1
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Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Lehr S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Dev Cell 2024:S1534-5807(24)00297-1. [PMID: 38776925 DOI: 10.1016/j.devcel.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 03/08/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable "winning" floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering.
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Affiliation(s)
- Teresa Krammer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Hannah T Stuart
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; The Francis Crick Institute, London, UK
| | - Elena Gromberg
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Keisuke Ishihara
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Dillon Cislo
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA
| | | | - Fernando Becerril Perez
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Elena Costantini
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Stefanie Lehr
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Laura Arbanas
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | | | | | - Nicola Elvassore
- Department of Industrial Engineering, University of Padova & Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Eric Siggia
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA
| | | | - Anna Kicheva
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
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2
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Chang Y, Bach L, Hasiuk M, Wen L, Elmzzahi T, Tsui C, Gutiérrez-Melo N, Steffen T, Utzschneider DT, Raj T, Jost PJ, Heink S, Cheng J, Burton OT, Zeiträg J, Alterauge D, Dahlström F, Becker JC, Kastl M, Symeonidis K, van Uelft M, Becker M, Reschke S, Krebs S, Blum H, Abdullah Z, Paeschke K, Ohnmacht C, Neumann C, Liston A, Meissner F, Korn T, Hasenauer J, Heissmeyer V, Beyer M, Kallies A, Jeker LT, Baumjohann D. TGF-β specifies T FH versus T H17 cell fates in murine CD4 + T cells through c-Maf. Sci Immunol 2024; 9:eadd4818. [PMID: 38427718 DOI: 10.1126/sciimmunol.add4818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 01/05/2024] [Indexed: 03/03/2024]
Abstract
T follicular helper (TFH) cells are essential for effective antibody responses, but deciphering the intrinsic wiring of mouse TFH cells has long been hampered by the lack of a reliable protocol for their generation in vitro. We report that transforming growth factor-β (TGF-β) induces robust expression of TFH hallmark molecules CXCR5 and Bcl6 in activated mouse CD4+ T cells in vitro. TGF-β-induced mouse CXCR5+ TFH cells are phenotypically, transcriptionally, and functionally similar to in vivo-generated TFH cells and provide critical help to B cells. The study further reveals that TGF-β-induced CXCR5 expression is independent of Bcl6 but requires the transcription factor c-Maf. Classical TGF-β-containing T helper 17 (TH17)-inducing conditions also yield separate CXCR5+ and IL-17A-producing cells, highlighting shared and distinct cell fate trajectories of TFH and TH17 cells. We demonstrate that excess IL-2 in high-density T cell cultures interferes with the TGF-β-induced TFH cell program, that TFH and TH17 cells share a common developmental stage, and that c-Maf acts as a switch factor for TFH versus TH17 cell fates in TGF-β-rich environments in vitro and in vivo.
