dexamethasone, vincristine, or doxorubicin, three drugs currently used for the treatment of ALL. EXPERIMENTAL DESIGN First, we searched for the most synergistic combination of KPT-8602 with dexamethasone, vincristine, or doxorubicin in vitro in both B-ALL and T-ALL cell lines using proliferation and apoptosis as a readout. Next, we validated this synergistic effect by treatment of clinically relevant B- and T-ALL patient-derived xenograft models in vivo. Finally, we performed RNA-sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to determine the mechanism of synergy. RESULTS KPT-8602 showed strong synergism with dexamethasone on human B-ALL and T-ALL cell lines as well as in vivo in three patient-derived ALL xenografts. Compared with single-drug treatment, the drug combination caused increased apoptosis and led to histone depletion. Mechanistically, integration of ChIP-seq and RNA-seq data revealed that addition of KPT-8602 to dexamethasone enhanced the activity of the glucocorticoid receptor (NR3C1) and led to increased inhibition of E2F-mediated transcription. We observed strong inhibition of E2F target genes related to cell cycle, DNA replication, and transcriptional regulation. CONCLUSIONS Our preclinical study demonstrates that KPT-8602 enhances the effects of dexamethasone to inhibit B-ALL and T-ALL cells via NR3C1- and E2F-mediated transcriptional complexes, allowing to achieve increased dexamethasone effects for patients.
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Affiliation(s)
- Delphine Verbeke
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Sofie Demeyer
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Cristina Prieto
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Charles E de Bock
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, New South Wales, Australia
| | - Jolien De Bie
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Laboratory Medicine, UZ Leuven, Leuven, Belgium
| | - Olga Gielen
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Kris Jacobs
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Nicole Mentens
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Bronte Manouk Verhoeven
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
| | - Anne Uyttebroeck
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Pediatric Oncology, UZ Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Department of Laboratory Medicine, UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Kim De Keersmaecker
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Johan Maertens
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Hematology, UZ Leuven, Leuven, Belgium
| | - Heidi Segers
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
- Department of Pediatric Oncology, UZ Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium.
- Center for Cancer Biology, VIB, Leuven, Belgium
- Leuvens Kanker Instituut (LKI), KU Leuven - UZ Leuven, Leuven, Belgium
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24
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Van Oijstaeijen W, Van Passel S, Cools J. Urban green infrastructure: A review on valuation toolkits from an urban planning perspective. J Environ Manage 2020; 267:110603. [PMID: 32349950 DOI: 10.1016/j.jenvman.2020.110603] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/02/2020] [Accepted: 04/10/2020] [Indexed: 05/10/2023]
Abstract
As a response to increasing urbanization and changing weather and climatic patterns, urban green infrastructure (UGI) emerged as a concept to increase resilience within the urban boundaries. Given that implementing these (semi-) natural solutions in practice requires a clear overview of the costs and benefits, valuation becomes ever important. A range of decision-support tools for green infrastructure and ecosystem services exist, developed for various purposes. This paper reviews the potential of 10 shortlisted and existing valuation tools to support investment decisions of urban green infrastructure. In the assessment, the functionality is regarded specifically from the urban planning and decision-making viewpoint. The toolkits were evaluated on 12 different criteria. After analyzing the toolkits on these criteria, the findings are evaluated on the (mis)match with specific requirements in the urban planning and management context. Secondly, recommendations and guidelines are formulated to support the design of simple valuation tools, tailored to support the development of green infrastructure in urban areas. Approaching the valuation toolkits biophysically and (socio-)economically provides an integral overview of the challenges and opportunities of the capacities of each framework. It was found that most tools are not designed for the peculiarities of the urban context. Several elements contribute to the hampering uptake of GI valuation tools. Firstly, the limited effort in the economic case for green infrastructure remains a burden to use toolkits to compare grey and green alternatives. Secondly, tools are currently seldom designed for the peculiarities of cities: urban ecosystem (dis)services, multi-scalability, life-span assessments of co-benefits and the importance of social benefits. Thirdly, toolkits should be the result of co-development between the scientific community and local authorities in order to create toolkits that are tailor made to the specific needs in the urban planning process. It can be concluded that current tools, are not readily applicable to support decision making as such. However, if applied cautiously, they can have an indicative role to pinpoint further targeted and in-depth analyses.
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Affiliation(s)
- Wito Van Oijstaeijen
- Department of Engineering Management, Institute of Environment and Sustainable Development University of Antwerp, Belgium.
| | - Steven Van Passel
- Department of Engineering Management University of Antwerp, Belgium.
| | - Jan Cools
- Institute of Environment and Sustainable Development University of Antwerp, Belgium.
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25
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Schmidt T, Kharabi Masouleh B, Loges S, Cauwenberghs S, Fraisl P, Maes C, Jonckx B, De Keersmaecker K, Kleppe M, Tjwa M, Schenk T, Vinckier S, Fragoso R, De Mol M, Beel K, Dias S, Verfaillie C, Clark RE, Brümmendorf TH, Vandenberghe P, Rafii S, Holyoake T, Hochhaus A, Cools J, Karin M, Carmeliet G, Dewerchin M, Carmeliet P. Loss or Inhibition of Stromal-Derived PlGF Prolongs Survival of Mice with Imatinib-Resistant Bcr-Abl1 + Leukemia. Cancer Cell 2020; 37:135-136. [PMID: 31935370 DOI: 10.1016/j.ccell.2019.12.010] [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: 10/25/2022]
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26
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Loontiens S, Durinck K, Vanhauwaert S, Depestel L, Oliveira ML, Dewyn G, Bock CD, Barata JT, Langenau D, Cools J, Taghon T, Vlierberghe PV, Speleman F. Abstract 3696: PHF6loss drives IL7R oncogene addiction in TLX1 driven T-ALL. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease. The PHF6 gene is frequently targeted by loss-of-function mutations or deletions, with the highest prevalence in TLX1 or TLX3 rearranged T-ALLs. To gain insights into the putative function of PHF6 as a tumor suppressor in the T-cell lineage, we investigated the effects of PHF6 knock down during normal and malignant thymocytes. Notably, we observed broad effects on the investigated transcriptomes suggesting an important role for PHF6 in gene regulation. Furthermore, IL7R was identified as a common transcriptional target that was significantly upregulated upon PHF6 knockdown in both normal and malignant T cells. IL7R encodes a cytokine receptor critically involved in normal thymic development and which also acts as a bona fide oncogene in subset of primary T-ALLs. Thus, loss of PHF6 might further boost oncogenic addiction of leukemic T-cell lymphoblast to IL7-induced JAK-STAT signaling.
To further explore the role of PHF6 inactivation in TLX1 driven leukemogenesis in vivo, we performed zebrafish modeling. For this, we generated a stable tg(rag2:TLX1, rag2:GFP) overexpressing as well as a phf6 knock out zebrafish line. These lines were crossed and offspring was monitored for T-ALL formation. Interestingly, three fish out of a cohort of 80 animals developed leukemia between 10 to 18 months of age. These leukemias originated from the thymus, spreaded throughout the whole body and were transplantable. Thus far, no leukemia was detected in PHF6 mutated or TLX1 overexpressing only zebrafish. Leukemic cells obtained from tumors that developed in the PHF6null TLX1rag2-TLX1/GFP animals were subjected to RNA-, ATAC- and H3K27ac ChIP-sequencing to assess the epigenetic status of the IL7R locus. In addition, exome-, and CNV-sequencing was performed to identify somatic lesions that cooperated loss of Phf6 during TLX1 driven T-cell transformation in zebrafish. Furthermore, additional injections of TLX1 in combination with an activating IL7R mutant into phf6 mutant zebrafish are currently ongoing to monitor additional effects on accelerated tumor formation. In conclusion, our data suggest that loss of PHF6 drives TLX1 mediated leukemogenesis, at least in part, by increasing surface IL7R expression. Therefore, we believe that increased addiction to oncogenic JAK-STAT signaling may render PHF6 mutant leukemic cells more sensitive to JAK inhibitors, a notion that we are currently investigating in our TLX1/PHF6 and TLX1/PHF6/IL7R zebrafish models.
Citation Format: Siebe Loontiens, Kaat Durinck, Suzanne Vanhauwaert, Lisa Depestel, Mariana L. Oliveira, Givani Dewyn, Charles De Bock, João T. Barata, David Langenau, Jan Cools, Tom Taghon, Pieter Van Vlierberghe, Frank Speleman. PHF6loss drives IL7R oncogene addiction in TLX1 driven T-ALL [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3696.
