1
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Miao B, Hu Z, Mezzadra R, Hoeijmakers L, Fauster A, Du S, Yang Z, Sator-Schmitt M, Engel H, Li X, Broderick C, Jin G, Gomez-Eerland R, Rozeman L, Lei X, Matsuo H, Yang C, Hofland I, Peters D, Broeks A, Laport E, Fitz A, Zhao X, Mahmoud MAA, Ma X, Sander S, Liu HK, Cui G, Gan Y, Wu W, Xiao Y, Heck AJR, Guan W, Lowe SW, Horlings HM, Wang C, Brummelkamp TR, Blank CU, Schumacher TNM, Sun C. CMTM6 shapes antitumor T cell response through modulating protein expression of CD58 and PD-L1. Cancer Cell 2023; 41:1817-1828.e9. [PMID: 37683639 DOI: 10.1016/j.ccell.2023.08.008] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/02/2023] [Accepted: 08/15/2023] [Indexed: 09/10/2023]
Abstract
The dysregulated expression of immune checkpoint molecules enables cancer cells to evade immune destruction. While blockade of inhibitory immune checkpoints like PD-L1 forms the basis of current cancer immunotherapies, a deficiency in costimulatory signals can render these therapies futile. CD58, a costimulatory ligand, plays a crucial role in antitumor immune responses, but the mechanisms controlling its expression remain unclear. Using two systematic approaches, we reveal that CMTM6 positively regulates CD58 expression. Notably, CMTM6 interacts with both CD58 and PD-L1, maintaining the expression of these two immune checkpoint ligands with opposing functions. Functionally, the presence of CMTM6 and CD58 on tumor cells significantly affects T cell-tumor interactions and response to PD-L1-PD-1 blockade. Collectively, these findings provide fundamental insights into CD58 regulation, uncover a shared regulator of stimulatory and inhibitory immune checkpoints, and highlight the importance of tumor-intrinsic CMTM6 and CD58 expression in antitumor immune responses.
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Affiliation(s)
- Beiping Miao
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaoqing Hu
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Riccardo Mezzadra
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lotte Hoeijmakers
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Astrid Fauster
- Division of Biochemistry, Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Shangce Du
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Medicine, Heidelberg University, 69120 Heidelberg, Germany
| | - Zhi Yang
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Melanie Sator-Schmitt
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Helena Engel
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Xueshen Li
- Department of Biomedical Engineering, Stevens Institute of Technology, Hoboken, NJ 07030, USA
| | - Caroline Broderick
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Guangzhi Jin
- Department of Interventional Radiology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, No. 1111, Xianxia Road, Shanghai 200336, China
| | - Raquel Gomez-Eerland
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Lisette Rozeman
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Xin Lei
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - Hitoshi Matsuo
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Chen Yang
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ingrid Hofland
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Dennis Peters
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Elke Laport
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Annika Fitz
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Xiyue Zhao
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Mohamed A A Mahmoud
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Xiujian Ma
- Faculty of Medicine, Heidelberg University, 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ) Heidelberg, Division Molecular Neurogenetics, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sandrine Sander
- German Cancer Research Center (DKFZ) Heidelberg, Division Adaptive Immunity and Lymphoma , Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Hai-Kun Liu
- German Cancer Research Center (DKFZ) Heidelberg, Division Molecular Neurogenetics, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Guoliang Cui
- German Cancer Research Center (DKFZ) Heidelberg, Division T Cell Metabolism, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Yu Gan
- Department of Biomedical Engineering, Stevens Institute of Technology, Hoboken, NJ 07030, USA
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138648, Singapore; Department of Pharmacy, National University of Singapore, Singapore 117543, Singapore
| | - Yanling Xiao
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Wenxian Guan
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hugo M Horlings
- Department of Pathology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Cun Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Thijn R Brummelkamp
- Division of Biochemistry, Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Christian U Blank
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Medical Oncology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Medical Oncology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands.
| | - Ton N M Schumacher
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute, Oncode Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Hematology, Leiden University Medical Center (LUMC), Leiden, the Netherlands.
| | - Chong Sun
- German Cancer Research Center (DKFZ) Heidelberg, Division Immune Regulation in Cancer, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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2
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McLelland GL, Lopez-Osias M, Verzijl CRC, Ellenbroek BD, Oliveira RA, Boon NJ, Dekker M, van den Hengel LG, Ali R, Janssen H, Song JY, Krimpenfort P, van Zutphen T, Jonker JW, Brummelkamp TR. Identification of an alternative triglyceride biosynthesis pathway. Nature 2023; 621:171-178. [PMID: 37648867 PMCID: PMC10482677 DOI: 10.1038/s41586-023-06497-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Triacylglycerols (TAGs) are the main source of stored energy in the body, providing an important substrate pool for mitochondrial beta-oxidation. Imbalances in the amount of TAGs are associated with obesity, cardiac disease and various other pathologies1,2. In humans, TAGs are synthesized from excess, coenzyme A-conjugated fatty acids by diacylglycerol O-acyltransferases (DGAT1 and DGAT2)3. In other organisms, this activity is complemented by additional enzymes4, but whether such alternative pathways exist in humans remains unknown. Here we disrupt the DGAT pathway in haploid human cells and use iterative genetics to reveal an unrelated TAG-synthesizing system composed of a protein we called DIESL (also known as TMEM68, an acyltransferase of previously unknown function) and its regulator TMX1. Mechanistically, TMX1 binds to and controls DIESL at the endoplasmic reticulum, and loss of TMX1 leads to the unconstrained formation of DIESL-dependent lipid droplets. DIESL is an autonomous TAG synthase, and expression of human DIESL in Escherichia coli endows this organism with the ability to synthesize TAG. Although both DIESL and the DGATs function as diacylglycerol acyltransferases, they contribute to the cellular TAG pool under specific conditions. Functionally, DIESL synthesizes TAG at the expense of membrane phospholipids and maintains mitochondrial function during periods of extracellular lipid starvation. In mice, DIESL deficiency impedes rapid postnatal growth and affects energy homeostasis during changes in nutrient availability. We have therefore identified an alternative TAG biosynthetic pathway driven by DIESL under potent control by TMX1.
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Affiliation(s)
- Gian-Luca McLelland
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Marta Lopez-Osias
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cristy R C Verzijl
- Department of Pediatrics, Section of Molecular Metabolism and Nutrition, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Brecht D Ellenbroek
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rafaela A Oliveira
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nicolaas J Boon
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marleen Dekker
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lisa G van den Hengel
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rahmen Ali
- Animal Modeling Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hans Janssen
- Electron Microscope Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ji-Ying Song
- Animal Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Krimpenfort
- Animal Modeling Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tim van Zutphen
- Department of Pediatrics, Section of Molecular Metabolism and Nutrition, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Faculty Campus Fryslân, University of Groningen, Leeuwarden, The Netherlands
| | - Johan W Jonker
- Department of Pediatrics, Section of Molecular Metabolism and Nutrition, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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3
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Mazouzi A, Moser SC, Abascal F, van den Broek B, Del Castillo Velasco-Herrera M, van der Heijden I, Hekkelman M, Drenth AP, van der Burg E, Kroese LJ, Jalink K, Adams DJ, Jonkers J, Brummelkamp TR. FIRRM/C1orf112 mediates resolution of homologous recombination intermediates in response to DNA interstrand crosslinks. Sci Adv 2023; 9:eadf4409. [PMID: 37256941 PMCID: PMC10413679 DOI: 10.1126/sciadv.adf4409] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
DNA interstrand crosslinks (ICLs) pose a major obstacle for DNA replication and transcription if left unrepaired. The cellular response to ICLs requires the coordination of various DNA repair mechanisms. Homologous recombination (HR) intermediates generated in response to ICLs, require efficient and timely conversion by structure-selective endonucleases. Our knowledge on the precise coordination of this process remains incomplete. Here, we designed complementary genetic screens to map the machinery involved in the response to ICLs and identified FIRRM/C1orf112 as an indispensable factor in maintaining genome stability. FIRRM deficiency leads to hypersensitivity to ICL-inducing compounds, accumulation of DNA damage during S-G2 phase of the cell cycle, and chromosomal aberrations, and elicits a unique mutational signature previously observed in HR-deficient tumors. In addition, FIRRM is recruited to ICLs, controls MUS81 chromatin loading, and thereby affects resolution of HR intermediates. FIRRM deficiency in mice causes early embryonic lethality and accelerates tumor formation. Thus, FIRRM plays a critical role in the response to ICLs encountered during DNA replication.
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Affiliation(s)
- Abdelghani Mazouzi
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Amsterdam, Netherlands
| | - Sarah C. Moser
- Oncode Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Bram van den Broek
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, Netherlands
- BioImaging Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Ingrid van der Heijden
- Oncode Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Maarten Hekkelman
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anne Paulien Drenth
- Oncode Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Eline van der Burg
- Oncode Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Lona J. Kroese
- Animal Modeling Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Kees Jalink
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - David J. Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Jos Jonkers
- Oncode Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Thijn R. Brummelkamp
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Amsterdam, Netherlands
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4
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Koob L, Friskes A, van Bergen L, Feringa FM, van den Broek B, Koeleman ES, van Beek E, Schubert M, Blomen VA, Brummelkamp TR, Krenning L, Medema RH. MND1 enables homologous recombination in somatic cells primarily outside the context of replication. Mol Oncol 2023. [PMID: 37195379 DOI: 10.1002/1878-0261.13448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 05/18/2023] Open
Abstract
Faithful and timely repair of DNA double-strand breaks (DSBs) is fundamental for the maintenance of genomic integrity. Here, we demonstrate that the meiotic recombination co-factor MND1 facilitates the repair of DSBs in somatic cells. We show that MND1 localizes to DSBs, where it stimulates DNA repair through homologous recombination (HR). Importantly, MND1 is not involved in the response to replication-associated DSBs, implying that it is dispensable for HR-mediated repair of one-ended DSBs. Instead, we find that MND1 specifically plays a role in the response to two-ended DSBs that are induced by irradiation (IR) or various chemotherapeutic drugs. Surprisingly, we find that MND1 is specifically active in G2 phase, whereas it only marginally affects repair during S phase. MND1 localization to DSBs is dependent on resection of the DNA ends, and seemingly occurs through direct binding of MND1 to RAD51- coated ssDNA. Importantly, the lack of MND1-driven HR repair directly potentiates the toxicity of IR-induced damage, which could open new possibilities for therapeutic intervention, specifically in HR-proficient tumors.
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Affiliation(s)
- Lisa Koob
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Anoek Friskes
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Louise van Bergen
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Femke M Feringa
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam, 1081, Amsterdam, The Netherlands
| | - Bram van den Broek
- Bioimaging facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Emma S Koeleman
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Chromatin Networks, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Ellis van Beek
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Michael Schubert
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Vincent A Blomen
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Scenic Biotech, 1098 XG, Amsterdam, The Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
| | - Lenno Krenning
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
- Crown Bioscience, 3584 CM, Utrecht, The Netherlands
| | - René H Medema
- Oncode Institute, Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066, CX, Amsterdam, The Netherlands
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5
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Bak J, Landskron L, Brummelkamp TR, Perrakis A. Extracting Modified Microtubules from Mammalian Cells to Study Microtubule-Protein Complexes by Cryo-Electron Microscopy. J Vis Exp 2023. [PMID: 36939268 DOI: 10.3791/65126] [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] [Indexed: 03/06/2023] Open
Abstract
Microtubules are an important part of the cytoskeleton and are involved in intracellular organization, cell division, and migration. Depending on the posttranslational modifications, microtubules can form complexes with various interacting proteins. These microtubule-protein complexes are often implicated in human diseases. Understanding the structure of such complexes is useful for elucidating their mechanisms of action and can be studied by cryo-electron microscopy (cryo-EM). To obtain such complexes for structural studies, it is important to extract microtubules containing or lacking specific posttranslational modifications. Here, we describe a simplified protocol to extract endogenous tubulin from genetically modified mammalian cells, involving microtubule polymerization, followed by sedimentation using ultracentrifugation. The extracted tubulin can then be used to prepare cryo-electron microscope grids with microtubules that are bound to a purified microtubule-binding protein of interest. As an example, we demonstrate the extraction of fully tyrosinated microtubules from cell lines engineered to lack the three known tubulin-detyrosinating enzymes. These microtubules are then used to make a protein complex with enzymatically inactive microtubule-associated tubulin detyrosinase on cryo-EM grids.
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Affiliation(s)
- Jitske Bak
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute
| | - Lisa Landskron
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute
| | | | - Anastassis Perrakis
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute;
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6
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Haahr P, Galli RA, van den Hengel LG, Bleijerveld OB, Kazokaitė-Adomaitienė J, Song JY, Kroese LJ, Krimpenfort P, Baltissen MP, Vermeulen M, Ottenheijm CAC, Brummelkamp TR. Actin maturation requires the ACTMAP/C19orf54 protease. Science 2022; 377:1533-1537. [PMID: 36173861 DOI: 10.1126/science.abq5082] [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: 11/02/2022]
Abstract
Protein synthesis generally starts with a methionine that is removed during translation. However, cytoplasmic actin defies this rule because its synthesis involves noncanonical excision of the acetylated methionine by an unidentified enzyme after translation. Here, we identified C19orf54, named ACTMAP (actin maturation protease), as this enzyme. Its ablation resulted in viable mice in which the cytoskeleton was composed of immature actin molecules across all tissues. However, in skeletal muscle, the lengths of sarcomeric actin filaments were shorter, muscle function was decreased, and centralized nuclei, a common hallmark of myopathies, progressively accumulated. Thus, ACTMAP encodes the missing factor required for the synthesis of mature actin and regulates specific actin-dependent traits in vivo.