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Affiliation(s)
- Yinshui Chang
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Luisa Bach
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Marko Hasiuk
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Lifen Wen
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Tarek Elmzzahi
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Immunogenomics and Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Carlson Tsui
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Nicolás Gutiérrez-Melo
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Teresa Steffen
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Daniel T Utzschneider
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Timsse Raj
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Paul Jonas Jost
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Sylvia Heink
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine, 81675 Munich, Germany
| | - Jingyuan Cheng
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Oliver T Burton
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Julia Zeiträg
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Dominik Alterauge
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Frank Dahlström
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Jennifer-Christin Becker
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Melanie Kastl
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Konstantinos Symeonidis
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Martina van Uelft
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Matthias Becker
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | - Sarah Reschke
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Zeinab Abdullah
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Katrin Paeschke
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Caspar Ohnmacht
- Center of Allergy and Environment (ZAUM), Technical University and Helmholtz Center Munich, Munich, Germany
| | - Christian Neumann
- Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Adrian Liston
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Felix Meissner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Systems Immunology and Proteomics, Institute of Innate Immunity, Medical Faculty, University of Bonn, Germany
| | - Thomas Korn
- Institute for Experimental Neuroimmunology, Technical University of Munich School of Medicine, 81675 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Jan Hasenauer
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
- Center for Mathematics, Technical University of Munich, Garching, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Feodor-Lynen-Str. 21, 81377 Munich, Germany
| | - Marc Beyer
- Immunogenomics and Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
| | - Axel Kallies
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Dirk Baumjohann
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
- Institute for Immunology, Faculty of Medicine, Biomedical Center, LMU Munich, Grosshaderner Str. 9, 82152 Planegg-Martinsried, Germany
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3
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Beirute-Herrera J, López-Amo Calvo B, Edenhofer F, Esk C. The promise of genetic screens in human in vitro brain models. Biol Chem 2024; 405:13-24. [PMID: 37697643 DOI: 10.1515/hsz-2023-0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/21/2023] [Indexed: 09/13/2023]
Abstract
Advances of in vitro culture models have allowed unprecedented insights into human neurobiology. At the same time genetic screening has matured into a robust and accessible experimental strategy allowing for the simultaneous study of many genes in parallel. The combination of both technologies is a newly emerging tool for neuroscientists, opening the door to identifying causal cell- and tissue-specific developmental and disease mechanisms. However, with complex experimental genetic screening set-ups new challenges in data interpretation and experimental scope arise that require a deep understanding of the benefits and challenges of individual approaches. In this review, we summarize the literature that applies genetic screening to in vitro brain models, compare experimental strengths and weaknesses and point towards future directions of these promising approaches.
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Affiliation(s)
- Julianne Beirute-Herrera
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Beatriz López-Amo Calvo
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Frank Edenhofer
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Christopher Esk
- Institute of Molecular Biology, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Center for Molecular Biosciences, University Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
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4
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Ito Y, Inoue S, Nakashima T, Zhang H, Li Y, Kasuya H, Matsukawa T, Wu Z, Yoshikawa T, Kataoka M, Ishikawa T, Kagoya Y. Epigenetic profiles guide improved CRISPR/Cas9-mediated gene knockout in human T cells. Nucleic Acids Res 2024; 52:141-153. [PMID: 37985205 PMCID: PMC10783505 DOI: 10.1093/nar/gkad1076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023] Open
Abstract
Genetic modification of specific genes is emerging as a useful tool to enhance the functions of antitumor T cells in adoptive immunotherapy. Current advances in CRISPR/Cas9 technology enable gene knockout during in vitro preparation of infused T-cell products through transient transfection of a Cas9-guide RNA (gRNA) ribonucleoprotein complex. However, selecting optimal gRNAs remains a major challenge for efficient gene ablation. Although multiple in silico tools to predict the targeting efficiency have been developed, their performance has not been validated in cultured human T cells. Here, we explored a strategy to select optimal gRNAs using our pooled data on CRISPR/Cas9-mediated gene knockout in human T cells. The currently available prediction tools alone were insufficient to accurately predict the indel percentage in T cells. We used data on the epigenetic profiles of cultured T cells obtained from transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Combining the epigenetic information with sequence-based prediction tools significantly improved the gene-editing efficiency. We further demonstrate that epigenetically closed regions can be targeted by designing two gRNAs in adjacent regions. Finally, we demonstrate that the gene-editing efficiency of unstimulated T cells can be enhanced through pretreatment with IL-7. These findings enable more efficient gene editing in human T cells.