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27
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Habets RA, de Bock CE, Serneels L, Lodewijckx I, Verbeke D, Nittner D, Narlawar R, Demeyer S, Dooley J, Liston A, Taghon T, Cools J, de Strooper B. Safe targeting of T cell acute lymphoblastic leukemia by pathology-specific NOTCH inhibition. Sci Transl Med 2019; 11:11/494/eaau6246. [DOI: 10.1126/scitranslmed.aau6246] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/18/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
Given the high frequency of activating NOTCH1 mutations in T cell acute lymphoblastic leukemia (T-ALL), inhibition of the γ-secretase complex remains an attractive target to prevent ligand-independent release of the cytoplasmic tail and oncogenic NOTCH1 signaling. However, four different γ-secretase complexes exist, and available inhibitors block all complexes equally. As a result, these cause severe “on-target” gastrointestinal tract, skin, and thymus toxicity, limiting their therapeutic application. Here, we demonstrate that genetic deletion or pharmacologic inhibition of the presenilin-1 (PSEN1) subclass of γ-secretase complexes is highly effective in decreasing leukemia while avoiding dose-limiting toxicities. Clinically, T-ALL samples were found to selectively express only PSEN1-containing γ-secretase complexes. The conditional knockout of Psen1 in developing T cells attenuated the development of a mutant NOTCH1-driven leukemia in mice in vivo but did not abrogate normal T cell development. Treatment of T-ALL cell lines with the selective PSEN1 inhibitor MRK-560 effectively decreased mutant NOTCH1 processing and led to cell cycle arrest. These observations were extended to T-ALL patient-derived xenografts in vivo, demonstrating that MRK-560 treatment decreases leukemia burden and increased overall survival without any associated gut toxicity. Therefore, PSEN1-selective compounds provide a potential therapeutic strategy for safe and effective targeting of T-ALL and possibly also for other diseases in which NOTCH signaling plays a role.
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28
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Kampen KR, Sulima SO, Verbelen B, Girardi T, Vereecke S, Fancello L, Rinaldi G, Verbeeck J, Op de Beeck J, Uyttebroeck A, Meijerink JPP, Moorman AV, Harrison CJ, Spincemaille P, Cools J, Cassiman D, Fendt SM, Vermeersch P, De Keersmaecker K. Correction: The ribosomal RPL10 R98S mutation drives IRES-dependent BCL-2 translation in T-ALL. Leukemia 2019; 33:1055-1062. [PMID: 30850735 PMCID: PMC6756081 DOI: 10.1038/s41375-019-0424-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kim R Kampen
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Sergey O Sulima
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Benno Verbelen
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Tiziana Girardi
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Stijn Vereecke
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Laura Fancello
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Gianmarco Rinaldi
- Laboratory of Cellular Metabolism and Metabolic Regulation, Center for Cancer Biology, VIB, Leuven, Belgium.,Department of Oncology, Laboratory of Cellular Metabolism and Metabolic Regulation, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Jelle Verbeeck
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Joyce Op de Beeck
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Anne Uyttebroeck
- Department of Pediatric Oncology & Hematology, University Hospitals Leuven, Leuven, Belgium
| | | | - Anthony V Moorman
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Pieter Spincemaille
- Department of Gastroenterology-Hepatology and Metabolic Center, University Hospitals Leuven, Leuven, Belgium
| | - Jan Cools
- Laboratory of Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium.,Laboratory of Molecular Biology of Leukemia, Center for Cancer Biology, VIB, Leuven, Belgium
| | - David Cassiman
- Department of Gastroenterology-Hepatology and Metabolic Center, University Hospitals Leuven, Leuven, Belgium
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, Center for Cancer Biology, VIB, Leuven, Belgium.,Department of Oncology, Laboratory of Cellular Metabolism and Metabolic Regulation, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Pieter Vermeersch
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Kim De Keersmaecker
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium.
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29
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Kampen KR, Sulima SO, Verbelen B, Girardi T, Vereecke S, Rinaldi G, Verbeeck J, Op de Beeck J, Uyttebroeck A, Meijerink JPP, Moorman AV, Harrison CJ, Spincemaille P, Cools J, Cassiman D, Fendt SM, Vermeersch P, De Keersmaecker K. The ribosomal RPL10 R98S mutation drives IRES-dependent BCL-2 translation in T-ALL. Leukemia 2019; 33:319-332. [PMID: 29930300 PMCID: PMC6169730 DOI: 10.1038/s41375-018-0176-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 12/11/2022]
Abstract
The R98S mutation in ribosomal protein L10 (RPL10 R98S) affects 8% of pediatric T-cell acute lymphoblastic leukemia (T-ALL) cases, and was previously described to impair cellular proliferation. The current study reveals that RPL10 R98S cells accumulate reactive oxygen species which promotes mitochondrial dysfunction and reduced ATP levels, causing the proliferation defect. RPL10 R98S mutant leukemia cells can survive high oxidative stress levels via a specific increase of IRES-mediated translation of the anti-apoptotic factor B-cell lymphoma 2 (BCL-2), mediating BCL-2 protein overexpression. RPL10 R98S selective sensitivity to the clinically available Bcl-2 inhibitor Venetoclax (ABT-199) was supported by suppression of splenomegaly and the absence of human leukemia cells in the blood of T-ALL xenografted mice. These results shed new light on the oncogenic function of ribosomal mutations in cancer, provide a novel mechanism for BCL-2 upregulation in leukemia, and highlight BCL-2 inhibition as a novel therapeutic opportunity in RPL10 R98S defective T-ALL.
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Affiliation(s)
- Kim R Kampen
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Sergey O Sulima
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Benno Verbelen
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Tiziana Girardi
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Stijn Vereecke
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Gianmarco Rinaldi
- Laboratory of Cellular Metabolism and Metabolic Regulation, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Oncology, Laboratory of Cellular Metabolism and Metabolic Regulation, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Jelle Verbeeck
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Joyce Op de Beeck
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Anne Uyttebroeck
- Department of Pediatric Oncology & Hematology, University Hospitals Leuven, Leuven, Belgium
| | | | - Anthony V Moorman
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Christine J Harrison
- Leukaemia Research Cytogenetics Group, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Pieter Spincemaille
- Department of Gastroenterology-Hepatology and Metabolic Center, University Hospitals Leuven, Leuven, Belgium
| | - Jan Cools
- Laboratory of Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
- Laboratory of Molecular Biology of Leukemia, Center for Cancer Biology, VIB, Leuven, Belgium
| | - David Cassiman
- Department of Gastroenterology-Hepatology and Metabolic Center, University Hospitals Leuven, Leuven, Belgium
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Oncology, Laboratory of Cellular Metabolism and Metabolic Regulation, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Pieter Vermeersch
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Kim De Keersmaecker
- Department of Oncology, Laboratory for Disease Mechanisms in Cancer, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium.