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Affiliation(s)
- Peter Haahr
- Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands.,Novo Nordisk Foundation Center for Protein Research (NNF-CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ricardo A Galli
- Department of Physiology, Amsterdam UMC (VUmc), 1081HV Amsterdam, Netherlands
| | - Lisa G van den Hengel
- Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands.,Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | | | - Ji-Ying Song
- Animal Pathology, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Lona J Kroese
- Animal Modeling Facility, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Paul Krimpenfort
- Animal Modeling Facility, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525GA Nijmegen, Netherlands
| | - Coen A C Ottenheijm
- Department of Physiology, Amsterdam UMC (VUmc), 1081HV Amsterdam, Netherlands
| | - Thijn R Brummelkamp
- Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands.,Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
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7
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van Ruiten MS, van Gent D, Sedeño Cacciatore Á, Fauster A, Willems L, Hekkelman ML, Hoekman L, Altelaar M, Haarhuis JHI, Brummelkamp TR, de Wit E, Rowland BD. The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism. Nat Struct Mol Biol 2022; 29:586-591. [PMID: 35710836 PMCID: PMC9205776 DOI: 10.1038/s41594-022-00773-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 12/15/2021] [Accepted: 04/05/2022] [Indexed: 12/16/2022]
Abstract
Cohesin structures the genome through the formation of chromatin loops and by holding together the sister chromatids. The acetylation of cohesin's SMC3 subunit is a dynamic process that involves the acetyltransferase ESCO1 and deacetylase HDAC8. Here we show that this cohesin acetylation cycle controls the three-dimensional genome in human cells. ESCO1 restricts the length of chromatin loops, and of architectural stripes emanating from CTCF sites. HDAC8 conversely promotes the extension of such loops and stripes. This role in controlling loop length turns out to be distinct from the canonical role of cohesin acetylation that protects against WAPL-mediated DNA release. We reveal that acetylation controls the interaction of cohesin with PDS5A to restrict chromatin loop length. Our data support a model in which this PDS5A-bound state acts as a brake that enables the pausing and restart of loop enlargement. The cohesin acetylation cycle hereby provides punctuation in the process of genome folding.
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Affiliation(s)
- Marjon S van Ruiten
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Démi van Gent
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Astrid Fauster
- Division of Biochemistry, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Laureen Willems
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maarten L Hekkelman
- Division of Biochemistry, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, the Netherlands
| | - Judith H I Haarhuis
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Thijn R Brummelkamp
- Division of Biochemistry, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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8
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Landskron L, Bak J, Adamopoulos A, Kaplani K, Moraiti M, van den Hengel LG, Song JY, Bleijerveld OB, Nieuwenhuis J, Heidebrecht T, Henneman L, Moutin MJ, Barisic M, Taraviras S, Perrakis A, Brummelkamp TR. Posttranslational modification of microtubules by the MATCAP detyrosinase. Science 2022; 376:eabn6020. [PMID: 35482892 DOI: 10.1126/science.abn6020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The detyrosination-tyrosination cycle involves the removal and religation of the C-terminal tyrosine of α-tubulin and is implicated in cognitive, cardiac, and mitotic defects. The vasohibin-small vasohibin-binding protein (SVBP) complex underlies much, but not all, detyrosination. We used haploid genetic screens to identify an unannotated protein, microtubule associated tyrosine carboxypeptidase (MATCAP), as a remaining detyrosinating enzyme. X-ray crystallography and cryo-electron microscopy structures established MATCAP's cleaving mechanism, substrate specificity, and microtubule recognition. Paradoxically, whereas abrogation of tyrosine religation is lethal in mice, codeletion of MATCAP and SVBP is not. Although viable, defective detyrosination caused microcephaly, associated with proliferative defects during neurogenesis, and abnormal behavior. Thus, MATCAP is a missing component of the detyrosination-tyrosination cycle, revealing the importance of this modification in brain formation.
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Affiliation(s)
- Lisa Landskron
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Jitske Bak
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Athanassios Adamopoulos
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Konstantina Kaplani
- Department of Physiology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Maria Moraiti
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Lisa G van den Hengel
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Ji-Ying Song
- Experimental Animal Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Joppe Nieuwenhuis
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, Netherlands
| | - Tatjana Heidebrecht
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Linda Henneman
- Transgenic Core Facility, Mouse Clinic for Cancer and Aging (MCCA), Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Marie-Jo Moutin
- Université Grenoble Alpes, INSERM, U1216, CNRS, Grenoble Institut Neurosciences, 38000 Grenoble, France
| | - Marin Barisic
- Cell Division and Cytoskeleton, Danish Cancer Society Research Center (DCRC), 2100 Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Anastassis Perrakis
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
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9
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Haarhuis JHI, van der Weide RH, Blomen VA, Flach KD, Teunissen H, Willems L, Brummelkamp TR, Rowland BD, de Wit E. A Mediator-cohesin axis controls heterochromatin domain formation. Nat Commun 2022; 13:754. [PMID: 35136067 PMCID: PMC8826356 DOI: 10.1038/s41467-022-28377-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 01/20/2022] [Indexed: 02/06/2023] Open
Abstract
The genome consists of regions of transcriptionally active euchromatin and more silent heterochromatin. We reveal that the formation of heterochromatin domains requires cohesin turnover on DNA. Stabilization of cohesin on DNA through depletion of its release factor WAPL leads to a near-complete loss of heterochromatin domains. We observe the opposite phenotype in cells deficient for subunits of the Mediator-CDK module, with an almost binary partition of the genome into dense H3K9me3 domains, and regions devoid of H3K9me3 spanning the rest of the genome. We suggest that the Mediator-CDK module might contribute to gene expression by limiting the formation of dense heterochromatin domains. WAPL deficiency prevents the formation of heterochromatin domains, and allows for gene expression even in the absence of the Mediator-CDK subunit MED12. We propose that cohesin and Mediator affect heterochromatin in different ways to enable the correct distribution of epigenetic marks, and thus to ensure proper gene expression.
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Affiliation(s)
- Judith H I Haarhuis
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Robin H van der Weide
- Division of Gene Regulation, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Hubrecht Institute-KNAW, Utrecht, The Netherlands
| | - Vincent A Blomen
- Division of Biochemistry, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Koen D Flach
- Division of Gene Regulation, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Laureen Willems
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Thijn R Brummelkamp
- Division of Biochemistry, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Benjamin D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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10
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Jongsma MLM, de Waard AA, Raaben M, Zhang T, Cabukusta B, Platzer R, Blomen VA, Xagara A, Verkerk T, Bliss S, Kong X, Gerke C, Janssen L, Stickel E, Holst S, Plomp R, Mulder A, Ferrone S, Claas FHJ, Heemskerk MHM, Griffioen M, Halenius A, Overkleeft H, Huppa JB, Wuhrer M, Brummelkamp TR, Neefjes J, Spaapen RM. The SPPL3-Defined Glycosphingolipid Repertoire Orchestrates HLA Class I-Mediated Immune Responses. Immunity 2021; 54:132-150.e9. [PMID: 33271119 PMCID: PMC8722104 DOI: 10.1016/j.immuni.2020.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/25/2020] [Accepted: 11/06/2020] [Indexed: 12/26/2022]
Abstract
HLA class I (HLA-I) glycoproteins drive immune responses by presenting antigens to cognate CD8+ T cells. This process is often hijacked by tumors and pathogens for immune evasion. Because options for restoring HLA-I antigen presentation are limited, we aimed to identify druggable HLA-I pathway targets. Using iterative genome-wide screens, we uncovered that the cell surface glycosphingolipid (GSL) repertoire determines effective HLA-I antigen presentation. We show that absence of the protease SPPL3 augmented B3GNT5 enzyme activity, resulting in upregulation of surface neolacto-series GSLs. These GSLs sterically impeded antibody and receptor interactions with HLA-I and diminished CD8+ T cell activation. Furthermore, a disturbed SPPL3-B3GNT5 pathway in glioma correlated with decreased patient survival. We show that the immunomodulatory effect could be reversed through GSL synthesis inhibition using clinically approved drugs. Overall, our study identifies a GSL signature that inhibits immune recognition and represents a potential therapeutic target in cancer, infection, and autoimmunity.
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Affiliation(s)
- Marlieke L M Jongsma
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands; Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - Antonius A de Waard
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Matthijs Raaben
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tao Zhang
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Birol Cabukusta
- Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - René Platzer
- Institut für Hygiene und Angewandte Immunologie, Vienna, Austria
| | - Vincent A Blomen
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Anastasia Xagara
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Tamara Verkerk
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Sophie Bliss
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Xiangrui Kong
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Carolin Gerke
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lennert Janssen
- Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - Elmer Stickel
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Stephanie Holst
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Rosina Plomp
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Arend Mulder
- Department of Immunology, LUMC, Leiden, the Netherlands
| | - Soldano Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Anne Halenius
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hermen Overkleeft
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Johannes B Huppa
- Institut für Hygiene und Angewandte Immunologie, Vienna, Austria
| | - Manfred Wuhrer
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Cancer Genomics Center, Amsterdam, the Netherlands
| | - Jacques Neefjes
- Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - Robbert M Spaapen
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands.
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11
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De Zan E, van Stiphout R, Gapp BV, Blomen VA, Brummelkamp TR, Nijman SMB. Quantitative genetic screening reveals a Ragulator-FLCN feedback loop that regulates the mTORC1 pathway. Sci Signal 2020; 13:13/649/eaba5665. [PMID: 32934076 DOI: 10.1126/scisignal.aba5665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Forward genetic screens in mammalian cell lines, such as RNAi and CRISPR-Cas9 screens, have made major contributions to the elucidation of diverse signaling pathways. Here, we exploited human haploid cells as a robust comparative screening platform and report a set of quantitative forward genetic screens for identifying regulatory mechanisms of mTORC1 signaling, a key growth control pathway that senses diverse metabolic states. Selected chemical and genetic perturbations in this screening platform, including rapamycin treatment and genetic ablation of the Ragulator subunit LAMTOR4, revealed the known core mTORC1 regulatory signaling complexes and the intimate interplay of the mTORC1 pathway with lysosomal function, validating the approach. In addition, we identified a differential requirement for LAMTOR4 and LAMTOR5 in regulating the mTORC1 pathway under fed and starved conditions. Furthermore, we uncovered a previously unknown "synthetic-sick" interaction between the tumor suppressor folliculin and LAMTOR4, which may have therapeutic implications in cancer treatment. Together, our study demonstrates the use of iterative "perturb and observe" genetic screens to uncover regulatory mechanisms driving complex mammalian signaling networks.
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Affiliation(s)
- Erica De Zan
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK
| | - Ruud van Stiphout
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK
| | - Bianca V Gapp
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK
| | | | | | - Sebastian M B Nijman
- Ludwig Institute for Cancer Research, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK.
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12
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Surface LE, Burrow DT, Li J, Park J, Kumar S, Lyu C, Song N, Yu Z, Rajagopal A, Bae Y, Lee BH, Mumm S, Gu CC, Baker JC, Mohseni M, Sum M, Huskey M, Duan S, Bijanki VN, Civitelli R, Gardner MJ, McAndrew CM, Ricci WM, Gurnett CA, Diemer K, Wan F, Costantino CL, Shannon KM, Raje N, Dodson TB, Haber DA, Carette JE, Varadarajan M, Brummelkamp TR, Birsoy K, Sabatini DM, Haller G, Peterson TR. ATRAID regulates the action of nitrogen-containing bisphosphonates on bone. Sci Transl Med 2020; 12:eaav9166. [PMID: 32434850 PMCID: PMC7882121 DOI: 10.1126/scitranslmed.aav9166] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/28/2020] [Accepted: 04/29/2020] [Indexed: 11/02/2022]
Abstract
Nitrogen-containing bisphosphonates (N-BPs), such as alendronate, are the most widely prescribed medications for diseases involving bone, with nearly 200 million prescriptions written annually. Recently, widespread use of N-BPs has been challenged due to the risk of rare but traumatic side effects such as atypical femoral fracture (AFF) and osteonecrosis of the jaw (ONJ). N-BPs bind to and inhibit farnesyl diphosphate synthase, resulting in defects in protein prenylation. Yet, it remains poorly understood what other cellular factors might allow N-BPs to exert their pharmacological effects. Here, we performed genome-wide studies in cells and patients to identify the poorly characterized gene, ATRAID Loss of ATRAID function results in selective resistance to N-BP-mediated loss of cell viability and the prevention of alendronate-mediated inhibition of prenylation. ATRAID is required for alendronate inhibition of osteoclast function, and ATRAID-deficient mice have impaired therapeutic responses to alendronate in both postmenopausal and senile (old age) osteoporosis models. Last, we performed exome sequencing on patients taking N-BPs that suffered ONJ or an AFF. ATRAID is one of three genes that contain rare nonsynonymous coding variants in patients with ONJ or an AFF that is also differentially expressed in poor outcome groups of patients treated with N-BPs. We functionally validated this patient variation in ATRAID as conferring cellular hypersensitivity to N-BPs. Our work adds key insight into the mechanistic action of N-BPs and the processes that might underlie differential responsiveness to N-BPs in people.