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Affiliation(s)
- Yusuke Ito
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Satoshi Inoue
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Takahiro Nakashima
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Haosong Zhang
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yang Li
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hitomi Kasuya
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Tetsuya Matsukawa
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Zhiwen Wu
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Toshiaki Yoshikawa
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Mirei Kataoka
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Tetsuo Ishikawa
- Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Yokohama, Japan
- Collective Intelligence Research Laboratory, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuki Kagoya
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
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5
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Niwa R, Sakai K, Lung MSY, Matsumoto T, Mikawa R, Maehana S, Suzuki M, Yamamoto Y, Maurissen TL, Hirabayashi A, Noda T, Kubo M, Gotoh S, Woltjen K. ACE2 knockout hinders SARS-CoV-2 propagation in iPS cell-derived airway and alveolar epithelial cells. Front Cell Dev Biol 2023; 11:1290876. [PMID: 38149046 PMCID: PMC10750251 DOI: 10.3389/fcell.2023.1290876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/26/2023] [Indexed: 12/28/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continues to spread around the world with serious cases and deaths. It has also been suggested that different genetic variants in the human genome affect both the susceptibility to infection and severity of disease in COVID-19 patients. Angiotensin-converting enzyme 2 (ACE2) has been identified as a cell surface receptor for SARS-CoV and SARS-CoV-2 entry into cells. The construction of an experimental model system using human iPS cells would enable further studies of the association between viral characteristics and genetic variants. Airway and alveolar epithelial cells are cell types of the lung that express high levels of ACE2 and are suitable for in vitro infection experiments. Here, we show that human iPS cell-derived airway and alveolar epithelial cells are highly susceptible to viral infection of SARS-CoV-2. Using gene knockout with CRISPR-Cas9 in human iPS cells we demonstrate that ACE2 plays an essential role in the airway and alveolar epithelial cell entry of SARS-CoV-2 in vitro. Replication of SARS-CoV-2 was strongly suppressed in ACE2 knockout (KO) lung cells. Our model system based on human iPS cell-derived lung cells may be applied to understand the molecular biology regulating viral respiratory infection leading to potential therapeutic developments for COVID-19 and the prevention of future pandemics.
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Affiliation(s)
- Ryo Niwa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kouji Sakai
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mandy Siu Yu Lung
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomoko Matsumoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ryuta Mikawa
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shotaro Maehana
- Department of Microbiology, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
- Regenerative Medicine and Cell Design Research Facility, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuki Yamamoto
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Thomas L. Maurissen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ai Hirabayashi
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Makoto Kubo
- Department of Microbiology, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
- Regenerative Medicine and Cell Design Research Facility, Kitasato University School of Allied Health Sciences, Kanagawa, Japan
| | - Shimpei Gotoh
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
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6
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Slyskova J, Muniesa-Vargas A, da Silva I, Drummond R, Park J, Häckes D, Poetsch I, Ribeiro-Silva C, Moretton A, Heffeter P, Schärer O, Vermeulen W, Lans H, Loizou J. Detection of oxaliplatin- and cisplatin-DNA lesions requires different global genome repair mechanisms that affect their clinical efficacy. NAR Cancer 2023; 5:zcad057. [PMID: 38058548 PMCID: PMC10696645 DOI: 10.1093/narcan/zcad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 11/02/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023] Open
Abstract
The therapeutic efficacy of cisplatin and oxaliplatin depends on the balance between the DNA damage induction and the DNA damage response of tumor cells. Based on clinical evidence, oxaliplatin is administered to cisplatin-unresponsive cancers, but the underlying molecular causes for this tumor specificity are not clear. Hence, stratification of patients based on DNA repair profiling is not sufficiently utilized for treatment selection. Using a combination of genetic, transcriptomics and imaging approaches, we identified factors that promote global genome nucleotide excision repair (GG-NER) of DNA-platinum adducts induced by oxaliplatin, but not by cisplatin. We show that oxaliplatin-DNA lesions are a poor substrate for GG-NER initiating factor XPC and that DDB2 and HMGA2 are required for efficient binding of XPC to oxaliplatin lesions and subsequent GG-NER initiation. Loss of DDB2 and HMGA2 therefore leads to hypersensitivity to oxaliplatin but not to cisplatin. As a result, low DDB2 levels in different colon cancer cells are associated with GG-NER deficiency and oxaliplatin hypersensitivity. Finally, we show that colon cancer patients with low DDB2 levels have a better prognosis after oxaliplatin treatment than patients with high DDB2 expression. We therefore propose that DDB2 is a promising predictive marker of oxaliplatin treatment efficiency in colon cancer.