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30
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de Bock CE, Down M, Baidya K, Sweron B, Boyd AW, Fiers M, Burns GF, Molloy TJ, Lock RB, Soulier J, Taghon T, Van Vlierberghe P, Cools J, Holst J, Thorne RF. T-cell acute lymphoblastic leukemias express a unique truncated FAT1 isoform that cooperates with NOTCH1 in leukemia development. Haematologica 2018; 104:e204-e207. [PMID: 30514801 DOI: 10.3324/haematol.2018.198424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Charles E de Bock
- KU Leuven, Center for Human Genetics, Belgium .,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Michelle Down
- Leukaemia Foundation Laboratory, QIMR-Berghofer Medical Research Institute, Brisbane, Australia
| | - Kinsha Baidya
- School of Medical Sciences and Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
| | - Bram Sweron
- KU Leuven, Center for Human Genetics, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Andrew W Boyd
- Leukaemia Foundation Laboratory, QIMR-Berghofer Medical Research Institute, Brisbane, Australia
| | - Mark Fiers
- VIB-KU Leuven Center for Brain & Disease Research, Belgium
| | - Gordon F Burns
- Cancer Research Unit, The University of Newcastle, Callaghan, NSW, Australia
| | - Timothy J Molloy
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Richard B Lock
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Jean Soulier
- U944 INSERM and Hematology laboratory, St-Louis Hospital, APHP, Hematology University Institute, University Paris-Diderot, France
| | - Tom Taghon
- Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Belgium
| | - Pieter Van Vlierberghe
- Center for Medical Genetics, Ghent University Hospital, Belgium Cancer Research Institute Ghent (CRIG), Belgium
| | - Jan Cools
- KU Leuven, Center for Human Genetics, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Jeff Holst
- Translational Cancer Metabolism Laboratory, Lowy Cancer Research Centre, University of New South Wales, Sydney, Australia
| | - Rick F Thorne
- Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Henan University, Zhengzhou, China .,School of Environmental and Life Sciences, University of Newcastle, NSW, Australia
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31
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Simonetti G, Padella A, do Valle IF, Fontana MC, Fonzi E, Bruno S, Baldazzi C, Guadagnuolo V, Manfrini M, Ferrari A, Paolini S, Papayannidis C, Marconi G, Franchini E, Zuffa E, Laginestra MA, Zanotti F, Astolfi A, Iacobucci I, Bernardi S, Sazzini M, Ficarra E, Hernandez JM, Vandenberghe P, Cools J, Bullinger L, Ottaviani E, Testoni N, Cavo M, Haferlach T, Castellani G, Remondini D, Martinelli G. Aneuploid acute myeloid leukemia exhibits a signature of genomic alterations in the cell cycle and protein degradation machinery. Cancer 2018; 125:712-725. [PMID: 30480765 PMCID: PMC6587451 DOI: 10.1002/cncr.31837] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/08/2018] [Accepted: 06/26/2018] [Indexed: 12/19/2022]
Abstract
Background Aneuploidy occurs in more than 20% of acute myeloid leukemia (AML) cases and correlates with an adverse prognosis. Methods To understand the molecular bases of aneuploid acute myeloid leukemia (A‐AML), this study examined the genomic profile in 42 A‐AML cases and 35 euploid acute myeloid leukemia (E‐AML) cases. Results A‐AML was characterized by increased genomic complexity based on exonic variants (an average of 26 somatic mutations per sample vs 15 for E‐AML). The integration of exome, copy number, and gene expression data revealed alterations in genes involved in DNA repair (eg, SLX4IP, RINT1, HINT1, and ATR) and the cell cycle (eg, MCM2, MCM4, MCM5, MCM7, MCM8, MCM10, UBE2C, USP37, CK2, CK3, CK4, BUB1B, NUSAP1, and E2F) in A‐AML, which was associated with a 3‐gene signature defined by PLK1 and CDC20 upregulation and RAD50 downregulation and with structural or functional silencing of the p53 transcriptional program. Moreover, A‐AML was enriched for alterations in the protein ubiquitination and degradation pathway (eg, increased levels of UHRF1 and UBE2C and decreased UBA3 expression), response to reactive oxygen species, energy metabolism, and biosynthetic processes, which may help in facing the unbalanced protein load. E‐AML was associated with BCOR/BCORL1 mutations and HOX gene overexpression. Conclusions These findings indicate that aneuploidy‐related and leukemia‐specific alterations cooperate to tolerate an abnormal chromosome number in AML, and they point to the mitotic and protein degradation machineries as potential therapeutic targets. Aneuploid acute myeloid leukemia (A‐AML) is associated with genomic and transcriptional alterations in the cell cycle and protein degradation pathways. The upregulation of PLK1 and CDC20 and the downregulation of RAD50 and of a p53‐related signature are hallmarks of A‐AML.
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Affiliation(s)
- Giorgia Simonetti
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Antonella Padella
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Italo Farìa do Valle
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy.,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Maria Chiara Fontana
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Eugenio Fonzi
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Samantha Bruno
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Carmen Baldazzi
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Viviana Guadagnuolo
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Marco Manfrini
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Anna Ferrari
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Stefania Paolini
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Cristina Papayannidis
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Giovanni Marconi
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Eugenia Franchini
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Elisa Zuffa
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Maria Antonella Laginestra
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Federica Zanotti
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Annalisa Astolfi
- Giorgio Prodi Cancer Research Center, University of Bologna, Bologna, Italy
| | - Ilaria Iacobucci
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Simona Bernardi
- Unit of Blood Diseases and Stem Cell Transplantation, University of Brescia, Brescia, Italy
| | - Marco Sazzini
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | | | - Jesus Maria Hernandez
- Fundación de Investigación del Cáncer de la Universidad de Salamanca, Salamanca, Spain
| | | | - Jan Cools
- Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Emanuela Ottaviani
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Nicoletta Testoni
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | - Michele Cavo
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
| | | | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna and L. e A. Seràgnoli Institute of Hematology, Bologna, Italy
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32
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Baens M, Stirparo R, Lampi Y, Verbeke D, Vandepoel R, Cools J, Marynen P, de Bock CE, Bornschein S. Malt1 self-cleavage is critical for regulatory T cell homeostasis and anti-tumor immunity in mice. Eur J Immunol 2018; 48:1728-1738. [PMID: 30025160 PMCID: PMC6220888 DOI: 10.1002/eji.201847597] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/04/2018] [Accepted: 07/13/2018] [Indexed: 12/31/2022]
Abstract
Mucosa-associated lymphoid tissue 1 (Malt1) regulates immune cell function by mediating the activation of nuclear factor κB (NF-κB) signaling through both its adaptor and proteolytic function. Malt1 is also a target of its own protease activity and this self-cleavage further contributes to NF-κB activity. Until now, the functional distinction between Malt1 self-cleavage and its general protease function in regulating NF-κB signaling and immune activation remained unclear. Here we demonstrate, using a new mouse model, the importance of Malt1 self-cleavage in regulating expression of NF-κB target genes and subsequent T cell activation. Significantly, we further establish that Treg homeostasis is critically linked to Malt1 function via a Treg intrinsic and extrinsic mechanism. TCR-mediated Malt1 proteolytic activity and self-cleavage was found to drive Il2 expression in conventional CD4+ T cells, thereby regulating Il2 availability for Treg homeostasis. Remarkably, the loss of Malt1-mediated self-cleavage alone was sufficient to cause a significant Treg deficit resulting in increased anti-tumor immune reactivity without associated autoimmunity complications. These results establish for the first time that inhibition of MALT1 proteolytic activity could be a viable therapeutic strategy to augment anti-tumor immunity.
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Affiliation(s)
- Mathijs Baens
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Cistim Leuven vzwLeuvenBelgium
| | - Rocco Stirparo
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
| | - Youlia Lampi
- Switch LaboratoryVIBLeuvenBelgium
- KU Leuven Department for Cellular and MolecularLeuvenBelgium
| | - Delphine Verbeke
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
| | - Roel Vandepoel
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
| | - Jan Cools
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
| | | | - Charles E. de Bock
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
| | - Simon Bornschein
- KU Leuven Department of Human GeneticsLeuvenBelgium
- VIB Center for Cancer BiologyLeuvenBelgium
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33
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Brajic A, Franckaert D, Burton O, Bornschein S, Calvanese AL, Demeyer S, Cools J, Dooley J, Schlenner S, Liston A. The Long Non-coding RNA Flatr Anticipates Foxp3 Expression in Regulatory T Cells. Front Immunol 2018; 9:1989. [PMID: 30319599 PMCID: PMC6167443 DOI: 10.3389/fimmu.2018.01989] [Citation(s) in RCA: 27] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/13/2018] [Indexed: 12/30/2022] Open
Abstract
Mammalian genomes encode a plethora of long non-coding RNA (lncRNA). These transcripts are thought to regulate gene expression, influencing biological processes from development to pathology. Results from the few lncRNA that have been studied in the context of the immune system have highlighted potentially critical functions as network regulators. Here we explored the nature of the lncRNA transcriptome in regulatory T cells (Tregs), a subset of CD4+ T cells required to establish and maintain immunological self-tolerance. The identified Treg lncRNA transcriptome showed distinct differences from that of non-regulatory CD4+ T cells, with evidence of direct shaping of the lncRNA transcriptome by Foxp3, the master transcription factor driving the distinct mRNA profile of Tregs. Treg lncRNA changes were disproportionally reversed in the absence of Foxp3, with an enrichment for colocalisation with Foxp3 DNA binding sites, indicating a direct coordination of transcription by Foxp3 independent of the mRNA coordination function. We further identified a novel lncRNA Flatr, as a member of the core Treg lncRNA transcriptome. Flatr expression anticipates Foxp3 expression during in vitro Treg conversion, and Flatr-deficient mice show a mild delay in in vitro and peripheral Treg induction. These results implicate Flatr as part of the upstream cascade leading to Treg conversion, and may provide clues as to the nature of this process.