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Affiliation(s)
- Lauren E Surface
- Department of Molecular and Cellular Biology, Department of Chemistry and Chemical Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Damon T Burrow
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Jinmei Li
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Jiwoong Park
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Sandeep Kumar
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Cheng Lyu
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Niki Song
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Zhou Yu
- Department of Molecular and Cellular Biology, Department of Chemistry and Chemical Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Abbhirami Rajagopal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yangjin Bae
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brendan H Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven Mumm
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospital for Children, St. Louis, MO 63110, USA
| | - Charles C Gu
- Division of Biostatistics, Washington University School of Medicine, 660 S. Euclid Ave., Campus Box 8067, St. Louis, MO 63110, USA
| | - Jonathan C Baker
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, 510 S. Kingshighway Blvd., St. Louis, MO 63110, USA
| | - Mahshid Mohseni
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Melissa Sum
- Division of Endocrinology, Diabetes and Metabolism, NYU Langone Health, 530 1st Ave., Schwartz 5E., New York, NY 10016, USA
| | - Margaret Huskey
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Shenghui Duan
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Vinieth N Bijanki
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospital for Children, St. Louis, MO 63110, USA
| | - Roberto Civitelli
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Michael J Gardner
- Department of Orthopedic Surgery, Stanford University, 450 Broadway Street, Redwood City, CA 94063, USA
| | - Chris M McAndrew
- Department of Orthopedic Surgery, Washington University School of Medicine, 4938 Parkview Place, St. Louis, MO 63110, USA
| | - William M Ricci
- Hospital for Special Surgery Main Campus-Belaire Building, 525 East 71st Street 2nd Floor, New York, NY 10021, USA
| | - Christina A Gurnett
- Department of Orthopedic Surgery, Washington University School of Medicine, 4938 Parkview Place, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine, Campus Box 8111, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Kathryn Diemer
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Fei Wan
- Department of Surgery, Washington University School of Medicine, Campus Box 8109, 4590 Children's Place, Suite 9600, St. Louis, MO 63110, USA
| | - Christina L Costantino
- Massachusetts General Hospital Cancer Center and Department of Surgery, Harvard Medical School, Boston, MA 02114, USA
| | - Kristen M Shannon
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Noopur Raje
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Thomas B Dodson
- Department of Oral and Maxillofacial Surgery, Massachusetts General Hospital and Harvard School of Dental Medicine, Boston, MA 02114, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
- Howard Hughes Medical Institute (HHMI), Chevy Chase, MD 20815, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Malini Varadarajan
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, CA 02140, USA
| | - Thijn R Brummelkamp
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, Netherlands
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Cancer Genomics Center, Plesmanlaan 121, 1066CX Amsterdam, Netherlands
| | - Kivanc Birsoy
- The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
| | - David M Sabatini
- Howard Hughes Medical Institute (HHMI), Chevy Chase, MD 20815, USA
- Whitehead Institute, 9 Cambridge Center, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- David H. Koch Center for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gabe Haller
- Department of Neurology, Washington University School of Medicine, Campus Box 8111, 660 S. Euclid Ave., St. Louis, MO 63110, USA
- Department of Neurosurgery, Washington University School of Medicine, Campus Box 8057, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Timothy R Peterson
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, BJC Institute of Health, 425 S. Euclid Ave., St. Louis, MO 63110, USA.
- Department of Genetics, Washington University School of Medicine, 4515 McKinley Ave. Campus Box 8232, St. Louis, MO 63110, USA
- Institute for Public Health, Washington University School of Medicine, 600 S. Taylor Suite 2400, Campus Box 8217, St. Louis, MO 63110, USA
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13
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Bigenzahn JW, Collu GM, Kartnig F, Pieraks M, Vladimer GI, Heinz LX, Sedlyarov V, Schischlik F, Fauster A, Rebsamen M, Parapatics K, Blomen VA, Müller AC, Winter GE, Kralovics R, Brummelkamp TR, Mlodzik M, Superti-Furga G. Abstract A08: Genetic drug resistance screen identifies LZTR1 as regulator of RAS ubiquitination and signaling. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-a08] [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
Small-molecule tyrosine kinase inhibitor (TKI)-based treatment of chronic myeloid leukemia (CML), directed by the presence of the Philadelphia chromosome (Ph+) encoded BCR-ABL tyrosine kinase, is a paradigm of targeted cancer therapy. However, the development of TKI resistance limits the long-term success of these therapeutics. We used a genetic screening approach in the near-haploid CML cell line KBM-7 to identify six genes whose individual loss of function led to TKI drug resistance. We investigated in detail the role of the leucine zipper-like transcription regulator 1 (LZTR1) gene, as it was mechanistically enigmatic despite its involvement in many human developmental and oncologic diseases including glioblastoma, schwannomatosis and Noonan syndrome. We found that LZTR1 inactivation led to enhanced MAPK pathway activity and reduced TKI sensitivity of CML cells in a RAS-dependent way. LZTR1 missense mutations identified in human diseases failed to revert the loss-of-function phenotype. Knockdown of the LZTR1 orthologue CG3711 in Drosophila led to an increase in ectopic wing vein formation that could be rescued by impairment of RAS gene function, confirming the epistatic relationship and suggesting an evolutionary conserved role for LZTR1 in RAS regulation. Endogenous LZTR1 protein associated with the four main RAS isoforms KRAS4A, KRAS4B, NRAS and HRAS in proximity biotinylation proteomic and immunoprecipitation experiments in a manner that for KRAS required farnesylation and palmitoylation. Ectopic expression of LZTR1 along with all four RAS proteins led to their ubiquitination, compatible with the proposed role of LZTR1 as a cullin (CUL)-3 E3 ligase adaptor. Loss of LZTR1 led to reduced ubiquitination of endogenous KRAS and its increased abundance as well as enhanced localization at the plasma membrane. Together with the work on the role of LZTR1 in diseases driven by the dysregulation of RAS ubiquitination and signaling (Steklov, Pandolfi, Baietti et al., Anna Sablina lab, KU Leuven; see separate abstract), we propose that LZTR1 acts as a conserved regulator of RAS ubiquitination and MAPK pathway activation, providing a mechanistic explanation to its genetic involvement across a variety of human pathologies.
Citation Format: Johannes W. Bigenzahn, Giovanna M. Collu, Felix Kartnig, Melanie Pieraks, Gregory I. Vladimer, Leonhard X. Heinz, Vitaly Sedlyarov, Fiorella Schischlik, Astrid Fauster, Manuele Rebsamen, Katja Parapatics, Vincent A. Blomen, André C. Müller, Georg E. Winter, Robert Kralovics, Thijn R. Brummelkamp, Marek Mlodzik, Giulio Superti-Furga. Genetic drug resistance screen identifies LZTR1 as regulator of RAS ubiquitination and signaling [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A08.
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Affiliation(s)
| | | | - Felix Kartnig
- 1CeMM Center for Molecular Medicine, Vienna, Austria,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marek Mlodzik
- 2Icahn School of Medicine at Mount Sinai, New York, NY,
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14
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Luteijn RD, van Diemen F, Blomen VA, Boer IGJ, Manikam Sadasivam S, van Kuppevelt TH, Drexler I, Brummelkamp TR, Lebbink RJ, Wiertz EJ. A Genome-Wide Haploid Genetic Screen Identifies Heparan Sulfate-Associated Genes and the Macropinocytosis Modulator TMED10 as Factors Supporting Vaccinia Virus Infection. J Virol 2019; 93:e02160-18. [PMID: 30996093 PMCID: PMC6580964 DOI: 10.1128/jvi.02160-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/11/2019] [Indexed: 12/15/2022] Open
Abstract
Vaccinia virus is a promising viral vaccine and gene delivery candidate and has historically been used as a model to study poxvirus-host cell interactions. We employed a genome-wide insertional mutagenesis approach in human haploid cells to identify host factors crucial for vaccinia virus infection. A library of mutagenized HAP1 cells was exposed to modified vaccinia virus Ankara (MVA). Deep-sequencing analysis of virus-resistant cells identified host factors involved in heparan sulfate synthesis, Golgi organization, and vesicular protein trafficking. We validated EXT1, TM9SF2, and TMED10 (TMP21/p23/p24δ) as important host factors for vaccinia virus infection. The critical roles of EXT1 in heparan sulfate synthesis and vaccinia virus infection were confirmed. TM9SF2 was validated as a player mediating heparan sulfate expression, explaining its contribution to vaccinia virus infection. In addition, TMED10 was found to be crucial for virus-induced plasma membrane blebbing and phosphatidylserine-induced macropinocytosis, presumably by regulating the cell surface expression of the TAM receptor Axl.IMPORTANCE Poxviruses are large DNA viruses that can infect a wide range of host species. A number of these viruses are clinically important to humans, including variola virus (smallpox) and vaccinia virus. Since the eradication of smallpox, zoonotic infections with monkeypox virus and cowpox virus are emerging. Additionally, poxviruses can be engineered to specifically target cancer cells and are used as a vaccine vector against tuberculosis, influenza, and coronaviruses. Poxviruses rely on host factors for most stages of their life cycle, including attachment to the cell and entry. These host factors are crucial for virus infectivity and host cell tropism. We used a genome-wide knockout library of host cells to identify host factors necessary for vaccinia virus infection. We confirm a dominant role for heparin sulfate in mediating virus attachment. Additionally, we show that TMED10, previously not implicated in virus infections, facilitates virus uptake by modulating the cellular response to phosphatidylserine.
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Affiliation(s)
- Rutger D Luteijn
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ferdy van Diemen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Ingrid G J Boer
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Toin H van Kuppevelt
- Department of Biochemistry, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ingo Drexler
- Institute for Virology, Universitätsklinikum Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | | | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emmanuel J Wiertz
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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15
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Mezzadra R, de Bruijn M, Jae LT, Gomez-Eerland R, Duursma A, Scheeren FA, Brummelkamp TR, Schumacher TN. SLFN11 can sensitize tumor cells towards IFN-γ-mediated T cell killing. PLoS One 2019; 14:e0212053. [PMID: 30753225 PMCID: PMC6372190 DOI: 10.1371/journal.pone.0212053] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/15/2018] [Indexed: 12/21/2022] Open
Abstract
Experimental and clinical observations have highlighted the role of cytotoxic T cells in human tumor control. However, the parameters that control tumor cell sensitivity to T cell attack remain incompletely understood. To identify modulators of tumor cell sensitivity to T cell effector mechanisms, we performed a whole genome haploid screen in HAP1 cells. Selection of tumor cells by exposure to tumor-specific T cells identified components of the interferon-γ (IFN-γ) receptor (IFNGR) signaling pathway, and tumor cell killing by cytotoxic T cells was shown to be in large part mediated by the pro-apoptotic effects of IFN-γ. Notably, we identified schlafen 11 (SLFN11), a known modulator of DNA damage toxicity, as a regulator of tumor cell sensitivity to T cell-secreted IFN-γ. SLFN11 does not influence IFNGR signaling, but couples IFNGR signaling to the induction of the DNA damage response (DDR) in a context dependent fashion. In line with this role of SLFN11, loss of SLFN11 can reduce IFN-γ mediated toxicity. Collectively, our data indicate that SLFN11 can couple IFN-γ exposure of tumor cells to DDR and cellular apoptosis. Future work should reveal the mechanistic basis for the link between IFNGR signaling and DNA damage response, and identify tumor cell types in which SLFN11 contributes to the anti-tumor activity of T cells.
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Affiliation(s)
- Riccardo Mezzadra
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marjolein de Bruijn
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lucas T. Jae
- Division of Biochemistry, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Raquel Gomez-Eerland
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anja Duursma
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ferenc A. Scheeren
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Thijn R. Brummelkamp
- Division of Biochemistry, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Cancergenomics.nl, Amsterdam, The Netherlands
| | - Ton N. Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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16
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Bigenzahn JW, Collu GM, Kartnig F, Pieraks M, Vladimer GI, Heinz LX, Sedlyarov V, Schischlik F, Fauster A, Rebsamen M, Parapatics K, Blomen VA, Müller AC, Winter GE, Kralovics R, Brummelkamp TR, Mlodzik M, Superti-Furga G. LZTR1 is a regulator of RAS ubiquitination and signaling. Science 2018; 362:1171-1177. [PMID: 30442766 DOI: 10.1126/science.aap8210] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 06/26/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
In genetic screens aimed at understanding drug resistance mechanisms in chronic myeloid leukemia cells, inactivation of the cullin 3 adapter protein-encoding leucine zipper-like transcription regulator 1 (LZTR1) gene led to enhanced mitogen-activated protein kinase (MAPK) pathway activity and reduced sensitivity to tyrosine kinase inhibitors. Knockdown of the Drosophila LZTR1 ortholog CG3711 resulted in a Ras-dependent gain-of-function phenotype. Endogenous human LZTR1 associates with the main RAS isoforms. Inactivation of LZTR1 led to decreased ubiquitination and enhanced plasma membrane localization of endogenous KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog). We propose that LZTR1 acts as a conserved regulator of RAS ubiquitination and MAPK pathway activation. Because LZTR1 disease mutations failed to revert loss-of-function phenotypes, our findings provide a molecular rationale for LZTR1 involvement in a variety of inherited and acquired human disorders.
