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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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2
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Kogler M, Tortola L, Negri GL, Leopoldi A, El-Naggar AM, Mereiter S, Gomez-Diaz C, Nitsch R, Tortora D, Kavirayani AM, Gapp BV, Rao S, Uribesalgo I, Hoffmann D, Cikes D, Novatchkova M, Williams DA, Trent JM, Ikeda F, Daugaard M, Hagelkruys A, Sorensen PH, Penninger JM. HACE1 Prevents Lung Carcinogenesis via Inhibition of RAC-Family GTPases. Cancer Res 2020; 80:3009-3022. [PMID: 32366477 PMCID: PMC7611202 DOI: 10.1158/0008-5472.can-19-2270] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 07/24/2019] [Revised: 03/21/2020] [Accepted: 04/29/2020] [Indexed: 12/19/2022]
Abstract
HACE1 is an E3 ubiquitin ligase with important roles in tumor biology and tissue homeostasis. Loss or mutation of HACE1 has been associated with the occurrence of a variety of neoplasms, but the underlying mechanisms have not been defined yet. Here, we report that HACE1 is frequently mutated in human lung cancer. In mice, loss of Hace1 led to enhanced progression of KRasG12D -driven lung tumors. Additional ablation of the oncogenic GTPase Rac1 partially reduced progression of Hace1-/- lung tumors. RAC2, a novel ubiquitylation target of HACE1, could compensate for the absence of its homolog RAC1 in Hace1-deficient, but not in HACE1-sufficient tumors. Accordingly, ablation of both Rac1 and Rac2 fully averted the increased progression of KRasG12D -driven lung tumors in Hace1-/- mice. In patients with lung cancer, increased expression of HACE1 correlated with reduced levels of RAC1 and RAC2 and prolonged survival, whereas elevated expression of RAC1 and RAC2 was associated with poor prognosis. This work defines HACE1 as a crucial regulator of the oncogenic activity of RAC-family GTPases in lung cancer development. SIGNIFICANCE: These findings reveal that mutation of the tumor suppressor HACE1 disrupts its role as a regulator of the oncogenic activity of RAC-family GTPases in human and murine lung cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/14/3009/F1.large.jpg.
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Affiliation(s)
- Melanie Kogler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Luigi Tortola
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria.
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Switzerland
| | - Gian Luca Negri
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Alexandra Leopoldi
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Amal M El-Naggar
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology, Faculty of Medicine, Menoufia University, Menoufia Governorate, Egypt
| | - Stefan Mereiter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Carlos Gomez-Diaz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Roberto Nitsch
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
- Advanced Medicines Safety, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Davide Tortora
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | | | - Bianca V Gapp
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Shuan Rao
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Iris Uribesalgo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - David Hoffmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Domagoj Cikes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Maria Novatchkova
- Research Institute of Molecular Pathology, Vienna BioCentre, Vienna, Austria
| | - David A Williams
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Jeffrey M Trent
- Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Mads Daugaard
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Astrid Hagelkruys
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria
| | - Poul H Sorensen
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCentre, Vienna, Austria.
- Department of Medical Genetics, Life Science Institute, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Forment JV, Herzog M, Coates J, Konopka T, Gapp BV, Nijman SM, Adams DJ, Keane TM, Jackson SP. Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells. Nat Chem Biol 2017; 13:12-14. [PMID: 27820796 PMCID: PMC5164930 DOI: 10.1038/nchembio.2226] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 03/29/2016] [Accepted: 08/24/2016] [Indexed: 12/21/2022]
Abstract
In model organisms, classical genetic screening via random mutagenesis provides key insights into the molecular bases of genetic interactions, helping to define synthetic lethality, synthetic viability and drug-resistance mechanisms. The limited genetic tractability of diploid mammalian cells, however, precludes this approach. Here, we demonstrate the feasibility of classical genetic screening in mammalian systems by using haploid cells, chemical mutagenesis and next-generation sequencing, providing a new tool to explore mammalian genetic interactions.
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Affiliation(s)
- Josep V. Forment
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Mareike Herzog
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Julia Coates
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tomasz Konopka
- Ludwig Institute for Cancer Research Ltd. and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bianca V. Gapp
- Ludwig Institute for Cancer Research Ltd. and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sebastian M. Nijman
- Ludwig Institute for Cancer Research Ltd. and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - Stephen P. Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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Abstract
Reverse genetic screens have driven gene annotation and target discovery in model organisms. However, many disease‐relevant genotypes and phenotypes cannot be studied in lower organisms. It is therefore essential to overcome technical hurdles associated with large‐scale reverse genetics in human cells. Here, we establish a reverse genetic approach based on highly robust and sensitive multiplexed RNA sequencing of mutant human cells. We conduct 10 parallel screens using a collection of engineered haploid isogenic cell lines with knockouts covering tyrosine kinases and identify known and unexpected effects on signaling pathways. Our study provides proof of concept for a scalable approach to link genotype to phenotype in human cells, which has broad applications. In particular, it clears the way for systematic phenotyping of still poorly characterized human genes and for systematic study of uncharacterized genomic features associated with human disease.
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Affiliation(s)
- Bianca V Gapp
- Nuffield Department of Clinical Medicine, Ludwig Cancer Research Ltd. University of Oxford, Oxford, UK
| | - Tomasz Konopka
- Nuffield Department of Clinical Medicine, Ludwig Cancer Research Ltd. University of Oxford, Oxford, UK
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vineet Dalal
- Nuffield Department of Clinical Medicine, Ludwig Cancer Research Ltd. University of Oxford, Oxford, UK
| | | | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Sebastian Mb Nijman
- Nuffield Department of Clinical Medicine, Ludwig Cancer Research Ltd. University of Oxford, Oxford, UK CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria Nuffield Department of Clinical Medicine, Target Discovery Institute University of Oxford, Oxford, UK
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5
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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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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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7
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Abstract
The great majority of targeted anticancer drugs inhibit mutated oncogenes that display increased activity. Yet many tumors do not contain such actionable aberrations, such as those harboring loss-of-function mutations. The notion of targeting synthetic lethal vulnerabilities in cancer cells has provided an alternative approach to exploiting more of the genetic and epigenetic changes acquired during tumorigenesis. Here, we review synthetic lethality as a therapeutic concept that exploits the inherent differences between normal cells and cancer cells. Furthermore, we provide an overview of the screening approaches that can be used to identify synthetic lethal interactions in human cells and present several recently identified interactions that may be pharmacologically exploited. Finally, we indicate some of the challenges of translating synthetic lethal interactions into the clinic and how these may be overcome.
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Affiliation(s)
- Ferran Fece de la Cruz
- CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, A1090 Vienna, Austria;
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8
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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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