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Affiliation(s)
- Aleksandra Brajic
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Dean Franckaert
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Oliver Burton
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Simon Bornschein
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium.,VIB Cancer Research Center, VIB, Leuven, Belgium
| | - Anna L Calvanese
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | | | - Jan Cools
- VIB Cancer Research Center, VIB, Leuven, Belgium
| | - James Dooley
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Susan Schlenner
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Adrian Liston
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
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34
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Degryse S, de Bock CE, Demeyer S, Govaerts I, Bornschein S, Verbeke D, Jacobs K, Binos S, Skerrett-Byrne DA, Murray HC, Verrills NM, Van Vlierberghe P, Cools J, Dun MD. Correction: Mutant JAK3 phosphoproteomic profiling predicts synergism between JAK3 inhibitors and MEK/BCL2 inhibitors for the treatment of T-cell acute lymphoblastic leukemia. Leukemia 2018; 32:2731. [PMID: 30232463 PMCID: PMC7609275 DOI: 10.1038/s41375-018-0241-7] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- S Degryse
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - C E de Bock
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - S Demeyer
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - I Govaerts
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - S Bornschein
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - D Verbeke
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - K Jacobs
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - S Binos
- Thermo Fisher Scientific, Scoresby, VIC, Australia
| | - D A Skerrett-Byrne
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - H C Murray
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - N M Verrills
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - P Van Vlierberghe
- Department of Pediatrics and Genetics, Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - J Cools
- VIB Center for Cancer Biology, Leuven, Belgium. .,KU Leuven Center for Human Genetics, Leuven, Belgium.
| | - M D Dun
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia. .,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia.
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35
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Vicente C, Stirparo R, Demeyer S, de Bock CE, Gielen O, Atkins M, Yan J, Halder G, Hassan BA, Cools J. The CCR4-NOT complex is a tumor suppressor in Drosophila melanogaster eye cancer models. J Hematol Oncol 2018; 11:108. [PMID: 30144809 PMCID: PMC6109294 DOI: 10.1186/s13045-018-0650-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/13/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The CNOT3 protein is a subunit of the CCR4-NOT complex, which is involved in mRNA degradation. We recently identified CNOT3 loss-of-function mutations in patients with T-cell acute lymphoblastic leukemia (T-ALL). METHODS Here, we use different Drosophila melanogaster eye cancer models to study the potential tumor suppressor function of Not3, the CNOT3 orthologue, and other members of the CCR4-NOT complex. RESULTS Our data show that knockdown of Not3, the structural components Not1/Not2, and the deadenylases twin/Pop2 all result in increased tumor formation. In addition, overexpression of Not3 could reduce tumor formation. Not3 downregulation has a mild but broad effect on gene expression and leads to increased levels of genes involved in DNA replication and ribosome biogenesis. CycB upregulation also contributes to the Not3 tumor phenotype. Similar findings were obtained in human T-ALL cell lines, pointing out the conserved function of Not3. CONCLUSIONS Together, our data establish a critical role for Not3 and the entire CCR4-NOT complex as tumor suppressor.
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Affiliation(s)
- Carmen Vicente
- Center for Cancer Biology, VIB, Leuven, Belgium. .,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium. .,Centro de Investigación Médica Aplicada, Av. de Pío XII, 55, 31008, Pamplona, Spain.
| | - Rocco Stirparo
- Center for Cancer Biology, VIB, Leuven, Belgium.,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium
| | - Sofie Demeyer
- Center for Cancer Biology, VIB, Leuven, Belgium.,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium
| | - Charles E de Bock
- Center for Cancer Biology, VIB, Leuven, Belgium.,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium
| | - Olga Gielen
- Center for Cancer Biology, VIB, Leuven, Belgium.,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium
| | - Mardelle Atkins
- Center for Cancer Biology, VIB, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Jiekun Yan
- Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium.,Center for Brain & Disease Research, VIB, Leuven, Belgium
| | - Georg Halder
- Center for Cancer Biology, VIB, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Bassem A Hassan
- Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium.,Center for Brain & Disease Research, VIB, Leuven, Belgium.,Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, UPMC, Sorbonne Universités, Inserm, CNRS, Paris, France
| | - Jan Cools
- Center for Cancer Biology, VIB, Leuven, Belgium. .,Center for Human Genetics, KU Leuven, Herestraat 49, box 912, B-3000, Leuven, Belgium.
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36
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Vanden Bempt M, Demeyer S, Broux M, De Bie J, Bornschein S, Mentens N, Vandepoel R, Geerdens E, Radaelli E, Bornhauser BC, Kulozik AE, Meijerink JP, Bourquin JP, de Bock CE, Cools J. Cooperative Enhancer Activation by TLX1 and STAT5 Drives Development of NUP214-ABL1/TLX1-Positive T Cell Acute Lymphoblastic Leukemia. Cancer Cell 2018; 34:271-285.e7. [PMID: 30107177 PMCID: PMC6097876 DOI: 10.1016/j.ccell.2018.07.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 05/04/2018] [Accepted: 07/18/2018] [Indexed: 01/01/2023]
Abstract
The NUP214-ABL1 fusion is a constitutively activated tyrosine kinase that is significantly associated with overexpression of the TLX1 and TLX3 transcription factors in T cell acute lymphoblastic leukemia (T-ALL). Here we show that NUP214-ABL1 cooperates with TLX1 in driving T-ALL development using a transgenic mouse model and human T-ALL cells. Using integrated ChIP-sequencing, ATAC-sequencing, and RNA-sequencing data, we demonstrate that TLX1 and STAT5, the downstream effector of NUP214-ABL1, co-bind poised enhancer regions, and cooperatively activate the expression of key proto-oncogenes such as MYC and BCL2. Inhibition of STAT5, downregulation of TLX1 or MYC, or interference with enhancer function through BET-inhibitor treatment leads to reduction of target gene expression and induction of leukemia cell death.
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Affiliation(s)
- Marlies Vanden Bempt
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Sofie Demeyer
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Michaël Broux
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Jolien De Bie
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Simon Bornschein
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Nicole Mentens
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Roel Vandepoel
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Ellen Geerdens
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Enrico Radaelli
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Beat C Bornhauser
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Andreas E Kulozik
- Department of Pediatric Hematology and Oncology, Heidelberg University Children's Hospital, Heidelberg, Germany; Hopp Children's Cancer Center at the NCT Heidelberg, Heidelberg, Germany
| | - Jules P Meijerink
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jean-Pierre Bourquin
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Charles E de Bock
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium.
| | - Jan Cools
- KU Leuven Center for Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium.
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37
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Verboom K, Van Loocke W, Volders PJ, Decaesteker B, Cobos FA, Bornschein S, de Bock CE, Atak ZK, Clappier E, Aerts S, Cools J, Soulier J, Taghon T, Van Vlierberghe P, Vandesompele J, Speleman F, Durinck K. A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing. Haematologica 2018; 103:e585-e589. [PMID: 29954933 DOI: 10.3324/haematol.2018.190587] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Karen Verboom
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium
| | - Wouter Van Loocke
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium
| | - Pieter-Jan Volders
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium.,Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks, BIG N2N, Belgium
| | - Bieke Decaesteker
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium
| | - Francisco Avila Cobos
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks, BIG N2N, Belgium
| | - Simon Bornschein
- KU Leuven Center for Human Genetics, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Charles E de Bock
- KU Leuven Center for Human Genetics, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Zeynep Kalender Atak
- KU Leuven Center for Human Genetics, Belgium.,VIB Center for Brain & Disease Research, Laboratory of Computational Biology, Leuven, Belgium
| | | | - Stein Aerts
- KU Leuven Center for Human Genetics, Belgium.,VIB Center for Brain & Disease Research, Laboratory of Computational Biology, Leuven, Belgium
| | - Jan Cools
- KU Leuven Center for Human Genetics, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Jean Soulier
- Hôpital Saint Louis, Institut Universitaire d'Hématologie, Paris, France
| | - Tom Taghon
- Cancer Research Institute Ghent, Belgium.,Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Belgium
| | - Pieter Van Vlierberghe
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks, BIG N2N, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Belgium.,Cancer Research Institute Ghent, Belgium
| | - Kaat Durinck
- Center for Medical Genetics, Ghent University, Belgium .,Cancer Research Institute Ghent, Belgium
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38
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de Bock CE, Cools J. JAK3 mutations and HOXA9 expression are important cooperating events in T-cell acute lymphoblastic leukemia. Mol Cell Oncol 2018; 5:e1458014. [PMID: 30250904 PMCID: PMC6149783 DOI: 10.1080/23723556.2018.1458014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 03/13/2018] [Accepted: 03/13/2018] [Indexed: 11/28/2022]
Abstract
Sequencing data from large cohorts of T-cell acute lymphoblastic leukemia patients identified a significant association between the presence of JAK3 mutations and ectopic HOXA9 expression. Mouse models using a constitutive or novel inducible retroviral expression vector to express the JAK3(M511I) mutant and HOXA9 led to the development of an aggressive leukemia in vivo, with shorter latency than JAK3(M511I) or HOXA9 alone. This was primarily due to the co-binding of STAT5 and HOXA9 to the same genomic loci leading to increased oncogenic JAK-STAT signaling.