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Affiliation(s)
- Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Giovanna M Collu
- Department of Cell, Developmental, and Regenerative Biology and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Felix Kartnig
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Melanie Pieraks
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gregory I Vladimer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Leonhard X Heinz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Fiorella Schischlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Astrid Fauster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vincent A Blomen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Thijn R Brummelkamp
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.,Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.,Cancer Genomics Center (CGC.nl), Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Marek Mlodzik
- Department of Cell, Developmental, and Regenerative Biology and Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria. .,Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
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17
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Spel L, Nieuwenhuis J, Haarsma R, Stickel E, Bleijerveld OB, Altelaar M, Boelens JJ, Brummelkamp TR, Nierkens S, Boes M. Nedd4-Binding Protein 1 and TNFAIP3-Interacting Protein 1 Control MHC-1 Display in Neuroblastoma. Cancer Res 2018; 78:6621-6631. [DOI: 10.1158/0008-5472.can-18-0545] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 06/20/2018] [Accepted: 09/10/2018] [Indexed: 11/16/2022]
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18
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Hoffmann HH, Schneider WM, Blomen VA, Scull MA, Hovnanian A, Brummelkamp TR, Rice CM. Diverse Viruses Require the Calcium Transporter SPCA1 for Maturation and Spread. Cell Host Microbe 2018; 22:460-470.e5. [PMID: 29024641 DOI: 10.1016/j.chom.2017.09.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 04/04/2017] [Revised: 07/05/2017] [Accepted: 09/06/2017] [Indexed: 10/18/2022]
Abstract
Respiratory and arthropod-borne viral infections are a global threat due to the lack of effective antivirals and vaccines. A potential strategy is to target host proteins required for viruses but non-essential for the host. To identify such proteins, we performed a genome-wide knockout screen in human haploid cells and identified the calcium pump SPCA1. SPCA1 is required by viruses from the Paramyxoviridae, Flaviviridae, and Togaviridae families, including measles, dengue, West Nile, Zika, and chikungunya viruses. Calcium transport activity is required for SPCA1 to promote virus spread. SPCA1 regulates proteases within the trans-Golgi network that require calcium for their activity and are critical for virus glycoprotein maturation. Consistent with these findings, viral glycoproteins fail to mature in SPCA1-deficient cells preventing viral spread, which is evident even in cells with partial loss of SPCA1. Thus, SPCA1 is an attractive antiviral host target for a broad spectrum of established and emerging viral infections.
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Affiliation(s)
- H-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - William M Schneider
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Vincent A Blomen
- Biochemistry Division, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Margaret A Scull
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Alain Hovnanian
- INSERM UMR 1163 and Imagine Institute, 75015 Paris, France; Université Paris V Descartes - Sorbonne Paris Cité, 75006 Paris, France; Department of Genetics, Necker Hospital, 75015 Paris, France
| | - Thijn R Brummelkamp
- Biochemistry Division, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Cancer Genomics Centre, 3584 CG Utrecht, The Netherlands
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
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19
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Raaben M, Jae LT, Herbert AS, Kuehne AI, Stubbs SH, Chou YY, Blomen VA, Kirchhausen T, Dye JM, Brummelkamp TR, Whelan SP. NRP2 and CD63 Are Host Factors for Lujo Virus Cell Entry. Cell Host Microbe 2018; 22:688-696.e5. [PMID: 29120745 DOI: 10.1016/j.chom.2017.10.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/13/2017] [Accepted: 10/06/2017] [Indexed: 01/13/2023]
Abstract
Arenaviruses cause fatal hemorrhagic disease in humans. Old World arenavirus glycoproteins (GPs) mainly engage α-dystroglycan as a cell-surface receptor, while New World arenaviruses hijack transferrin receptor. However, the Lujo virus (LUJV) GP does not cluster with New or Old World arenaviruses. Using a recombinant vesicular stomatitis virus containing LUJV GP as its sole attachment and fusion protein (VSV-LUJV), we demonstrate that infection is independent of known arenavirus receptor genes. A genome-wide haploid genetic screen identified the transmembrane protein neuropilin 2 (NRP2) and tetraspanin CD63 as factors for LUJV GP-mediated infection. LUJV GP binds the N-terminal domain of NRP2, while CD63 stimulates pH-activated LUJV GP-mediated membrane fusion. Overexpression of NRP2 or its N-terminal domain enhances VSV-LUJV infection, and cells lacking NRP2 are deficient in wild-type LUJV infection. These findings uncover this distinct set of host cell entry factors in LUJV infection and are attractive focus points for therapeutic intervention.
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Affiliation(s)
- Matthijs Raaben
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Lucas T Jae
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Virology Division, 1425 Porter Street, Fort Detrick, MD 21702-5011, USA
| | - Ana I Kuehne
- U.S. Army Medical Research Institute of Infectious Diseases, Virology Division, 1425 Porter Street, Fort Detrick, MD 21702-5011, USA
| | - Sarah H Stubbs
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yi-Ying Chou
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Vincent A Blomen
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Tomas Kirchhausen
- Department of Cell Biology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Virology Division, 1425 Porter Street, Fort Detrick, MD 21702-5011, USA
| | - Thijn R Brummelkamp
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; CGC.nl; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 14 Vienna, Austria.
| | - Sean P Whelan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
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20
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Abstract
In order to replicate, most pathogens need to enter their target cells. Many viruses enter the host cell through an endocytic pathway and hijack endosomes for their journey towards sites of replication. For delivery of their genome to the host cell cytoplasm and to avoid degradation, viruses have to escape this endosomal compartment without host detection. Viruses have developed complex mechanisms to penetrate the endosomal membrane and have evolved to co-opt several host factors to facilitate endosomal escape. Conversely, there is an extensive variety of cellular mechanisms to counteract or impede viral replication. At the level of cell entry, there are cellular defense mechanisms that recognize endosomal membrane damage caused by virus-induced membrane fusion and pore formation, as well as restriction factors that block these processes. In this Cell Science at a Glance article and accompanying poster, we describe the different mechanisms that viruses have evolved to escape the endosomal compartment, as well as the counteracting cellular protection mechanisms. We provide examples for enveloped and non-enveloped viruses, for which we discuss some unique and unexpected cellular responses to virus-entry-induced membrane damage.
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Affiliation(s)
- Jacqueline Staring
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Department of Biochemistry, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Matthijs Raaben
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Thijn R Brummelkamp
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands .,Department of Biochemistry, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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21
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Staring J, van den Hengel LG, Raaben M, Blomen VA, Carette JE, Brummelkamp TR. KREMEN1 Is a Host Entry Receptor for a Major Group of Enteroviruses. Cell Host Microbe 2018; 23:636-643.e5. [DOI: 10.1016/j.chom.2018.03.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/19/2018] [Accepted: 03/26/2018] [Indexed: 01/23/2023]
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22
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Gerhards NM, Blomen VA, Mutlu M, Nieuwenhuis J, Howald D, Guyader C, Jonkers J, Brummelkamp TR, Rottenberg S. Haploid genetic screens identify genetic vulnerabilities to microtubule-targeting agents. Mol Oncol 2018; 12:953-971. [PMID: 29689640 PMCID: PMC5983209 DOI: 10.1002/1878-0261.12307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022] Open
Abstract
The absence of biomarkers to accurately predict anticancer therapy response remains a major obstacle in clinical oncology. We applied a genome‐wide loss‐of‐function screening approach in human haploid cells to characterize genetic vulnerabilities to classical microtubule‐targeting agents. Using docetaxel and vinorelbine, two well‐established chemotherapeutic agents, we sought to identify genetic alterations sensitizing human HAP1 cells to these drugs. Despite the fact that both drugs act on microtubules, a set of distinct genes were identified whose disruption affects drug sensitivity. For docetaxel, this included a number of genes with a function in mitosis, while for vinorelbine we identified inactivation of FBXW7,RB1, and NF2, three frequently mutated tumor suppressor genes, as sensitizing factors. We validated these genes using independent knockout clones and confirmed FBXW7 as an important regulator of the mitotic spindle assembly. Upon FBXW7 depletion, vinorelbine treatment led to decreased survival of cells due to defective mitotic progression and subsequent mitotic catastrophe. We show that haploid insertional mutagenesis screens are a useful tool to study genetic vulnerabilities to classical chemotherapeutic drugs by identifying thus far unknown sensitivity factors. These results provide a rationale for investigating patient response to vinca alkaloid‐based anticancer treatment in relation to the mutational status of these three tumor suppressor genes, and could in the future lead to the establishment of novel predictive biomarkers or suggest new drug combinations based on molecular mechanisms of drug sensitivity.
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Affiliation(s)
- Nora M Gerhards
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Vincent A Blomen
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Merve Mutlu
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Joppe Nieuwenhuis
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Denise Howald
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Charlotte Guyader
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Thijn R Brummelkamp
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Switzerland.,Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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23
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Maroofian R, Riemersma M, Jae LT, Zhianabed N, Willemsen MH, Wissink-Lindhout WM, Willemsen MA, de Brouwer APM, Mehrjardi MYV, Ashrafi MR, Kusters B, Kleefstra T, Jamshidi Y, Nasseri M, Pfundt R, Brummelkamp TR, Abbaszadegan MR, Lefeber DJ, van Bokhoven H. B3GALNT2 mutations associated with non-syndromic autosomal recessive intellectual disability reveal a lack of genotype-phenotype associations in the muscular dystrophy-dystroglycanopathies. Genome Med 2017; 9:118. [PMID: 29273094 PMCID: PMC5740572 DOI: 10.1186/s13073-017-0505-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 07/16/2017] [Accepted: 12/05/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The phenotypic severity of congenital muscular dystrophy-dystroglycanopathy (MDDG) syndromes associated with aberrant glycosylation of α-dystroglycan ranges from the severe Walker-Warburg syndrome or muscle-eye-brain disease to mild, late-onset, isolated limb-girdle muscular dystrophy without neural involvement. However, muscular dystrophy is invariably found across the spectrum of MDDG patients. METHODS Using linkage mapping and whole-exome sequencing in two families with an unexplained neurodevelopmental disorder, we have identified homozygous and compound heterozygous mutations in B3GALNT2. RESULTS The first family comprises two brothers of Dutch non-consanguineous parents presenting with mild ID and behavioral problems. Immunohistochemical analysis of muscle biopsy revealed no significant aberrations, in line with the absence of a muscular phenotype in the affected siblings. The second family includes five affected individuals from an Iranian consanguineous kindred with mild-to-moderate intellectual disability (ID) and epilepsy without any notable neuroimaging, muscle, or eye abnormalities. Complementation assays of the compound heterozygous mutations identified in the two brothers had a comparable effect on the O-glycosylation of α-dystroglycan as previously reported mutations that are associated with severe muscular phenotypes. CONCLUSIONS In conclusion, we show that mutations in B3GALNT2 can give rise to a novel MDDG syndrome presentation, characterized by ID associated variably with seizure, but without any apparent muscular involvement. Importantly, B3GALNT2 activity does not fully correlate with the severity of the phenotype as assessed by the complementation assay.