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Affiliation(s)
- Jana Slyskova
- Center for Cancer Research, Medical University of Vienna, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
| | - Alba Muniesa-Vargas
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Israel Tojal da Silva
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, São Paulo 01508-010, Brazil
| | - Rodrigo Drummond
- Laboratory of Bioinformatics and Computational Biology, A.C. Camargo Cancer Center, São Paulo 01508-010, Brazil
| | - Jiyeong Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Isabella Poetsch
- Center for Cancer Research, Medical University of Vienna, A-1090 Vienna, Austria
- Research Cluster “Translational Cancer Therapy Research”, A-1090 Vienna, Austria
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Amandine Moretton
- Center for Cancer Research, Medical University of Vienna, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
| | - Petra Heffeter
- Center for Cancer Research, Medical University of Vienna, A-1090 Vienna, Austria
- Research Cluster “Translational Cancer Therapy Research”, A-1090 Vienna, Austria
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Joanna I Loizou
- Center for Cancer Research, Medical University of Vienna, A-1090 Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria
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7
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Xue G, Xie J, Hinterndorfer M, Cigler M, Dötsch L, Imrichova H, Lampe P, Cheng X, Adariani SR, Winter GE, Waldmann H. Discovery of a Drug-like, Natural Product-Inspired DCAF11 Ligand Chemotype. Nat Commun 2023; 14:7908. [PMID: 38036533 PMCID: PMC10689823 DOI: 10.1038/s41467-023-43657-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Targeted proteasomal and autophagic protein degradation, often employing bifunctional modalities, is a new paradigm for modulation of protein function. In an attempt to explore protein degradation by means of autophagy we combine arylidene-indolinones reported to bind the autophagy-related LC3B-protein and ligands of the PDEδ lipoprotein chaperone, the BRD2/3/4-bromodomain containing proteins and the BTK- and BLK kinases. Unexpectedly, the resulting bifunctional degraders do not induce protein degradation by means of macroautophagy, but instead direct their targets to the ubiquitin-proteasome system. Target and mechanism identification reveal that the arylidene-indolinones covalently bind DCAF11, a substrate receptor in the CUL4A/B-RBX1-DDB1-DCAF11 E3 ligase. The tempered α, β-unsaturated indolinone electrophiles define a drug-like DCAF11-ligand class that enables exploration of this E3 ligase in chemical biology and medicinal chemistry programs. The arylidene-indolinone scaffold frequently occurs in natural products which raises the question whether E3 ligand classes can be found more widely among natural products and related compounds.
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Affiliation(s)
- Gang Xue
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jianing Xie
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lara Dötsch
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp Lampe
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Xiufen Cheng
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Soheila Rezaei Adariani
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
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8
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Herzfeldt AK, Gamez MP, Martin E, Boryn LM, Baskaran P, Huber HJ, Schuler M, Park JE, Swee LK. Complementary CRISPR screen highlights the contrasting role of membrane-bound and soluble ICAM-1 in regulating antigen-specific tumor cell killing by cytotoxic T cells. eLife 2023; 12:e84314. [PMID: 37732732 PMCID: PMC10586807 DOI: 10.7554/elife.84314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 09/20/2023] [Indexed: 09/22/2023] Open
Abstract
Cytotoxic CD8 +T lymphocytes (CTLs) are key players of adaptive anti-tumor immunity based on their ability to specifically recognize and destroy tumor cells. Many cancer immunotherapies rely on unleashing CTL function. However, tumors can evade killing through strategies which are not yet fully elucidated. To provide deeper insight into tumor evasion mechanisms in an antigen-dependent manner, we established a human co-culture system composed of tumor and primary immune cells. Using this system, we systematically investigated intrinsic regulators of tumor resistance by conducting a complementary CRISPR screen approach. By harnessing CRISPR activation (CRISPRa) and CRISPR knockout (KO) technology in parallel, we investigated gene gain-of-function as well as loss-of-function across genes with annotated function in a colon carcinoma cell line. CRISPRa and CRISPR KO screens uncovered 187 and 704 hits, respectively, with 60 gene hits overlapping between both. These data confirmed the role of interferon-γ (IFN-γ), tumor necrosis factor α (TNF-α) and autophagy pathways and uncovered novel genes implicated in tumor resistance to killing. Notably, we discovered that ILKAP encoding the integrin-linked kinase-associated serine/threonine phosphatase 2 C, a gene previously unknown to play a role in antigen specific CTL-mediated killing, mediate tumor resistance independently from regulating antigen presentation, IFN-γ or TNF-α responsiveness. Moreover, our work describes the contrasting role of soluble and membrane-bound ICAM-1 in regulating tumor cell killing. The deficiency of membrane-bound ICAM-1 (mICAM-1) or the overexpression of soluble ICAM-1 (sICAM-1) induced resistance to CTL killing, whereas PD-L1 overexpression had no impact. These results highlight the essential role of ICAM-1 at the immunological synapse between tumor and CTL and the antagonist function of sICAM-1.