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Affiliation(s)
- Charles E de Bock
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Jan Cools
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
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39
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de Bock CE, Demeyer S, Degryse S, Verbeke D, Sweron B, Gielen O, Vandepoel R, Vicente C, Vanden Bempt M, Dagklis A, Geerdens E, Bornschein S, Gijsbers R, Soulier J, Meijerink JP, Heinäniemi M, Teppo S, Bouvy-Liivrand M, Lohi O, Radaelli E, Cools J. HOXA9 Cooperates with Activated JAK/STAT Signaling to Drive Leukemia Development. Cancer Discov 2018; 8:616-631. [PMID: 29496663 DOI: 10.1158/2159-8290.cd-17-0583] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 01/26/2018] [Accepted: 02/22/2018] [Indexed: 11/16/2022]
Abstract
Leukemia is caused by the accumulation of multiple genomic lesions in hematopoietic precursor cells. However, how these events cooperate during oncogenic transformation remains poorly understood. We studied the cooperation between activated JAK3/STAT5 signaling and HOXA9 overexpression, two events identified as significantly co-occurring in T-cell acute lymphoblastic leukemia. Expression of mutant JAK3 and HOXA9 led to a rapid development of leukemia originating from multipotent or lymphoid-committed progenitors, with a significant decrease in disease latency compared with JAK3 or HOXA9 alone. Integrated RNA sequencing, chromatin immunoprecipitation sequencing, and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) revealed that STAT5 and HOXA9 have co-occupancy across the genome, resulting in enhanced STAT5 transcriptional activity and ectopic activation of FOS/JUN (AP1). Our data suggest that oncogenic transcription factors such as HOXA9 provide a fertile ground for specific signaling pathways to thrive, explaining why JAK/STAT pathway mutations accumulate in HOXA9-expressing cells.Significance: The mechanism of oncogene cooperation in cancer development remains poorly characterized. In this study, we model the cooperation between activated JAK/STAT signaling and ectopic HOXA9 expression during T-cell leukemia development. We identify a direct cooperation between STAT5 and HOXA9 at the transcriptional level and identify PIM1 kinase as a possible drug target in mutant JAK/STAT/HOXA9-positive leukemia cases. Cancer Discov; 8(5); 616-31. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Charles E de Bock
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Sofie Demeyer
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Sandrine Degryse
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Delphine Verbeke
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Bram Sweron
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Olga Gielen
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Roel Vandepoel
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Carmen Vicente
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Marlies Vanden Bempt
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Antonis Dagklis
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Ellen Geerdens
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Simon Bornschein
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Rik Gijsbers
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jean Soulier
- U944 INSERM and Hematology Laboratory, St-Louis Hospital, APHP, Hematology University Institute, University Paris-Diderot, Paris, France
| | - Jules P Meijerink
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Susanna Teppo
- Tampere Centre for Child Health Research, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Maria Bouvy-Liivrand
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Olli Lohi
- Tampere Centre for Child Health Research, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Enrico Radaelli
- KU Leuven, Center for Human Genetics, Leuven, Belgium.,VIB, Center for Cancer Biology, Leuven, Belgium
| | - Jan Cools
- KU Leuven, Center for Human Genetics, Leuven, Belgium. .,VIB, Center for Cancer Biology, Leuven, Belgium
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40
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Degryse S, de Bock CE, Demeyer S, Govaerts I, Bornschein S, Verbeke D, Jacobs K, Binos S, Skerrett-Byrne DA, Murray HC, Verrills NM, Van Vlierberghe P, Cools J, Dun MD. Mutant JAK3 phosphoproteomic profiling predicts synergism between JAK3 inhibitors and MEK/BCL2 inhibitors for the treatment of T-cell acute lymphoblastic leukemia. Leukemia 2017; 32:788-800. [PMID: 28852199 PMCID: PMC5843905 DOI: 10.1038/leu.2017.276] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/17/2017] [Accepted: 08/15/2017] [Indexed: 02/06/2023]
Abstract
Mutations in the interleukin-7 receptor (IL7R) or the Janus kinase 3 (JAK3) kinase occur frequently in T-cell acute lymphoblastic leukemia (T-ALL) and both are able to drive cellular transformation and the development of T-ALL in mouse models. However, the signal transduction pathways downstream of JAK3 mutations remain poorly characterized. Here we describe the phosphoproteome downstream of the JAK3(L857Q)/(M511I) activating mutations in transformed Ba/F3 lymphocyte cells. Signaling pathways regulated by JAK3 mutants were assessed following acute inhibition of JAK1/JAK3 using the JAK kinase inhibitors ruxolitinib or tofacitinib. Comprehensive network interrogation using the phosphoproteomic signatures identified significant changes in pathways regulating cell cycle, translation initiation, mitogen-activated protein kinase and phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)/AKT signaling, RNA metabolism, as well as epigenetic and apoptotic processes. Key regulatory proteins within pathways that showed altered phosphorylation following JAK inhibition were targeted using selumetinib and trametinib (MEK), buparlisib (PI3K) and ABT-199 (BCL2), and found to be synergistic in combination with JAK kinase inhibitors in primary T-ALL samples harboring JAK3 mutations. These data provide the first detailed molecular characterization of the downstream signaling pathways regulated by JAK3 mutations and provide further understanding into the oncogenic processes regulated by constitutive kinase activation aiding in the development of improved combinatorial treatment regimens.
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Affiliation(s)
- S Degryse
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - C E de Bock
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - S Demeyer
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - I Govaerts
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - S Bornschein
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - D Verbeke
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - K Jacobs
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - S Binos
- Thermo Fisher Scientific, Scoresby, Victoria, Australia
| | - D A Skerrett-Byrne
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - H C Murray
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - N M Verrills
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia
| | - P Van Vlierberghe
- Department of Pediatrics and Genetics, Center for Medical Genetics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - J Cools
- VIB Center for Cancer Biology, Leuven, Belgium.,KU Leuven Center for Human Genetics, Leuven, Belgium
| | - M D Dun
- Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales, Australia.,Cancer Research Program, School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, New South Wales, Australia
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41
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van der Krogt JA, Bempt MV, Ferreiro JF, Mentens N, Jacobs K, Pluys U, Doms K, Geerdens E, Uyttebroeck A, Pierre P, Michaux L, Devos T, Vandenberghe P, Tousseyn T, Cools J, Wlodarska I. Anaplastic lymphoma kinase-positive anaplastic large cell lymphoma with the variant RNF213-, ATIC- and TPM3-ALK fusions is characterized by copy number gain of the rearranged ALK gene. Haematologica 2017; 102:1605-1616. [PMID: 28659337 PMCID: PMC5685221 DOI: 10.3324/haematol.2016.146571] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 03/24/2016] [Accepted: 06/26/2017] [Indexed: 12/11/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK)-positive anaplastic large cell lymphoma is characterized by 2p23/ALK aberrations, including the classic t(2;5)(p23;q35)/NPM1-ALK rearrangement present in ~80% of cases and several variant t(2p23/ALK) occurring in the remaining cases. The ALK fusion partners play a key role in the constitutive activation of the chimeric protein and its subcellular localization. Using various molecular technologies, we have characterized ALK fusions in eight recently diagnosed anaplastic large cell lymphoma cases with cytoplasmic-only ALK expression. The identified partner genes included EEF1G (one case), RNF213/ALO17 (one case), ATIC (four cases) and TPM3 (two cases). Notably, all cases showed copy number gain of the rearranged ALK gene, which is never observed in NPM1-ALK-positive lymphomas. We hypothesized that this could be due to lower expression levels and/or lower oncogenic potential of the variant ALK fusions. Indeed, all partner genes, except EEF1G, showed lower expression in normal and malignant T cells, in comparison with NPM1. In addition, we investigated the transformation potential of endogenous Npm1-Alk and Atic-Alk fusions generated by clustered regularly interspaced short palindromic repeats/Cas9 genome editing in Ba/F3 cells. We found that Npm1-Alk has a stronger transformation potential than Atic-Alk, and we observed a subclonal gain of Atic-Alk after a longer culture period, which was not observed for Npm1-Alk. Taken together, our data illustrate that lymphomas driven by the variant ATIC-ALK fusion (and likely by RNF213-ALK and TPM3-ALK), but not the classic NPM1-ALK, require an increased dosage of the ALK hybrid gene to compensate for the relatively low and insufficient expression and signaling properties of the chimeric gene.