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Affiliation(s)
- Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Moniek Riemersma
- Department of Neurology, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
- Department of Laboratory Medicine, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
- Department of Human Genetics 855, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Lucas T Jae
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377, Munich, Germany
| | | | - Marjolein H Willemsen
- Department of Human Genetics 855, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Willemijn M Wissink-Lindhout
- Department of Human Genetics 855, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Michèl A Willemsen
- Department of Neurology, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Arjan P M de Brouwer
- Department of Human Genetics 855, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | | | - Mahmoud Reza Ashrafi
- Department of Child Neurology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Benno Kusters
- Department of Pathology, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6229 HX, Maastricht, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics 855, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Yalda Jamshidi
- Genetics and Molecular Cell Sciences Research Centre, St George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Mojila Nasseri
- Pardis Clinical and Genetics Laboratory, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rolph Pfundt
- Department of Human Genetics 855, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Thijn R Brummelkamp
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377, Munich, Germany
| | - Mohammad Reza Abbaszadegan
- Pardis Clinical and Genetics Laboratory, Mashhad, Iran
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Dirk J Lefeber
- Department of Neurology, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
- Department of Laboratory Medicine, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics 855, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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Nieuwenhuis J, Adamopoulos A, Bleijerveld OB, Mazouzi A, Stickel E, Celie P, Altelaar M, Knipscheer P, Perrakis A, Blomen VA, Brummelkamp TR. Vasohibins encode tubulin detyrosinating activity. Science 2017; 358:1453-1456. [PMID: 29146869 DOI: 10.1126/science.aao5676] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/03/2017] [Indexed: 12/14/2022]
Abstract
Tubulin is subjected to a number of posttranslational modifications to generate heterogeneous microtubules. The modifications include removal and ligation of the C-terminal tyrosine of ⍺-tubulin. The enzymes responsible for detyrosination, an activity first observed 40 years ago, have remained elusive. We applied a genetic screen in haploid human cells to find regulators of tubulin detyrosination. We identified SVBP, a peptide that regulates the abundance of vasohibins (VASH1 and VASH2). Vasohibins, but not SVBP alone, increased detyrosination of ⍺-tubulin, and purified vasohibins removed the C-terminal tyrosine of ⍺-tubulin. We found that vasohibins play a cell type-dependent role in detyrosination, although cells also contain an additional detyrosinating activity. Thus, vasohibins, hitherto studied as secreted angiogenesis regulators, constitute a long-sought missing link in the tubulin tyrosination cycle.
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Affiliation(s)
- Joppe Nieuwenhuis
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Athanassios Adamopoulos
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Onno B Bleijerveld
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Abdelghani Mazouzi
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Elmer Stickel
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Patrick Celie
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Maarten Altelaar
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands.,Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, Netherlands
| | - Puck Knipscheer
- Hubrecht Institute-KNAW, University Medical Center Utrecht, 3584 CT Utrecht, Netherlands.,CGC.nl, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Anastassis Perrakis
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Vincent A Blomen
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands.
| | - Thijn R Brummelkamp
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands. .,CGC.nl, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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25
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Blomen VA, Brummelkamp TR. Abstract A19: Exploring genetic interactions in haploid human cells. Mol Cancer Ther 2017. [DOI: 10.1158/1538-8514.synthleth-a19] [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
Gene-associated phenotypes often depend on the activity of other genes resulting in genetic interactions. In model organisms, the large-scale generation of combinations of mutations has resulted in the identification of genetic interactions and provided insights into their contribution to complex phenotypes. Here we use haploid human cells combined with genome-wide mutagenesis to study genetic interactions. We have made a synthetic lethality network using query genes acting in the secretory pathway and observe that human genes frequently engage in genetic interactions. Beyond cell lethality, we search for genes, which upon loss deregulate cellular processes such as signaling pathways. Genetic modifier approaches in those mutants reveals back-up mechanisms or genetic networks contributing to the phenotype of interest. This provides a much-needed window into the robust genetic networks governing human cells.
Citation Format: Vincent A. Blomen, Thijn R. Brummelkamp. Exploring genetic interactions in haploid human cells [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr A19.
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26
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Sun C, Mezzadra R, Jae LT, Gomez-Eerland R, Vries ED, Wu W, Xiao Y, Heck AJ, Borst J, Brummelkamp TR, Schumacher TN. Abstract LB-291: Identification of CMTM6 and CMTM4 as PD-L1 protein regulators. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-291] [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
The clinical benefit in patients with diverse types of metastatic cancers that is observed upon blockade of the PD-1 - PD-L1 interaction has highlighted the importance of this inhibitory axis in the suppression of human tumor-specific T cell responses. In spite of the key role of PD-L1 expression by cells within the tumor microenvironment, our understanding of the regulation of the PD-L1 protein is limited. Using a haploid genetic screen, we here identify CMTM6, a poorly described type 3 transmembrane protein of previously unknown function, as a regulator of the PD-L1 protein. Interference with CMTM6 expression results in impaired PD-L1 protein expression in all tumor cell types tested and also in primary human dendritic cells. Furthermore, through both a haploid genetic modifier screen in CMTM6 deficient cells and genetic complementation experiments, we demonstrate that this function is shared by its closest family member CMTM4, but not by all other CMTM members tested. Notably, CMTM6 increases the PD-L1 protein pool without affecting PD-L1 transcript levels. Rather, we demonstrate that CMTM6 is present at the cell surface, associates with PD-L1 protein, and increases PD-L1 protein half-life. Consistent with this role, T cell inhibitory capacity of PD-L1 expressing tumor cells is enhanced by CMTM6. Collectively, our data reveal that PD-L1 relies on CMTM6/4 to efficiently carry out its inhibitory function, and suggest potential new avenues to block this pathway.
[C.S., R.M., and L.T.J. contributed equally to this work. T.R.B. and T.N.M.S. are both corresponding authors.]
Citation Format: Chong Sun, Riccardo Mezzadra, Lucas T. Jae, Raquel Gomez-Eerland, Evert de Vries, Wei Wu, Yanling Xiao, Albert J. Heck, Jannie Borst, Thijn R. Brummelkamp, Ton N. Schumacher. Identification of CMTM6 and CMTM4 as PD-L1 protein regulators [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-291. doi:10.1158/1538-7445.AM2017-LB-291
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Affiliation(s)
- Chong Sun
- 1The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Lucas T. Jae
- 1The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Evert de Vries
- 1The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Wei Wu
- 2Utrecht University, Utrecht, Netherlands
| | - Yanling Xiao
- 1The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Jannie Borst
- 1The Netherlands Cancer Institute, Amsterdam, Netherlands
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27
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Haarhuis JHI, van der Weide RH, Blomen VA, Yáñez-Cuna JO, Amendola M, van Ruiten MS, Krijger PHL, Teunissen H, Medema RH, van Steensel B, Brummelkamp TR, de Wit E, Rowland BD. The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension. Cell 2017; 169:693-707.e14. [PMID: 28475897 PMCID: PMC5422210 DOI: 10.1016/j.cell.2017.04.013] [Citation(s) in RCA: 454] [Impact Index Per Article: 64.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/21/2017] [Accepted: 04/10/2017] [Indexed: 12/30/2022]
Abstract
The spatial organization of chromosomes influences many nuclear processes including gene expression. The cohesin complex shapes the 3D genome by looping together CTCF sites along chromosomes. We show here that chromatin loop size can be increased and that the duration with which cohesin embraces DNA determines the degree to which loops are enlarged. Cohesin's DNA release factor WAPL restricts this loop extension and also prevents looping between incorrectly oriented CTCF sites. We reveal that the SCC2/SCC4 complex promotes the extension of chromatin loops and the formation of topologically associated domains (TADs). Our data support the model that cohesin structures chromosomes through the processive enlargement of loops and that TADs reflect polyclonal collections of loops in the making. Finally, we find that whereas cohesin promotes chromosomal looping, it rather limits nuclear compartmentalization. We conclude that the balanced activity of SCC2/SCC4 and WAPL enables cohesin to correctly structure chromosomes.
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Affiliation(s)
- Judith H I Haarhuis
- Division of Cell Biology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Robin H van der Weide
- Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Vincent A Blomen
- Division of Biochemistry, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - J Omar Yáñez-Cuna
- Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Mario Amendola
- Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Marjon S van Ruiten
- Division of Cell Biology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | | | - Hans Teunissen
- Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - René H Medema
- Division of Cell Biology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Thijn R Brummelkamp
- Division of Biochemistry, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Cancer Genomics Center, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
| | - Benjamin D Rowland
- Division of Cell Biology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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28
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Staring J, von Castelmur E, Blomen VA, van den Hengel LG, Brockmann M, Baggen J, Thibaut HJ, Nieuwenhuis J, Janssen H, van Kuppeveld FJM, Perrakis A, Carette JE, Brummelkamp TR. PLA2G16 represents a switch between entry and clearance of Picornaviridae. Nature 2017; 541:412-416. [PMID: 28077878 DOI: 10.1038/nature21032] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/06/2016] [Indexed: 12/20/2022]
Abstract
Picornaviruses are a leading cause of human and veterinary infections that result in various diseases, including polio and the common cold. As archetypical non-enveloped viruses, their biology has been extensively studied. Although a range of different cell-surface receptors are bound by different picornaviruses, it is unclear whether common host factors are needed for them to reach the cytoplasm. Using genome-wide haploid genetic screens, here we identify the lipid-modifying enzyme PLA2G16 (refs 8, 9, 10, 11) as a picornavirus host factor that is required for a previously unknown event in the viral life cycle. We find that PLA2G16 functions early during infection, enabling virion-mediated genome delivery into the cytoplasm, but not in any virion-assigned step, such as cell binding, endosomal trafficking or pore formation. To resolve this paradox, we screened for suppressors of the ΔPLA2G16 phenotype and identified a mechanism previously implicated in the clearance of intracellular bacteria. The sensor of this mechanism, galectin-8 (encoded by LGALS8), detects permeated endosomes and marks them for autophagic degradation, whereas PLA2G16 facilitates viral genome translocation and prevents clearance. This study uncovers two competing processes triggered by virus entry: activation of a pore-activated clearance pathway and recruitment of a phospholipase to enable genome release.
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Affiliation(s)
- Jacqueline Staring
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | | | - Vincent A Blomen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | | | - Markus Brockmann
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jim Baggen
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Hendrik Jan Thibaut
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Joppe Nieuwenhuis
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Hans Janssen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Anastassis Perrakis
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, California 94305, USA
| | - Thijn R Brummelkamp
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.,Cancer GenomiCs.nl (CGC.nl), Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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29
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Ng M, Ndungo E, Kaczmarek ME, Herbert AS, Binger T, Kuehne AI, Jangra RK, Hawkins JA, Gifford RJ, Biswas R, Demogines A, James RM, Yu M, Brummelkamp TR, Drosten C, Wang LF, Kuhn JH, Müller MA, Dye JM, Sawyer SL, Chandran K. Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats. eLife 2015; 4. [PMID: 26698106 PMCID: PMC4709267 DOI: 10.7554/elife.11785] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/19/2015] [Indexed: 12/13/2022] Open
Abstract
Biological factors that influence the host range and spillover of Ebola virus (EBOV) and other filoviruses remain enigmatic. While filoviruses infect diverse mammalian cell lines, we report that cells from African straw-colored fruit bats (Eidolon helvum) are refractory to EBOV infection. This could be explained by a single amino acid change in the filovirus receptor, NPC1, which greatly reduces the affinity of EBOV-NPC1 interaction. We found signatures of positive selection in bat NPC1 concentrated at the virus-receptor interface, with the strongest signal at the same residue that controls EBOV infection in Eidolon helvum cells. Our work identifies NPC1 as a genetic determinant of filovirus susceptibility in bats, and suggests that some NPC1 variations reflect host adaptations to reduce filovirus replication and virulence. A single viral mutation afforded escape from receptor control, revealing a pathway for compensatory viral evolution and a potential avenue for expansion of filovirus host range in nature. DOI:http://dx.doi.org/10.7554/eLife.11785.001 Ebola virus and other filoviruses can cause devastating diseases in humans and other apes. Numerous small outbreaks of Ebola virus disease have occurred in Africa over the past 40 years. However, in 2013–2015, the largest outbreak on record took place in three Western African nations with no previous history of the disease. Human outbreaks of Ebola virus disease likely begin when a person encounters an infected wild animal. Though it remains unclear precisely which animals harbor Ebola virus between outbreaks, and how they transmit the virus to humans or other primates, recent work showed that some filoviruses do infect specific types of bats in nature. Ng, Ndungo, Kaczmarek et al. sought to identify the genes that influence whether or not a type of bat is susceptible to infection by Ebola virus and other filoviruses. Several filoviruses, including Ebola virus, were tested to see if they could infect cells that had been collected from four types of African fruit bats. These bats are all found in areas where outbreaks have occurred in the past. The tests revealed that a small change in the sequence of the NPC1 gene in some bat cells greatly reduced their susceptibility to Ebola virus. NPC1 encodes a protein that mammals need in order to move cholesterol within their cells. In humans, the loss of the protein encoded by NPC1 causes a rare but very severe disease called Niemann-Pick type C disease. This protein also turns out to be a receptor that the filoviruses must bind to before they can infect the cells. Further analysis then revealed that NPC1 has evolved rapidly in bats, with changes concentrated in the parts of the receptor that interact with Ebola virus. Ng, Ndungo, Kaczmarek et al. went on to discover some changes in the genome sequence of Ebola virus that could compensate for the changes in the bat’s NPC1 gene. These findings hint at one way that a filovirus could evolve to better infect a host with receptors that were less than optimal. Following on from this work, the next challenges will be to expand the investigation to include additional types of bats, other types of mammals, and other host genes that could influence filovirus infection and disease. Further studies could also examine the other side of the arms race – that is, the evolution of viral genes in bats. However, such studies would be complicated by the lack of viral sequences that have been collected from bats, because to date most have been isolated from humans and other primates instead. DOI:http://dx.doi.org/10.7554/eLife.11785.002
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Affiliation(s)
- Melinda Ng
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
| | - Esther Ndungo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
| | - Maria E Kaczmarek
- Department of Integrative Biology, University of Texas at Austin, Austin, United States
| | - Andrew S Herbert
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, United States
| | - Tabea Binger
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - Ana I Kuehne
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, United States
| | - Rohit K Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
| | - John A Hawkins
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, United States
| | - Robert J Gifford
- University of Glasgow MRC Virology Unit, Glasgow, United Kingdom
| | - Rohan Biswas
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
| | - Ann Demogines
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States
| | - Rebekah M James
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, United States
| | - Meng Yu
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, , Singapore
| | | | - Christian Drosten
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany.,German Centre for Infectious Diseases Research, Bonn, Germany
| | - Lin-Fa Wang
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, , Singapore
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, United States
| | - Marcel A Müller
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, United States
| | - Sara L Sawyer
- Department of Molecular Biosciences, University of Texas at Austin, Austin, United States.,BioFrontiers Institute, University of Colorado Boulder, Boulder, United States.,Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
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30
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Lackner DH, Carré A, Guzzardo PM, Banning C, Mangena R, Henley T, Oberndorfer S, Gapp BV, Nijman SM, Brummelkamp TR, Bürckstümmer T. A generic strategy for CRISPR-Cas9-mediated gene tagging. Nat Commun 2015; 6:10237. [PMID: 26674669 PMCID: PMC4703899 DOI: 10.1038/ncomms10237] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/20/2015] [Indexed: 02/06/2023] Open
Abstract
Genome engineering has been greatly enhanced by the availability of Cas9 endonuclease that can be targeted to almost any genomic locus using so called guide RNAs (gRNAs). However, the introduction of foreign DNA sequences to tag an endogenous gene is still cumbersome as it requires the synthesis or cloning of homology templates. Here we present a strategy that enables the tagging of endogenous loci using one generic donor plasmid. It contains the tag of interest flanked by two gRNA recognition sites that allow excision of the tag from the plasmid. Co-transfection of cells with Cas9, a gRNA specifying the genomic locus of interest, the donor plasmid and a cassette-specific gRNA triggers the insertion of the tag by a homology-independent mechanism. The strategy is efficient and delivers clones that display a predictable integration pattern. As showcases we generated NanoLuc luciferase- and TurboGFP-tagged reporter cell lines.