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Affiliation(s)
- Ann-Kathrin Herzfeldt
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Marta Puig Gamez
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Eva Martin
- Department of Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | | | - Praveen Baskaran
- Department of Global Computational Biology and Digital Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - Heinrich J Huber
- Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - Michael Schuler
- Department of Drug Discovery Sciences, Boehringer IngelheimBiberach an der RissGermany
| | - John E Park
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
| | - Lee Kim Swee
- Department of Cancer Immunology and Immune Modulation, Boehringer IngelheimBiberach an der RissGermany
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9
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Ebner J, Schmoellerl J, Piontek M, Manhart G, Troester S, Carter BZ, Neubauer H, Moriggl R, Szakács G, Zuber J, Köcher T, Andreeff M, Sperr WR, Valent P, Grebien F. ABCC1 and glutathione metabolism limit the efficacy of BCL-2 inhibitors in acute myeloid leukemia. Nat Commun 2023; 14:5709. [PMID: 37726279 PMCID: PMC10509209 DOI: 10.1038/s41467-023-41229-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/25/2023] [Indexed: 09/21/2023] Open
Abstract
The BCL-2 inhibitor Venetoclax is a promising agent for the treatment of acute myeloid leukemia (AML). However, many patients are refractory to Venetoclax, and resistance develops quickly. ATP-binding cassette (ABC) transporters mediate chemotherapy resistance but their role in modulating the activity of targeted small-molecule inhibitors is unclear. Using CRISPR/Cas9 screening, we find that loss of ABCC1 strongly increases the sensitivity of AML cells to Venetoclax. Genetic and pharmacologic ABCC1 inactivation potentiates the anti-leukemic effects of BCL-2 inhibitors and efficiently re-sensitizes Venetoclax-resistant leukemia cells. Conversely, ABCC1 overexpression induces resistance to BCL-2 inhibitors by reducing intracellular drug levels, and high ABCC1 levels predicts poor response to Venetoclax therapy in patients. Consistent with ABCC1-specific export of glutathionylated substrates, inhibition of glutathione metabolism increases the potency of BCL-2 inhibitors. These results identify ABCC1 and glutathione metabolism as mechanisms limiting efficacy of BCL-2 inhibitors, which may pave the way to development of more effective therapies.
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Affiliation(s)
- Jessica Ebner
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Johannes Schmoellerl
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Martin Piontek
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gabriele Manhart
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Selina Troester
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Bing Z Carter
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heidi Neubauer
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Richard Moriggl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gergely Szakács
- Center for Cancer Research, Medical University Vienna, Vienna, Austria
- Institute of Enzymology, Research Centre of Natural Sciences, Eötvös Loránd Research Network, Budapest, Hungary
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Thomas Köcher
- Vienna BioCenter Core Facilities, Vienna BioCenter, Vienna, Austria
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wolfgang R Sperr
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Peter Valent
- Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria.