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Affiliation(s)
| | - Marlies Vanden Bempt
- Center for Human Genetics, KU Leuven, Belgium.,Center for Cancer Biology, VIB, Leuven, Belgium
| | | | - Nicole Mentens
- Center for Human Genetics, KU Leuven, Belgium.,Center for Cancer Biology, VIB, Leuven, Belgium
| | - Kris Jacobs
- Center for Human Genetics, KU Leuven, Belgium.,Center for Cancer Biology, VIB, Leuven, Belgium
| | | | | | - Ellen Geerdens
- Center for Human Genetics, KU Leuven, Belgium.,Center for Cancer Biology, VIB, Leuven, Belgium
| | | | - Pascal Pierre
- Department of Hematology, Cliniques Sud Luxembourg, Arlon, Belgium
| | | | - Timothy Devos
- Department of Hematology, University Hospitals Leuven, Belgium
| | - Peter Vandenberghe
- Center for Human Genetics, KU Leuven, Belgium.,Department of Hematology, University Hospitals Leuven, Belgium
| | - Thomas Tousseyn
- Translational Cell and Tissue Research KU Leuven, Belgium.,Department of Pathology, University Hospitals Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Belgium.,Center for Cancer Biology, VIB, Leuven, Belgium
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42
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Przybyl J, Kowalewska M, Quattrone A, Dewaele B, Vanspauwen V, Varma S, Vennam S, Newman AM, Swierniak M, Bakuła-Zalewska E, Siedlecki JA, Bidzinski M, Cools J, van de Rijn M, Debiec-Rychter M. Macrophage infiltration and genetic landscape of undifferentiated uterine sarcomas. JCI Insight 2017; 2:94033. [PMID: 28570276 DOI: 10.1172/jci.insight.94033] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Endometrial stromal tumors include translocation-associated low- and high-grade endometrial stromal sarcomas (ESS) and highly malignant undifferentiated uterine sarcomas (UUS). UUS is considered a poorly defined group of aggressive tumors and is often seen as a diagnosis of exclusion after ESS and leiomyosarcoma (LMS) have been ruled out. We performed a comprehensive analysis of gene expression, copy number variation, point mutations, and immune cell infiltrates in the largest series to date of all major types of uterine sarcomas to shed light on the biology of UUS and to identify potential novel therapeutic targets. We show that UUS tumors have a distinct molecular profile from LMS and ESS. Gene expression and immunohistochemical analyses revealed the presence of high numbers of tumor-associated macrophages (TAMs) in UUS, which makes UUS patients suitable candidates for therapies targeting TAMs. Our results show a high genomic instability of UUS and downregulation of several TP53-mediated tumor suppressor genes, such as NDN, CDH11, and NDRG4. Moreover, we demonstrate that UUS carry somatic mutations in several oncogenes and tumor suppressor genes implicated in RAS/PI3K/AKT/mTOR, ERBB3, and Hedgehog signaling.
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Affiliation(s)
- Joanna Przybyl
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland.,Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Magdalena Kowalewska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland.,Department of Immunology, Biochemistry and Nutrition, Medical University of Warsaw, Warsaw, Poland
| | - Anna Quattrone
- Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Barbara Dewaele
- Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Vanessa Vanspauwen
- Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Sujay Vennam
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine.,Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Michal Swierniak
- Human Cancer Genetics, Center of New Technologies, CENT, University of Warsaw, Warsaw, Poland
| | | | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland
| | - Mariusz Bidzinski
- Department of Gynecologic Oncology, Maria Sklodowska-Curie Institute-Oncology Center, Warsaw, Poland.,The Faculty of Medicine and Health Sciences, Jan Kochanowski University, Kielce, Poland
| | - Jan Cools
- KU Leuven and Flanders Interuniversity Institute for Biotechnology (VIB), Leuven, Belgium
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Maria Debiec-Rychter
- Department of Human Genetics, KU Leuven and University Hospitals Leuven, Leuven, Belgium
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43
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Vercruysse T, De Bie J, Neggers JE, Jacquemyn M, Vanstreels E, Schmid-Burgk JL, Hornung V, Baloglu E, Landesman Y, Senapedis W, Shacham S, Dagklis A, Cools J, Daelemans D. The Second-Generation Exportin-1 Inhibitor KPT-8602 Demonstrates Potent Activity against Acute Lymphoblastic Leukemia. Clin Cancer Res 2017; 23:2528-2541. [PMID: 27780859 DOI: 10.1158/1078-0432.ccr-16-1580] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/14/2016] [Accepted: 10/10/2016] [Indexed: 11/16/2022]
Abstract
Purpose: Human exportin-1 (XPO1) is the key nuclear-cytoplasmic transport protein that exports different cargo proteins out of the nucleus. Inducing nuclear accumulation of these proteins by inhibiting XPO1 causes cancer cell death. First clinical validation of pharmacological inhibition of XPO1 was obtained with the Selective Inhibitor of Nuclear Export (SINE) compound selinexor (KPT-330) demonstrating activity in phase-II/IIb clinical trials when dosed 1 to 3 times weekly. The second-generation SINE compound KPT-8602 shows improved tolerability and can be dosed daily. Here, we investigate and validate the drug-target interaction of KPT-8602 and explore its activity against acute lymphoblastic leukemia (ALL).Experimental Design: We examined the effect of KPT-8602 on XPO1 function and XPO1-cargo as well as on a panel of leukemia cell lines. Mutant XPO1 leukemia cells were designed to validate KPT-8602's drug-target interaction. In vivo, anti-ALL activity was measured in a mouse ALL model and patient-derived ALL xenograft models.Results: KPT-8602 induced caspase-dependent apoptosis in a panel of leukemic cell lines in vitro Using CRISPR/Cas9 genome editing, we demonstrated the specificity of KPT-8602 for cysteine 528 in the cargo-binding groove of XPO1 and validated the drug target interaction. In vivo, KPT-8602 showed potent anti-leukemia activity in a mouse ALL model as well as in patient-derived T- and B-ALL xenograft models without affecting normal hematopoiesis.Conclusions: KPT-8602 is highly specific for XPO1 inhibition and demonstrates potent anti-leukemic activity supporting clinical application of the second-generation SINE compound for the treatment of ALL. Clin Cancer Res; 23(10); 2528-41. ©2016 AACR.
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Affiliation(s)
- Thomas Vercruysse
- KU Leuven Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Leuven, Belgium
| | - Jolien De Bie
- KU Leuven Department of Human Genetics, Laboratory of Molecular Biology of Leukemia, Leuven, Belgium
- VIB Center for the Biology of Disease, Leuven, Belgium
| | - Jasper E Neggers
- KU Leuven Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Leuven, Belgium
| | - Maarten Jacquemyn
- KU Leuven Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Leuven, Belgium
| | - Els Vanstreels
- KU Leuven Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Leuven, Belgium
| | | | - Veit Hornung
- Institute of Molecular Medicine, University Hospital, University of Bonn, Bonn, Germany
| | | | | | | | | | - Antonis Dagklis
- KU Leuven Department of Human Genetics, Laboratory of Molecular Biology of Leukemia, Leuven, Belgium
- VIB Center for the Biology of Disease, Leuven, Belgium
| | - Jan Cools
- KU Leuven Department of Human Genetics, Laboratory of Molecular Biology of Leukemia, Leuven, Belgium
- VIB Center for the Biology of Disease, Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Leuven, Belgium.
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Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy caused by the accumulation of genomic lesions that affect the development of T cells. For many years, it has been established that deregulated expression of transcription factors, impairment of the CDKN2A/2B cell-cycle regulators, and hyperactive NOTCH1 signaling play prominent roles in the pathogenesis of this leukemia. In the past decade, systematic screening of T-ALL genomes by high-resolution copy-number arrays and next-generation sequencing technologies has revealed that T-cell progenitors accumulate additional mutations affecting JAK/STAT signaling, protein translation, and epigenetic control, providing novel attractive targets for therapy. In this review, we provide an update on our knowledge of T-ALL pathogenesis, the opportunities for the introduction of targeted therapy, and the challenges that are still ahead.