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Affiliation(s)
| | - Alexia Carré
- Horizon Genomics, Campus Vienna Biocenter 3, 1030 Vienna, Austria
| | | | - Carina Banning
- Horizon Genomics, Campus Vienna Biocenter 3, 1030 Vienna, Austria
| | - Ramu Mangena
- Horizon Discovery, 7100 Cambridge Research Park, Waterbeach, Cambridge CB25 9TL, UK
| | - Tom Henley
- Horizon Discovery, 7100 Cambridge Research Park, Waterbeach, Cambridge CB25 9TL, UK
| | | | - Bianca V. Gapp
- Ludwig Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Sebastian M.B. Nijman
- Ludwig Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
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31
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Planells-Cases R, Lutter D, Guyader C, Gerhards NM, Ullrich F, Elger DA, Kucukosmanoglu A, Xu G, Voss FK, Reincke SM, Stauber T, Blomen VA, Vis DJ, Wessels LF, Brummelkamp TR, Borst P, Rottenberg S, Jentsch TJ. Subunit composition of VRAC channels determines substrate specificity and cellular resistance to Pt-based anti-cancer drugs. EMBO J 2015; 34:2993-3008. [PMID: 26530471 PMCID: PMC4687416 DOI: 10.15252/embj.201592409] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [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: 06/30/2015] [Accepted: 10/05/2015] [Indexed: 11/25/2022] Open
Abstract
Although platinum‐based drugs are widely used chemotherapeutics for cancer treatment, the determinants of tumor cell responsiveness remain poorly understood. We show that the loss of subunits LRRC8A and LRRC8D of the heteromeric LRRC8 volume‐regulated anion channels (VRACs) increased resistance to clinically relevant cisplatin/carboplatin concentrations. Under isotonic conditions, about 50% of cisplatin uptake depended on LRRC8A and LRRC8D, but neither on LRRC8C nor on LRRC8E. Cell swelling strongly enhanced LRRC8‐dependent cisplatin uptake, bolstering the notion that cisplatin enters cells through VRAC. LRRC8A disruption also suppressed drug‐induced apoptosis independently from drug uptake, possibly by impairing VRAC‐dependent apoptotic cell volume decrease. Hence, by mediating cisplatin uptake and facilitating apoptosis, VRAC plays a dual role in the cellular drug response. Incorporation of the LRRC8D subunit into VRAC substantially increased its permeability for cisplatin and the cellular osmolyte taurine, indicating that LRRC8 proteins form the channel pore. Our work suggests that LRRC8D‐containing VRACs are crucial for cell volume regulation by an important organic osmolyte and may influence cisplatin/carboplatin responsiveness of tumors.
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Affiliation(s)
- Rosa Planells-Cases
- Leibniz-Institut für Molekulare Pharmakologie (FMP) Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Darius Lutter
- Leibniz-Institut für Molekulare Pharmakologie (FMP) Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Charlotte Guyader
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nora M Gerhards
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Florian Ullrich
- Leibniz-Institut für Molekulare Pharmakologie (FMP) Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Deborah A Elger
- Leibniz-Institut für Molekulare Pharmakologie (FMP) Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Asli Kucukosmanoglu
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Guotai Xu
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Felizia K Voss
- Leibniz-Institut für Molekulare Pharmakologie (FMP) Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - S Momsen Reincke
- Leibniz-Institut für Molekulare Pharmakologie (FMP) Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Tobias Stauber
- Leibniz-Institut für Molekulare Pharmakologie (FMP) Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Vincent A Blomen
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel J Vis
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk F Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Thijn R Brummelkamp
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Piet Borst
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Thomas J Jentsch
- Leibniz-Institut für Molekulare Pharmakologie (FMP) Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany NeuroCure Cluster of Excellence, Charité Universitätsmedizin, Berlin, Germany
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32
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Blomen VA, Májek P, Jae LT, Bigenzahn JW, Nieuwenhuis J, Staring J, Sacco R, van Diemen FR, Olk N, Stukalov A, Marceau C, Janssen H, Carette JE, Bennett KL, Colinge J, Superti-Furga G, Brummelkamp TR. Gene essentiality and synthetic lethality in haploid human cells. Science 2015; 350:1092-6. [PMID: 26472760 DOI: 10.1126/science.aac7557] [Citation(s) in RCA: 553] [Impact Index Per Article: 61.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 10/01/2015] [Indexed: 12/11/2022]
Abstract
Although the genes essential for life have been identified in less complex model organisms, their elucidation in human cells has been hindered by technical barriers. We used extensive mutagenesis in haploid human cells to identify approximately 2000 genes required for optimal fitness under culture conditions. To study the principles of genetic interactions in human cells, we created a synthetic lethality network focused on the secretory pathway based exclusively on mutations. This revealed a genetic cross-talk governing Golgi homeostasis, an additional subunit of the human oligosaccharyltransferase complex, and a phosphatidylinositol 4-kinase β adaptor hijacked by viruses. The synthetic lethality map parallels observations made in yeast and projects a route forward to reveal genetic networks in diverse aspects of human cell biology.
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Affiliation(s)
- Vincent A Blomen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Peter Májek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Lucas T Jae
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Joppe Nieuwenhuis
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Jacqueline Staring
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Roberto Sacco
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Ferdy R van Diemen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Nadine Olk
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Caleb Marceau
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA
| | - Hans Janssen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, 299 Campus Drive, Stanford, CA 94305, USA
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria. University of Montpellier, Institut de Recherche en Cancérologie de Montpellier Inserm U1194, Institut régional du Cancer Montpellier, 34000 Montpellier, France.
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria. Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
| | - Thijn R Brummelkamp
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria. Cancer Genomics Center (CGC.nl), Plesmanlaan 121, 1066CX, Amsterdam, Netherlands.
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Tsvetkov P, Mendillo ML, Zhao J, Carette JE, Merrill PH, Cikes D, Varadarajan M, van Diemen FR, Penninger JM, Goldberg AL, Brummelkamp TR, Santagata S, Lindquist S. Compromising the 19S proteasome complex protects cells from reduced flux through the proteasome. eLife 2015; 4. [PMID: 26327695 PMCID: PMC4551903 DOI: 10.7554/elife.08467] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/29/2015] [Indexed: 12/11/2022] Open
Abstract
Proteasomes are central regulators of protein homeostasis in eukaryotes. Proteasome function is vulnerable to environmental insults, cellular protein imbalance and targeted pharmaceuticals. Yet, mechanisms that cells deploy to counteract inhibition of this central regulator are little understood. To find such mechanisms, we reduced flux through the proteasome to the point of toxicity with specific inhibitors and performed genome-wide screens for mutations that allowed cells to survive. Counter to expectation, reducing expression of individual subunits of the proteasome's 19S regulatory complex increased survival. Strong 19S reduction was cytotoxic but modest reduction protected cells from inhibitors. Protection was accompanied by an increased ratio of 20S to 26S proteasomes, preservation of protein degradation capacity and reduced proteotoxic stress. While compromise of 19S function can have a fitness cost under basal conditions, it provided a powerful survival advantage when proteasome function was impaired. This means of rebalancing proteostasis is conserved from yeast to humans.
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Affiliation(s)
- Peter Tsvetkov
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Marc L Mendillo
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Jinghui Zhao
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Parker H Merrill
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Domagoj Cikes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Ferdy R van Diemen
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Alfred L Goldberg
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Thijn R Brummelkamp
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sandro Santagata
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, United States
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Wijdeven RH, Pang B, van der Zanden SY, Qiao X, Blomen V, Hoogstraat M, Lips EH, Janssen L, Wessels L, Brummelkamp TR, Neefjes J. Genome-Wide Identification and Characterization of Novel Factors Conferring Resistance to Topoisomerase II Poisons in Cancer. Cancer Res 2015; 75:4176-87. [PMID: 26260527 DOI: 10.1158/0008-5472.can-15-0380] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/14/2015] [Indexed: 02/03/2023]
Abstract
The topoisomerase II poisons doxorubicin and etoposide constitute longstanding cornerstones of chemotherapy. Despite their extensive clinical use, many patients do not respond to these drugs. Using a genome-wide gene knockout approach, we identified Keap1, the SWI/SNF complex, and C9orf82 (CAAP1) as independent factors capable of driving drug resistance through diverse molecular mechanisms, all converging on the DNA double-strand break (DSB) and repair pathway. Loss of Keap1 or the SWI/SNF complex inhibits generation of DSB by attenuating expression and activity of topoisomerase IIα, respectively, whereas deletion of C9orf82 augments subsequent DSB repair. Their corresponding genes, frequently mutated or deleted in human tumors, may impact drug sensitivity, as exemplified by triple-negative breast cancer patients with diminished SWI/SNF core member expression who exhibit reduced responsiveness to chemotherapy regimens containing doxorubicin. Collectively, our work identifies genes that may predict the response of cancer patients to the broadly used topoisomerase II poisons and defines alternative pathways that could be therapeutically exploited in treatment-resistant patients.
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Affiliation(s)
- Ruud H Wijdeven
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Baoxu Pang
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Xiaohang Qiao
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Vincent Blomen
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marlous Hoogstraat
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands. Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands. Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lennert Janssen
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lodewyk Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Thijn R Brummelkamp
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jacques Neefjes
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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35
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Gerhards NM, Guyader C, Blomen VA, Küçükosmanoğlu A, van Tellingen O, Vis DJ, Wessels LF, Brummelkamp TR, Borst P, Rottenberg S. Abstract 3607: Loss-of-function screens using haploid KBM7 and HAP1 cells to identify mechanisms of anti-cancer drug resistance. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3607] [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
The lack of biomarkers to predict anti-cancer therapy response remains a major obstacle in the treatment of various cancers. This handicap not only affects novel targeted therapies. Also for classical chemotherapeutic drugs such as DNA cross-linking agents, topoisomerase inhibitors or microtubule-targeting compounds, which are all frequently used in the clinic, we do not understand well why some patients have a major benefit of the therapy whereas others do not. A decreased intracellular drug accumulation has been proposed as one potential mechanism, but the clinical relevance of known uptake and efflux mechanisms is still controversial for various chemotherapeutic drugs. To identify novel factors that may be relevant for the intracellular concentration of drugs, we carried out loss-of-function screens using haploid KBM7 and HAP1 cells. In particular, we used the PARP inhibitor olaparib, the topoisomerase I inhibitor topotecan, platinum drugs, and the microtubule-targeting compounds docetaxel and vinorelbine to select resistant clones. We will present results from these screens and their validation, including independent cell lines and TCGA data sets.