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
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10
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Li C, Fleck JS, Martins-Costa C, Burkard TR, Themann J, Stuempflen M, Peer AM, Vertesy Á, Littleboy JB, Esk C, Elling U, Kasprian G, Corsini NS, Treutlein B, Knoblich JA. Single-cell brain organoid screening identifies developmental defects in autism. Nature 2023; 621:373-380. [PMID: 37704762 PMCID: PMC10499611 DOI: 10.1038/s41586-023-06473-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/21/2023] [Indexed: 09/15/2023]
Abstract
The development of the human brain involves unique processes (not observed in many other species) that can contribute to neurodevelopmental disorders1-4. Cerebral organoids enable the study of neurodevelopmental disorders in a human context. We have developed the CRISPR-human organoids-single-cell RNA sequencing (CHOOSE) system, which uses verified pairs of guide RNAs, inducible CRISPR-Cas9-based genetic disruption and single-cell transcriptomics for pooled loss-of-function screening in mosaic organoids. Here we show that perturbation of 36 high-risk autism spectrum disorder genes related to transcriptional regulation uncovers their effects on cell fate determination. We find that dorsal intermediate progenitors, ventral progenitors and upper-layer excitatory neurons are among the most vulnerable cell types. We construct a developmental gene regulatory network of cerebral organoids from single-cell transcriptomes and chromatin modalities and identify autism spectrum disorder-associated and perturbation-enriched regulatory modules. Perturbing members of the BRG1/BRM-associated factor (BAF) chromatin remodelling complex leads to enrichment of ventral telencephalon progenitors. Specifically, mutating the BAF subunit ARID1B affects the fate transition of progenitors to oligodendrocyte and interneuron precursor cells, a phenotype that we confirmed in patient-specific induced pluripotent stem cell-derived organoids. Our study paves the way for high-throughput phenotypic characterization of disease susceptibility genes in organoid models with cell state, molecular pathway and gene regulatory network readouts.
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Affiliation(s)
- Chong Li
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Catarina Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jan Themann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Marlene Stuempflen
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Angela Maria Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Ábel Vertesy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jamie B Littleboy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Christopher Esk
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Gregor Kasprian
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
- Department of Neurology, Medical University of Vienna, Vienna, Austria.
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11
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Schwartz I, Vunjak M, Budroni V, Cantoran García A, Mastrovito M, Soderholm A, Hinterndorfer M, de Almeida M, Hacker K, Wang J, Froussios K, Jude J, Decker T, Zuber J, Versteeg GA. SPOP targets the immune transcription factor IRF1 for proteasomal degradation. eLife 2023; 12:e89951. [PMID: 37622993 PMCID: PMC10491434 DOI: 10.7554/elife.89951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Adaptation of the functional proteome is essential to counter pathogens during infection, yet precisely timed degradation of these response proteins after pathogen clearance is likewise key to preventing autoimmunity. Interferon regulatory factor 1 (IRF1) plays an essential role as a transcription factor in driving the expression of immune response genes during infection. The striking difference in functional output with other IRFs is that IRF1 also drives the expression of various cell cycle inhibiting factors, making it an important tumor suppressor. Thus, it is critical to regulate the abundance of IRF1 to achieve a 'Goldilocks' zone in which there is sufficient IRF1 to prevent tumorigenesis, yet not too much which could drive excessive immune activation. Using genetic screening, we identified the E3 ligase receptor speckle type BTB/POZ protein (SPOP) to mediate IRF1 proteasomal turnover in human and mouse cells. We identified S/T-rich degrons in IRF1 required for its SPOP MATH domain-dependent turnover. In the absence of SPOP, elevated IRF1 protein levels functionally increased IRF1-dependent cellular responses, underpinning the biological significance of SPOP in curtailing IRF1 protein abundance.