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Affiliation(s)
- Tiziana Girardi
- Department of Oncology, KU Leuven, Leuven, Belgium
- Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Carmen Vicente
- Leuven Cancer Institute (LKI), Leuven, Belgium
- VIB Center for the Biology of Disease, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Jan Cools
- Leuven Cancer Institute (LKI), Leuven, Belgium
- VIB Center for the Biology of Disease, Leuven, Belgium
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Kim De Keersmaecker
- Department of Oncology, KU Leuven, Leuven, Belgium
- Leuven Cancer Institute (LKI), Leuven, Belgium
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45
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46
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Affiliation(s)
- Carmen Vicente
- Center for Human Genetics, KU Leuven, Leuven Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven Center for the Biology of Disease, VIB, Leuven, Belgium
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47
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Daelemans D, Neggers JE, De Bie J, Jacquemyn M, D’Hoore A, Vanstreels E, Baloglu E, Landesman Y, Shacham S, Senapedis W, Dagklis A, Vercruysse T, Cools J. Abstract LB-210: KPT-8602 is a second-generation XPO1 inhibitor with improved in vivo tolerability that demonstrates potent acute lymphoblastic leukemia activity. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Human exportin-1 (XPO1) is the key nuclear-cytoplasmic transport protein that exports a wide variety of different cargo proteins including tumor suppressors out of the cell's nucleus. Inhibition of XPO1 function consequently restores nuclear localization of these proteins and is a promising therapeutic strategy for cancer. Selective inhibitor of nuclear export (SINE) compounds are inhibitors of the XPO1-mediated nuclear export with potent anti-cancer activity. The oral clinical candidate SINE selinexor (KPT-330) is currently in Phase-II/IIb clinical trials and demonstrated remission in patients as a single agent or in combination therapy in trials for pre-treated, relapsed and refractory hematological and solid tumor malignancies. The drug is generally well tolerated when dosed every other day 1-3 times a week. However, XPO1 inhibitors with improved tolerability allowing more frequent dosing can be expected to have a substantial clinical benefit.
Here we present the anti-leukemic activity of a second-generation XPO1 inhibitor KPT-8602 with improved tolerability allowing for a daily dosing regimen. First, its anti-XPO1 activity was assessed; KPT-8602 potently inhibited the XPO1-mediated nuclear protein export at nanomolar concentrations and it blocked the interaction of XPO1 with cargo protein. KPT-8602 also induced potent cytotoxicity on a panel of T-ALL and B-ALL cell lines. Cytotoxicity correlated with the induction of caspase-dependent apoptosis and the nuclear accumulation of p53 as well as the subsequent induction of p53 response. To further investigate the mechanism of action of KPT-8602 we applied CRISPR/Cas9 to introduce a Cys528Ser mutation in the XPO1 gene of four different leukemia cell lines. Mutant cells were over 100 times resistant to KPT-8602. In addition, drug-target interaction was confirmed by pull-down of wild-type XPO1 protein out of cells using biotinylated KPT-8602 while it was unable to pull down mutated XPO1C528S out of mutant cells. These results illustrate the highly specific interaction of the drug for its target and prove that the anti-leukemic activity of KPT-8602 is caused by inhibition of XPO1.
To examine the anti-leukemic activity of KPT-8062 in vivo, mice engrafted with patient-derived T-cell acute lymphoblastic leukemia were treated with KPT-8602 or placebo. Mice were daily treated by oral gavage for 3 weeks. Treatment with KPT-8602 led to a significant reduction of leukemia cell numbers in blood as measured by weekly blood counts, without affecting normal erythropoiesis. Animals treated with KPT-8602 had prolonged survival compared to placebo treated animals. KPT-8602 also showed potent anti-leukemia activity in a mouse T-ALL leukemia model.
In conclusion, KPT-8062 is a second-generation XPO1 inhibitor with high specificity for its target and with potent anti-ALL activity. It displays better tolerability as compared to the first-generation SINE selinexor allowing it for daily dosing resulting in effective anti-ALL activity in in vivo PDX models warranting further evaluation of this new drug in patients. As such, in January 2016 a phase I/II study with KPT-8602 has been initiated.
Citation Format: Dirk Daelemans, Jasper Edgar Neggers, Jolien De Bie, Maarten Jacquemyn, Astrid D’Hoore, Els Vanstreels, Erkan Baloglu, Yosef Landesman, Sharon Shacham, William Senapedis, Antonis Dagklis, Thomas Vercruysse, Jan Cools. KPT-8602 is a second-generation XPO1 inhibitor with improved in vivo tolerability that demonstrates potent acute lymphoblastic leukemia activity. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-210.
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Affiliation(s)
- Dirk Daelemans
- 1KU Leuven – University of Leuven, Rega Institute for Medical Research, Leuven, Belgium
| | - Jasper Edgar Neggers
- 1KU Leuven – University of Leuven, Rega Institute for Medical Research, Leuven, Belgium
| | - Jolien De Bie
- 2KU Leuven – University of Leuven, VIB Center for the Biology of Disease, Leuven, Belgium
| | - Maarten Jacquemyn
- 1KU Leuven – University of Leuven, Rega Institute for Medical Research, Leuven, Belgium
| | - Astrid D’Hoore
- 1KU Leuven – University of Leuven, Rega Institute for Medical Research, Leuven, Belgium
| | - Els Vanstreels
- 1KU Leuven – University of Leuven, Rega Institute for Medical Research, Leuven, Belgium
| | | | | | | | | | - Antonis Dagklis
- 2KU Leuven – University of Leuven, VIB Center for the Biology of Disease, Leuven, Belgium
| | - Thomas Vercruysse
- 1KU Leuven – University of Leuven, Rega Institute for Medical Research, Leuven, Belgium
| | - Jan Cools
- 2KU Leuven – University of Leuven, VIB Center for the Biology of Disease, Leuven, Belgium
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La Starza R, Barba G, Demeyer S, Pierini V, Di Giacomo D, Gianfelici V, Schwab C, Matteucci C, Vicente C, Cools J, Messina M, Crescenzi B, Chiaretti S, Foà R, Basso G, Harrison CJ, Mecucci C. Deletions of the long arm of chromosome 5 define subgroups of T-cell acute lymphoblastic leukemia. Haematologica 2016; 101:951-8. [PMID: 27151989 DOI: 10.3324/haematol.2016.143875] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/29/2016] [Indexed: 11/09/2022] Open
Abstract
Recurrent deletions of the long arm of chromosome 5 were detected in 23/200 cases of T-cell acute lymphoblastic leukemia. Genomic studies identified two types of deletions: interstitial and terminal. Interstitial 5q deletions, found in five cases, were present in both adults and children with a female predominance (chi-square, P=0.012). Interestingly, these cases resembled immature/early T-cell precursor acute lymphoblastic leukemia showing significant down-regulation of five out of the ten top differentially expressed genes in this leukemia group, including TCF7 which maps within the 5q31 common deleted region. Mutations of genes known to be associated with immature/early T-cell precursor acute lymphoblastic leukemia, i.e. WT1, ETV6, JAK1, JAK3, and RUNX1, were present, while CDKN2A/B deletions/mutations were never detected. All patients had relapsed/resistant disease and blasts showed an early differentiation arrest with expression of myeloid markers. Terminal 5q deletions, found in 18 of patients, were more prevalent in adults (chi-square, P=0.010) and defined a subgroup of HOXA-positive T-cell acute lymphoblastic leukemia characterized by 130 up- and 197 down-regulated genes. Down-regulated genes included TRIM41, ZFP62, MAPK9, MGAT1, and CNOT6, all mapping within the 1.4 Mb common deleted region at 5q35.3. Of interest, besides CNOT6 down-regulation, these cases also showed low BTG1 expression and a high incidence of CNOT3 mutations, suggesting that the CCR4-NOT complex plays a crucial role in the pathogenesis of HOXA-positive T-cell acute lymphoblastic leukemia with terminal 5q deletions. In conclusion, interstitial and terminal 5q deletions are recurrent genomic losses identifying distinct subtypes of T-cell acute lymphoblastic leukemia.