Citation Format: Nora M. Gerhards, Charlotte Guyader, Vincent A. Blomen, Aslı Küçükosmanoğlu, Olaf van Tellingen, Daniel J. Vis, Lodewyk F. Wessels, Thijn R. Brummelkamp, Piet Borst, Sven Rottenberg. Loss-of-function screens using haploid KBM7 and HAP1 cells to identify mechanisms of anti-cancer drug resistance. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3607. doi:10.1158/1538-7445.AM2015-3607
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Affiliation(s)
| | | | | | | | | | - Daniel J. Vis
- 2Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Piet Borst
- 2Netherlands Cancer Institute, Amsterdam, Netherlands
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36
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Affiliation(s)
- Thijn R Brummelkamp
- Division of Biochemistry and Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
| | - Bas van Steensel
- Department of Cell Biology, Erasmus University Medical Center, 3015 GE Rotterdam, Netherlands
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37
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Jae LT, Brummelkamp TR. Emerging intracellular receptors for hemorrhagic fever viruses. Trends Microbiol 2015; 23:392-400. [PMID: 26004032 DOI: 10.1016/j.tim.2015.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [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: 02/20/2015] [Revised: 04/10/2015] [Accepted: 04/21/2015] [Indexed: 01/05/2023]
Abstract
Ebola virus and Lassa virus belong to different virus families that can cause viral hemorrhagic fever, a life-threatening disease in humans with limited treatment options. To infect a target cell, Ebola and Lassa viruses engage receptors at the cell surface and are subsequently shuttled into the endosomal compartment. Upon arrival in late endosomes/lysosomes, the viruses trigger membrane fusion to release their genome into the cytoplasm. Although contact sites at the cell surface were recognized for Ebola virus and Lassa virus, it was postulated that Ebola virus requires a critical receptor inside the cell. Recent screens for host factors identified such internal receptors for both viruses: Niemann-Pick disease type C1 protein (NPC1) for Ebola virus and lysosome-associated membrane protein 1 (LAMP1) for Lassa virus. A cellular trigger is needed to permit binding of the viral envelope protein to these intracellular receptors. This 'receptor switch' represents a previously unnoticed step in virus entry with implications for host-pathogen interactions and viral tropism.
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Affiliation(s)
- Lucas T Jae
- Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, CX, 1066 The Netherlands
| | - Thijn R Brummelkamp
- Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, CX, 1066 The Netherlands.
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38
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Essletzbichler P, Konopka T, Santoro F, Chen D, Gapp BV, Kralovics R, Brummelkamp TR, Nijman SMB, Bürckstümmer T. Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line. Genome Res 2014; 24:2059-65. [PMID: 25373145 PMCID: PMC4248322 DOI: 10.1101/gr.177220.114] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Near-haploid human cell lines are instrumental for genetic screens and genome engineering as gene inactivation is greatly facilitated by the absence of a second gene copy. However, no completely haploid human cell line has been described, hampering the genetic accessibility of a subset of genes. The near-haploid human cell line HAP1 contains a single copy of all chromosomes except for a heterozygous 30-megabase fragment of Chromosome 15. This large fragment encompasses 330 genes and is integrated on the long arm of Chromosome 19. Here, we employ a CRISPR/Cas9-based genome engineering strategy to excise this sizeable chromosomal fragment and to efficiently and reproducibly derive clones that retain their haploid state. Importantly, spectral karyotyping and single-nucleotide polymorphism (SNP) genotyping revealed that engineered-HAPloid (eHAP) cells are fully haploid with no gross chromosomal aberrations induced by Cas9. Furthermore, whole-genome sequence and transcriptome analysis of the parental HAP1 and an eHAP cell line showed that transcriptional changes are limited to the excised Chromosome 15 fragment. Together, we demonstrate the feasibility of efficiently engineering megabase deletions with the CRISPR/Cas9 technology and report the first fully haploid human cell line.
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Affiliation(s)
| | - Tomasz Konopka
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090 Vienna, Austria
| | | | - Doris Chen
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090 Vienna, Austria
| | - Bianca V Gapp
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090 Vienna, Austria
| | - Robert Kralovics
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090 Vienna, Austria
| | - Thijn R Brummelkamp
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090 Vienna, Austria; The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Sebastian M B Nijman
- Haplogen GmbH, 1030 Vienna, Austria; Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090 Vienna, Austria
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39
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Oosterkamp HM, Hijmans EM, Brummelkamp TR, Canisius S, Wessels LFA, Zwart W, Bernards R. USP9X downregulation renders breast cancer cells resistant to tamoxifen. Cancer Res 2014; 74:3810-20. [PMID: 25028367 DOI: 10.1158/0008-5472.can-13-1960] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [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
Tamoxifen is one of the most widely used endocrine agents for the treatment of estrogen receptor α (ERα)-positive breast cancer. Although effective in most patients, resistance to tamoxifen is a clinically significant problem and the mechanisms responsible remain elusive. To address this problem, we performed a large scale loss-of-function genetic screen in ZR-75-1 luminal breast cancer cells to identify candidate resistance genes. In this manner, we found that loss of function in the deubiquitinase USP9X prevented proliferation arrest by tamoxifen, but not by the ER downregulator fulvestrant. RNAi-mediated attenuation of USP9X was sufficient to stabilize ERα on chromatin in the presence of tamoxifen, causing a global tamoxifen-driven activation of ERα-responsive genes. Using a gene signature defined by their differential expression after USP9X attenuation in the presence of tamoxifen, we were able to define patients with ERα-positive breast cancer experiencing a poor outcome after adjuvant treatment with tamoxifen. The signature was specific in its lack of correlation with survival in patients with breast cancer who did not receive endocrine therapy. Overall, our findings identify a gene signature as a candidate biomarker of response to tamoxifen in breast cancer.
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Affiliation(s)
- Hendrika M Oosterkamp
- Authors' Affiliations: Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands; and
| | - E Marielle Hijmans
- Authors' Affiliations: Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands; and
| | - Thijn R Brummelkamp
- Authors' Affiliations: Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands; and
| | - Sander Canisius
- Authors' Affiliations: Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands; and
| | - Lodewyk F A Wessels
- Authors' Affiliations: Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands; and
| | - Wilbert Zwart
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - René Bernards
- Authors' Affiliations: Division of Molecular Carcinogenesis and Cancer Genomics Center Netherlands; and
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40
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Tafesse FG, Guimaraes CP, Maruyama T, Carette JE, Lory S, Brummelkamp TR, Ploegh HL. GPR107, a G-protein-coupled receptor essential for intoxication by Pseudomonas aeruginosa exotoxin A, localizes to the Golgi and is cleaved by furin. J Biol Chem 2014; 289:24005-18. [PMID: 25031321 PMCID: PMC4148833 DOI: 10.1074/jbc.m114.589275] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/08/2014] [Indexed: 12/25/2022] Open
Abstract
A number of toxins, including exotoxin A (PE) of Pseudomonas aeruginosa, kill cells by inhibiting protein synthesis. PE kills by ADP-ribosylation of the translation elongation factor 2, but many of the host factors required for entry, membrane translocation, and intracellular transport remain to be elucidated. A genome-wide genetic screen in human KBM7 cells was performed to uncover host factors used by PE, several of which were confirmed by CRISPR/Cas9-gene editing in a different cell type. Several proteins not previously implicated in the PE intoxication pathway were identified, including GPR107, an orphan G-protein-coupled receptor. GPR107 localizes to the trans-Golgi network and is essential for retrograde transport. It is cleaved by the endoprotease furin, and a disulfide bond connects the two cleaved fragments. Compromising this association affects the function of GPR107. The N-terminal region of GPR107 is critical for its biological function. GPR107 might be one of the long-sought receptors that associates with G-proteins to regulate intracellular vesicular transport.
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Affiliation(s)
- Fikadu G Tafesse
- From the Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Carla P Guimaraes
- From the Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Takeshi Maruyama
- From the Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Jan E Carette
- the Stanford School of Medicine, Stanford, California 94305
| | - Stephen Lory
- the Harvard Medical School, Boston, Massachusetts 02115, and
| | - Thijn R Brummelkamp
- the Netherlands Cancer Institute, Postbus 90203, 1006 BE Amsterdam, The Netherlands
| | - Hidde L Ploegh
- From the Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142,
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41
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Winter GE, Radic B, Mayor-Ruiz C, Blomen VA, Trefzer C, Kandasamy RK, Huber KVM, Gridling M, Chen D, Klampfl T, Kralovics R, Kubicek S, Fernandez-Capetillo O, Brummelkamp TR, Superti-Furga G. The solute carrier SLC35F2 enables YM155-mediated DNA damage toxicity. Nat Chem Biol 2014; 10:768-773. [PMID: 25064833 DOI: 10.1038/nchembio.1590] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 06/19/2014] [Indexed: 01/09/2023]
Abstract
Genotoxic chemotherapy is the most common cancer treatment strategy. However, its untargeted generic DNA-damaging nature and associated systemic cytotoxicity greatly limit its therapeutic applications. Here, we used a haploid genetic screen in human cells to discover an absolute dependency of the clinically evaluated anticancer compound YM155 on solute carrier family member 35 F2 (SLC35F2), an uncharacterized member of the solute carrier protein family that is highly expressed in a variety of human cancers. YM155 generated DNA damage through intercalation, which was contingent on the expression of SLC35F2 and its drug-importing activity. SLC35F2 expression and YM155 sensitivity correlated across a panel of cancer cell lines, and targeted genome editing verified SLC35F2 as the main determinant of YM155-mediated DNA damage toxicity in vitro and in vivo. These findings suggest a new route to targeted DNA damage by exploiting tumor and patient-specific import of YM155.
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Affiliation(s)
- Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Branka Radic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Cristina Mayor-Ruiz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Vincent A Blomen
- Division of Biochemistry, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Claudia Trefzer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Richard K Kandasamy
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Kilian V M Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Manuela Gridling
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Doris Chen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Thorsten Klampfl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
| | | | - Thijn R Brummelkamp
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria.,Division of Biochemistry, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 1090 Vienna, Austria
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42
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Jae LT, Raaben M, Herbert AS, Kuehne AI, Wirchnianski AS, Soh TK, Stubbs SH, Janssen H, Damme M, Saftig P, Whelan SP, Dye JM, Brummelkamp TR. Virus entry. Lassa virus entry requires a trigger-induced receptor switch. Science 2014; 344:1506-10. [PMID: 24970085 DOI: 10.1126/science.1252480] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Lassa virus spreads from a rodent to humans and can lead to lethal hemorrhagic fever. Despite its broad tropism, chicken cells were reported 30 years ago to resist infection. We found that Lassa virus readily engaged its cell-surface receptor α-dystroglycan in avian cells, but virus entry in susceptible species involved a pH-dependent switch to an intracellular receptor, the lysosome-resident protein LAMP1. Iterative haploid screens revealed that the sialyltransferase ST3GAL4 was required for the interaction of the virus glycoprotein with LAMP1. A single glycosylated residue in LAMP1, present in susceptible species but absent in birds, was essential for interaction with the Lassa virus envelope protein and subsequent infection. The resistance of Lamp1-deficient mice to Lassa virus highlights the relevance of this receptor switch in vivo.
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Affiliation(s)
- Lucas T Jae
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Matthijs Raaben
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands. Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702-5011, USA
| | - Ana I Kuehne
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702-5011, USA
| | - Ariel S Wirchnianski
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702-5011, USA
| | - Timothy K Soh
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Sarah H Stubbs
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Hans Janssen
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands
| | - Markus Damme
- Biochemisches Institut, Christian Albrechts-Universität Kiel, 24118 Kiel, Germany
| | - Paul Saftig
- Biochemisches Institut, Christian Albrechts-Universität Kiel, 24118 Kiel, Germany
| | - Sean P Whelan
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, MD 21702-5011, USA.
| | - Thijn R Brummelkamp
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria. Cancer Genomics Center (CGC.nl), Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.
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43
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Segawa K, Kurata S, Yanagihashi Y, Brummelkamp TR, Matsuda F, Nagata S. Caspase-mediated cleavage of phospholipid flippase for apoptotic phosphatidylserine exposure. Science 2014; 344:1164-8. [PMID: 24904167 DOI: 10.1126/science.1252809] [Citation(s) in RCA: 364] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Phospholipids are asymmetrically distributed in the plasma membrane. This asymmetrical distribution is disrupted during apoptosis, exposing phosphatidylserine (PtdSer) on the cell surface. Using a haploid genetic screen in human cells, we found that ATP11C (adenosine triphosphatase type 11C) and CDC50A (cell division cycle protein 50A) are required for aminophospholipid translocation from the outer to the inner plasma membrane leaflet; that is, they display flippase activity. ATP11C contained caspase recognition sites, and mutations at these sites generated caspase-resistant ATP11C without affecting its flippase activity. Cells expressing caspase-resistant ATP11C did not expose PtdSer during apoptosis and were not engulfed by macrophages, which suggests that inactivation of the flippase activity is required for apoptotic PtdSer exposure. CDC50A-deficient cells displayed PtdSer on their surface and were engulfed by macrophages, indicating that PtdSer is sufficient as an "eat me" signal.
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Affiliation(s)
- Katsumori Segawa
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Yoshida-Konoe, Kyoto 606-8501, Japan
| | - Sachiko Kurata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Yoshida-Konoe, Kyoto 606-8501, Japan
| | - Yuichi Yanagihashi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Yoshida-Konoe, Kyoto 606-8501, Japan
| | - Thijn R Brummelkamp
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe, Kyoto 606-8501, Japan
| | - Shigekazu Nagata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Yoshida-Konoe, Kyoto 606-8501, Japan. Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Kyoto 606-8501, Japan.