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Affiliation(s)
- Irene Schwartz
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
| | - Milica Vunjak
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
| | - Valentina Budroni
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
| | - Adriana Cantoran García
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
| | - Marialaura Mastrovito
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
| | - Adrian Soderholm
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
| | - Matthias Hinterndorfer
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
| | - Melanie de Almeida
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BiocenterViennaAustria
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
| | - Kathrin Hacker
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
| | - Jingkui Wang
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
| | - Kimon Froussios
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
| | - Julian Jude
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
| | - Thomas Decker
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BiocenterViennaAustria
- Medical University of Vienna, Vienna BioCenterViennaAustria
| | - Gijs A Versteeg
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of ViennaViennaAustria
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12
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Jia X, Zhu J, Bian X, Liu S, Yu S, Liang W, Jiang L, Mao R, Zhang W, Rao Y. Importance of glutamine in synaptic vesicles revealed by functional studies of SLC6A17 and its mutations pathogenic for intellectual disability. eLife 2023; 12:RP86972. [PMID: 37440432 PMCID: PMC10393021 DOI: 10.7554/elife.86972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023] Open
Abstract
Human mutations in the gene encoding the solute carrier (SLC) 6A17 caused intellectual disability (ID). The physiological role of SLC6A17 and pathogenesis of SLC6A17-based-ID were both unclear. Here, we report learning deficits in Slc6a17 knockout and point mutant mice. Biochemistry, proteomic, and electron microscopy (EM) support SLC6A17 protein localization in synaptic vesicles (SVs). Chemical analysis of SVs by liquid chromatography coupled to mass spectrometry (LC-MS) revealed glutamine (Gln) in SVs containing SLC6A17. Virally mediated overexpression of SLC6A17 increased Gln in SVs. Either genetic or virally mediated targeting of Slc6a17 reduced Gln in SVs. One ID mutation caused SLC6A17 mislocalization while the other caused defective Gln transport. Multidisciplinary approaches with seven types of genetically modified mice have shown Gln as an endogenous substrate of SLC6A17, uncovered Gln as a new molecule in SVs, established the necessary and sufficient roles of SLC6A17 in Gln transport into SVs, and suggested SV Gln decrease as the key pathogenetic mechanism in human ID.
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Affiliation(s)
- Xiaobo Jia
- Chinese Institute for Brain ResearchBeijingChina
- Changping LaboratoryBeijingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
| | - Jiemin Zhu
- Laboratory of Neurochemical Biology, PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, School of Chemistry and Chemical Engineering, Peking UniversityBeijingChina
| | - Xiling Bian
- Laboratory of Neurochemical Biology, PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, School of Chemistry and Chemical Engineering, Peking UniversityBeijingChina
| | | | - Sihan Yu
- Chinese Institute for Brain ResearchBeijingChina
| | | | - Lifen Jiang
- Institute of Molecular Physiology, Shenzhen Bay LaboratoryShenzhenChina
| | - Renbo Mao
- Chinese Institute for Brain ResearchBeijingChina
| | - Wenxia Zhang
- Laboratory of Neurochemical Biology, PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, School of Chemistry and Chemical Engineering, Peking UniversityBeijingChina
| | - Yi Rao
- Chinese Institute for Brain ResearchBeijingChina
- Changping LaboratoryBeijingChina
- Research Unit of Medical Neurobiology, Chinese Academy of Medical SciencesBeijingChina
- Laboratory of Neurochemical Biology, PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, School of Chemistry and Chemical Engineering, Peking UniversityBeijingChina
- Institute of Molecular Physiology, Shenzhen Bay LaboratoryShenzhenChina
- Capital Medical UniversityBeijingChina
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13
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Welte T, Goulois A, Stadler MB, Hess D, Soneson C, Neagu A, Azzi C, Wisser MJ, Seebacher J, Schmidt I, Estoppey D, Nigsch F, Reece-Hoyes J, Hoepfner D, Großhans H. Convergence of multiple RNA-silencing pathways on GW182/TNRC6. Mol Cell 2023:S1097-2765(23)00423-9. [PMID: 37369201 DOI: 10.1016/j.molcel.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 04/02/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
The RNA-binding protein TRIM71/LIN-41 is a phylogenetically conserved developmental regulator that functions in mammalian stem cell reprogramming, brain development, and cancer. TRIM71 recognizes target mRNAs through hairpin motifs and silences them through molecular mechanisms that await identification. Here, we uncover that TRIM71 represses its targets through RNA-supported interaction with TNRC6/GW182, a core component of the miRNA-induced silencing complex (miRISC). We demonstrate that AGO2, TRIM71, and UPF1 each recruit TNRC6 to specific sets of transcripts to silence them. As cellular TNRC6 levels are limiting, competition occurs among the silencing pathways, such that the loss of AGO proteins or of AGO binding to TNRC6 enhances the activities of the other pathways. We conclude that a miRNA-like silencing activity is shared among different mRNA silencing pathways and that the use of TNRC6 as a central hub provides a means to integrate their activities.