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Affiliation(s)
- Roberta La Starza
- Molecular Medicine Laboratory, Center for Hemato-Oncology Research, University of Perugia, Italy
| | - Gianluca Barba
- Molecular Medicine Laboratory, Center for Hemato-Oncology Research, University of Perugia, Italy
| | - Sofie Demeyer
- Center for Human Genetics, KU Leuven, Belgium Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Valentina Pierini
- Molecular Medicine Laboratory, Center for Hemato-Oncology Research, University of Perugia, Italy
| | - Danika Di Giacomo
- Molecular Medicine Laboratory, Center for Hemato-Oncology Research, University of Perugia, Italy
| | - Valentina Gianfelici
- Hematology, Department of Cellular Biotechnologies and Hematology, "Sapienza" University, Rome, Italy
| | - Claire Schwab
- Leukaemia Research Cytogenetic Group, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Caterina Matteucci
- Molecular Medicine Laboratory, Center for Hemato-Oncology Research, University of Perugia, Italy
| | - Carmen Vicente
- Center for Human Genetics, KU Leuven, Belgium Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Belgium Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Monica Messina
- Hematology, Department of Cellular Biotechnologies and Hematology, "Sapienza" University, Rome, Italy
| | - Barbara Crescenzi
- Molecular Medicine Laboratory, Center for Hemato-Oncology Research, University of Perugia, Italy
| | - Sabina Chiaretti
- Hematology, Department of Cellular Biotechnologies and Hematology, "Sapienza" University, Rome, Italy
| | - Robin Foà
- Hematology, Department of Cellular Biotechnologies and Hematology, "Sapienza" University, Rome, Italy
| | - Giuseppe Basso
- Pediatric Hemato-Oncology, Department of Pediatrics "Salus Pueri", University of Padova, Italy
| | - Christine J Harrison
- Leukaemia Research Cytogenetic Group, Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Cristina Mecucci
- Molecular Medicine Laboratory, Center for Hemato-Oncology Research, University of Perugia, Italy
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49
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Gianfelici V, Chiaretti S, Demeyer S, Di Giacomo F, Messina M, La Starza R, Peragine N, Paoloni F, Geerdens E, Pierini V, Elia L, Mancini M, De Propris MS, Apicella V, Gaidano G, Testi AM, Vitale A, Vignetti M, Mecucci C, Guarini A, Cools J, Foà R. RNA sequencing unravels the genetics of refractory/relapsed T-cell acute lymphoblastic leukemia. Prognostic and therapeutic implications. Haematologica 2016; 101:941-50. [PMID: 27151993 DOI: 10.3324/haematol.2015.139410] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/29/2016] [Indexed: 01/12/2023] Open
Abstract
Despite therapeutic improvements, a sizable number of patients with T-cell acute lymphoblastic leukemia still have a poor outcome. To unravel the genomic background associated with refractoriness, we evaluated the transcriptome of 19 cases of refractory/early relapsed T-cell acute lymphoblastic leukemia (discovery cohort) by performing RNA-sequencing on diagnostic material. The incidence and prognostic impact of the most frequently mutated pathways were validated by Sanger sequencing on genomic DNA from diagnostic samples of an independent cohort of 49 cases (validation cohort), including refractory, relapsed and responsive cases. Combined gene expression and fusion transcript analyses in the discovery cohort revealed the presence of known oncogenes and identified novel rearrangements inducing overexpression, as well as inactivation of tumor suppressor genes. Mutation analysis identified JAK/STAT and RAS/PTEN as the most commonly disrupted pathways in patients with chemorefractory disease or early relapse, frequently in association with NOTCH1/FBXW7 mutations. The analysis on the validation cohort documented a significantly higher risk of relapse, inferior overall survival, disease-free survival and event-free survival in patients with JAK/STAT or RAS/PTEN alterations. Conversely, a significantly better survival was observed in patients harboring only NOTCH1/FBXW7 mutations: this favorable prognostic effect was abrogated by the presence of concomitant mutations. Preliminary in vitro assays on primary cells demonstrated sensitivity to specific inhibitors. These data document the negative prognostic impact of JAK/STAT and RAS/PTEN mutations in T-cell acute lymphoblastic leukemia and suggest the potential clinical application of JAK and PI3K/mTOR inhibitors in patients harboring mutations in these pathways.
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Affiliation(s)
- Valentina Gianfelici
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Sabina Chiaretti
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Sofie Demeyer
- Center for Human Genetics, KU Leuven, Belgium Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Filomena Di Giacomo
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy Department of Molecular Biotechnology and Health Science and Center for Experimental Research and Medical Studies (CeRMS), University of Turin, Italy
| | - Monica Messina
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Roberta La Starza
- Hematology and Bone Marrow Transplantation Unit, Department of Medicine, University of Perugia, Italy
| | - Nadia Peragine
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | | | - Ellen Geerdens
- Center for Human Genetics, KU Leuven, Belgium Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Valentina Pierini
- Hematology and Bone Marrow Transplantation Unit, Department of Medicine, University of Perugia, Italy
| | - Loredana Elia
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Marco Mancini
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | | | - Valerio Apicella
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Anna Maria Testi
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Antonella Vitale
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Marco Vignetti
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy GIMEMA Data Center, Rome, Italy
| | - Cristina Mecucci
- Hematology and Bone Marrow Transplantation Unit, Department of Medicine, University of Perugia, Italy
| | - Anna Guarini
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Belgium Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Robin Foà
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
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50
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Van Roosbroeck K, Ferreiro JF, Tousseyn T, van der Krogt JA, Michaux L, Pienkowska-Grela B, Theate I, De Paepe P, Dierickx D, Doyen C, Put N, Cools J, Vandenberghe P, Wlodarska I. Genomic alterations of the JAK2 and PDL loci occur in a broad spectrum of lymphoid malignancies. Genes Chromosomes Cancer 2016; 55:428-41. [PMID: 26850007 DOI: 10.1002/gcc.22345] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 12/18/2022] Open
Abstract
The recurrent 9p24.1 aberrations in lymphoid malignancies potentially involving four cancer-related and druggable genes (JAK2, CD274/PDL1, PDCD1LG2/PDL2, and KDM4C/JMJD2Cl) are incompletely characterized. To gain more insight into the anatomy of these abnormalities, at first we studied 9p24.1 alterations in 18 leukemia/lymphoma cases using cytogenetic and molecular techniques. The aberrations comprised structural (nine cases) and numerical (nine cases) alterations. The former lesions were heterogeneous but shared a common breakpoint region of 200 kb downstream of JAK2. The rearrangements predominantly targeted the PDL locus. We have identified five potential partner genes of PDL1/2: PHACTR4 (1p34), N4BP2 (4p14), EEF1A1 (6q13), JAK2 (9p24.1), and IGL (22q11). Interestingly, the cryptic JAK2-PDL1 rearrangement was generated by a microdeletion spanning the 3'JAK2-5'PDL1 region. JAK2 was additionally involved in a cytogenetically cryptic IGH-mediated t(9;14)(p24.1;q32) found in two patients. This rare but likely underestimated rearrangement highlights the essential role of JAK2 in B-cell neoplasms. Cases with amplification of 9p24.1 were diagnosed as primary mediastinal B-cell lymphoma (five cases) and T-cell lymphoma (four cases). The smallest amplified 9p24.1 region was restricted to the JAK2-PDL1/2-RANBP6 interval. In the next step, we screened 200 cases of classical Hodgkin lymphoma by interphase FISH and identified PDL1/2 rearrangement (CIITA- and IGH-negative) in four cases (2%), what is a novel finding. Forty (25%) cases revealed high level amplification of 9p24.1, including four cases with a selective amplification of PDL1/2. Altogether, the majority of 9p24.1 rearrangements occurring in lymphoid malignancies seem to target the programmed death-1 ligands, what potentiates the therapeutic activity of PD-1 blockade in these tumors. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Katrien Van Roosbroeck
- Center for Human Genetics, KU Leuven, Leuven, Belgium.,Center for the Biology of Disease, VIB, Leuven, Belgium
| | | | - Thomas Tousseyn
- Department of Pathology UZ Leuven, Translational Cell and Tissue Research, K.U. Leuven, Leuven, Belgium
| | | | | | - Barbara Pienkowska-Grela
- Department of Pathology and Laboratory Diagnostic, Maria Sklodowska-Curie Memorial Cancer Centre and Institute, Warsaw, Poland
| | - Ivan Theate
- Department of Pathology, Cliniques Universitaires Saint-Luc, Université Catholique De Louvain, Brussels, Belgium
| | | | - Daan Dierickx
- Department of Hematology, UZ Leuven, Leuven, Belgium
| | - Chantal Doyen
- Department of Hematology, Mont-Godinne University Hospital, Yvoir, Belgium
| | - Natalie Put
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium.,Center for the Biology of Disease, VIB, Leuven, Belgium
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