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44
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Chen WW, Birsoy K, Mihaylova MM, Snitkin H, Stasinski I, Yucel B, Bayraktar EC, Carette JE, Clish CB, Brummelkamp TR, Sabatini DD, Sabatini DM. Inhibition of ATPIF1 ameliorates severe mitochondrial respiratory chain dysfunction in mammalian cells. Cell Rep 2014; 7:27-34. [PMID: 24685140 PMCID: PMC4040975 DOI: 10.1016/j.celrep.2014.02.046] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [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: 12/30/2013] [Revised: 02/07/2014] [Accepted: 02/28/2014] [Indexed: 01/19/2023] Open
Abstract
Mitochondrial respiratory chain disorders are characterized by loss of electron transport chain (ETC) activity. Although the causes of many such diseases are known, there is a lack of effective therapies. To identify genes that confer resistance to severe ETC dysfunction when inactivated, we performed a genome-wide genetic screen in haploid human cells with the mitochondrial complex III inhibitor antimycin. This screen revealed that loss of ATPIF1 strongly protects against antimycin-induced ETC dysfunction and cell death by allowing for the maintenance of mitochondrial membrane potential. ATPIF1 loss protects against other forms of ETC dysfunction and is even essential for the viability of human ρ° cells lacking mitochondrial DNA, a system commonly used for studying ETC dysfunction. Importantly, inhibition of ATPIF1 ameliorates complex III blockade in primary hepatocytes, a cell type afflicted in severe mitochondrial disease. Altogether, these results suggest that inhibition of ATPIF1 can ameliorate severe ETC dysfunction in mitochondrial pathology.
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Affiliation(s)
- Walter W Chen
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute, Seven Cambridge Center, Cambridge, MA 02142, USA
- David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kivanc Birsoy
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute, Seven Cambridge Center, Cambridge, MA 02142, USA
- David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Maria M Mihaylova
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute, Seven Cambridge Center, Cambridge, MA 02142, USA
- David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Harriet Snitkin
- Department of Cell Biology, New York University School of Medicine, New York, New York, 10016, USA
| | - Iwona Stasinski
- Department of Cell Biology, New York University School of Medicine, New York, New York, 10016, USA
| | - Burcu Yucel
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute, Seven Cambridge Center, Cambridge, MA 02142, USA
- David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Erol C Bayraktar
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute, Seven Cambridge Center, Cambridge, MA 02142, USA
- David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Clary B Clish
- Broad Institute, Seven Cambridge Center, Cambridge, MA 02142, USA
| | - Thijn R Brummelkamp
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121 1066 CX, Amsterdam, The Netherlands
| | - David D Sabatini
- Department of Cell Biology, New York University School of Medicine, New York, New York, 10016, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute, Seven Cambridge Center, Cambridge, MA 02142, USA
- David H. Koch Institute for Integrative Cancer Research at MIT, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
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45
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Bürckstümmer T, Banning C, Hainzl P, Schobesberger R, Kerzendorfer C, Pauler FM, Chen D, Them N, Schischlik F, Rebsamen M, Smida M, Fece de la Cruz F, Lapao A, Liszt M, Eizinger B, Guenzl PM, Blomen VA, Konopka T, Gapp B, Parapatics K, Maier B, Stöckl J, Fischl W, Salic S, Taba Casari MR, Knapp S, Bennett KL, Bock C, Colinge J, Kralovics R, Ammerer G, Casari G, Brummelkamp TR, Superti-Furga G, Nijman SMB. A reversible gene trap collection empowers haploid genetics in human cells. Nat Methods 2013; 10:965-71. [PMID: 24161985 DOI: 10.1038/nmeth.2609] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 07/22/2013] [Indexed: 11/09/2022]
Abstract
Knockout collections are invaluable tools for studying model organisms such as yeast. However, there are no large-scale knockout collections of human cells. Using gene-trap mutagenesis in near-haploid human cells, we established a platform to generate and isolate individual 'gene-trapped cells' and used it to prepare a collection of human cell lines carrying single gene-trap insertions. In most cases, the insertion can be reversed. This growing library covers 3,396 genes, one-third of the expressed genome, is DNA-barcoded and allows systematic screens for a wide variety of cellular phenotypes. We examined cellular responses to TNF-α, TGF-β, IFN-γ and TNF-related apoptosis-inducing ligand (TRAIL), to illustrate the value of this unique collection of isogenic human cell lines.
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46
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Jae LT, Raaben M, Riemersma M, van Beusekom E, Blomen VA, Velds A, Kerkhoven RM, Carette JE, Topaloglu H, Meinecke P, Wessels MW, Lefeber DJ, Whelan SP, van Bokhoven H, Brummelkamp TR. Deciphering the glycosylome of dystroglycanopathies using haploid screens for lassa virus entry. Science 2013; 340:479-83. [PMID: 23519211 DOI: 10.1126/science.1233675] [Citation(s) in RCA: 221] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glycosylated α-dystroglycan (α-DG) serves as cellular entry receptor for multiple pathogens, and defects in its glycosylation cause hereditary Walker-Warburg syndrome (WWS). At least eight proteins are critical to glycosylate α-DG, but many genes mutated in WWS remain unknown. To identify modifiers of α-DG, we performed a haploid screen for Lassa virus entry, a hemorrhagic fever virus causing thousands of deaths annually that hijacks glycosylated α-DG to enter cells. In complementary screens, we profiled cells for absence of α-DG carbohydrate chains or biochemically related glycans. This revealed virus host factors and a suite of glycosylation units, including all known Walker-Warburg genes and five additional factors critical for the modification of α-DG. Our findings accentuate the complexity of this posttranslational feature and point out genes defective in dystroglycanopathies.
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Affiliation(s)
- Lucas T Jae
- Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, Netherlands
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47
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Jacobson LS, Lima H, Goldberg MF, Gocheva V, Tsiperson V, Sutterwala FS, Joyce JA, Gapp BV, Blomen VA, Chandran K, Brummelkamp TR, Diaz-Griffero F, Brojatsch J. Cathepsin-mediated necrosis controls the adaptive immune response by Th2 (T helper type 2)-associated adjuvants. J Biol Chem 2013; 288:7481-7491. [PMID: 23297415 DOI: 10.1074/jbc.m112.400655] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Immunologic adjuvants are critical components of vaccines, but it remains unclear how prototypical adjuvants enhance the adaptive immune response. Recent studies have shown that necrotic cells could trigger an immune response. Although most adjuvants have been shown to be cytotoxic, this activity has traditionally been considered a side effect. We set out to test the role of adjuvant-mediated cell death in immunity and found that alum, the most commonly used adjuvant worldwide, triggers a novel form of cell death in myeloid leukocytes characterized by cathepsin-dependent lysosome-disruption. We demonstrated that direct lysosome-permeabilization with a soluble peptide, Leu-Leu-OMe, mimics the alum-like form of necrotic cell death in terms of cathepsin dependence and cell-type specificity. Using a combination of a haploid genetic screen and cathepsin-deficient cells, we identified specific cathepsins that control lysosome-mediated necrosis. We identified cathepsin C as critical for Leu-Leu-OMe-induced cell death, whereas cathepsins B and S were required for alum-mediated necrosis. Consistent with a role of necrotic cell death in adjuvant effects, Leu-Leu-OMe replicated an alum-like immune response in vivo, characterized by dendritic cell activation, granulocyte recruitment, and production of Th2-associated antibodies. Strikingly, cathepsin C deficiency not only blocked Leu-Leu-OMe-mediated necrosis but also impaired Leu-Leu-OMe-enhanced immunity. Together our findings suggest that necrotic cell death is a powerful mediator of a Th2-associated immune response.
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Affiliation(s)
- Lee S Jacobson
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Heriberto Lima
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Michael F Goldberg
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Vasilena Gocheva
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering, New York, New York 10065
| | - Vladislav Tsiperson
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
| | | | - Johanna A Joyce
- Department of Cancer Biology and Genetics, Memorial Sloan-Kettering, New York, New York 10065
| | - Bianca V Gapp
- Department of Biochemistry, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Vincent A Blomen
- Department of Biochemistry, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Thijn R Brummelkamp
- Department of Biochemistry, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Jürgen Brojatsch
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461.
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48
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Birsoy K, Wang T, Possemato R, Yilmaz OH, Koch CE, Chen WW, Hutchins AW, Gultekin Y, Peterson TR, Carette JE, Brummelkamp TR, Clish CB, Sabatini DM. MCT1-mediated transport of a toxic molecule is an effective strategy for targeting glycolytic tumors. Nat Genet 2012. [PMID: 23202129 PMCID: PMC3530647 DOI: 10.1038/ng.2471] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is increasing evidence that oncogenic transformation modifies the metabolic program of cells. A common alteration is the upregulation of glycolysis, and efforts to target glycolytic enzymes for anti-cancer therapy are underway. Here, we performed a genome-wide haploid genetic screen to identify resistance mechanisms to 3-bromopyruvate (3-BrPA), a drug candidate that inhibits glycolysis in a poorly understood fashion. We identified the SLC16A1 gene product, MCT1, as the main determinant of 3-BrPA sensitivity. MCT1 is necessary and sufficient for 3-BrPA uptake by cancer cells. Additionally, MCT1 mRNA levels are the best predictor of 3-BrPA sensitivity and are most elevated in glycolytic cancer cells. Lastly, forced MCT1 expression in 3-BrPA resistant cancer cells sensitizes tumor xenografts to 3-BrPA treatment in vivo. Our results identify a potential biomarker for 3-BrPA sensitivity and provide proof of concept that the selectivity of cancer-expressed transporters can be exploited for delivering toxic molecules to tumors.
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Affiliation(s)
- Kivanç Birsoy
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
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49
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Miller EH, Obernosterer G, Raaben M, Herbert AS, Deffieu MS, Krishnan A, Ndungo E, Sandesara RG, Carette JE, Kuehne AI, Ruthel G, Pfeffer SR, Dye JM, Whelan SP, Brummelkamp TR, Chandran K. Ebola virus entry requires the host-programmed recognition of an intracellular receptor. EMBO J 2012; 31:1947-60. [PMID: 22395071 DOI: 10.1038/emboj.2012.53] [Citation(s) in RCA: 255] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 02/03/2012] [Indexed: 01/03/2023] Open
Abstract
Ebola and Marburg filoviruses cause deadly outbreaks of haemorrhagic fever. Despite considerable efforts, no essential cellular receptors for filovirus entry have been identified. We showed previously that Niemann-Pick C1 (NPC1), a lysosomal cholesterol transporter, is required for filovirus entry. Here, we demonstrate that NPC1 is a critical filovirus receptor. Human NPC1 fulfills a cardinal property of viral receptors: it confers susceptibility to filovirus infection when expressed in non-permissive reptilian cells. The second luminal domain of NPC1 binds directly and specifically to the viral glycoprotein, GP, and a synthetic single-pass membrane protein containing this domain has viral receptor activity. Purified NPC1 binds only to a cleaved form of GP that is generated within cells during entry, and only viruses containing cleaved GP can utilize a receptor retargeted to the cell surface. Our findings support a model in which GP cleavage by endosomal cysteine proteases unmasks the binding site for NPC1, and GP-NPC1 engagement within lysosomes promotes a late step in entry proximal to viral escape into the host cytoplasm. NPC1 is the first known viral receptor that recognizes its ligand within an intracellular compartment and not at the plasma membrane.
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Affiliation(s)
- Emily Happy Miller
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
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50
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Guimaraes CP, Carette JE, Varadarajan M, Antos J, Popp MW, Spooner E, Brummelkamp TR, Ploegh HL. Identification of host cell factors required for intoxication through use of modified cholera toxin. ACTA ACUST UNITED AC 2012; 195:751-64. [PMID: 22123862 PMCID: PMC3257576 DOI: 10.1083/jcb.201108103] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe a novel labeling strategy to site-specifically attach fluorophores, biotin, and proteins to the C terminus of the A1 subunit (CTA1) of cholera toxin (CTx) in an otherwise correctly assembled and active CTx complex. Using a biotinylated N-linked glycosylation reporter peptide attached to CTA1, we provide direct evidence that ~12% of the internalized CTA1 pool reaches the ER. We also explored the sortase labeling method to attach the catalytic subunit of diphtheria toxin as a toxic warhead to CTA1, thus converting CTx into a cytolethal toxin. This new toxin conjugate enabled us to conduct a genetic screen in human cells, which identified ST3GAL5, SLC35A2, B3GALT4, UGCG, and ELF4 as genes essential for CTx intoxication. The first four encode proteins involved in the synthesis of gangliosides, which are known receptors for CTx. Identification and isolation of the ST3GAL5 and SLC35A2 mutant clonal cells uncover a previously unappreciated differential contribution of gangliosides to intoxication by CTx.
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Affiliation(s)
- Carla P Guimaraes
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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