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Affiliation(s)
- Thomas Welte
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Department of Medicine IV, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Alison Goulois
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Charlotte Soneson
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Anca Neagu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Chiara Azzi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marlena J Wisser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Isabel Schmidt
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - David Estoppey
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Florian Nigsch
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - John Reece-Hoyes
- Department of Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Dominic Hoepfner
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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14
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Brandstoetter T, Schmoellerl J, Grausenburger R, Kollmann S, Doma E, Huuhtanen J, Klampfl T, Eder T, Grebien F, Hoermann G, Zuber J, Mustjoki S, Maurer B, Sexl V. SBNO2 is a critical mediator of STAT3-driven hematological malignancies. Blood 2023; 141:1831-1845. [PMID: 36630607 PMCID: PMC10646773 DOI: 10.1182/blood.2022018494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/12/2022] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Gain-of-function mutations in the signal transducer and activator of transcription 3 (STAT3) gene are recurrently identified in patients with large granular lymphocytic leukemia (LGLL) and in some cases of natural killer (NK)/T-cell and adult T-cell leukemia/lymphoma. To understand the consequences and molecular mechanisms contributing to disease development and oncogenic transformation, we developed murine hematopoietic stem and progenitor cell models that express mutated STAT3Y640F. These cells show accelerated proliferation and enhanced self-renewal potential. We integrated gene expression analyses and chromatin occupancy profiling of STAT3Y640F-transformed cells with data from patients with T-LGLL. This approach uncovered a conserved set of direct transcriptional targets of STAT3Y640F. Among these, strawberry notch homolog 2 (SBNO2) represents an essential transcriptional target, which was identified by a comparative genome-wide CRISPR/Cas9-based loss-of-function screen. The STAT3-SBNO2 axis is also present in NK-cell leukemia, T-cell non-Hodgkin lymphoma, and NPM-ALK-rearranged T-cell anaplastic large cell lymphoma (T-ALCL), which are driven by STAT3-hyperactivation/mutation. In patients with NPM-ALK+ T-ALCL, high SBNO2 expression correlates with shorter relapse-free and overall survival. Our findings identify SBNO2 as a potential therapeutic intervention site for STAT3-driven hematopoietic malignancies.
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Affiliation(s)
- Tania Brandstoetter
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Reinhard Grausenburger
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sebastian Kollmann
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Eszter Doma
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Thorsten Klampfl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Eder
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- ICAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Barbara Maurer
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
- University of Innsbruck, Innsbruck, Austria
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15
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Hu J, Sánchez-Rivera FJ, Wang Z, Johnson GN, Ho YJ, Ganesh K, Umeda S, Gan S, Mujal AM, Delconte RB, Hampton JP, Zhao H, Kottapalli S, de Stanchina E, Iacobuzio-Donahue CA, Pe'er D, Lowe SW, Sun JC, Massagué J. STING inhibits the reactivation of dormant metastasis in lung adenocarcinoma. Nature 2023; 616:806-813. [PMID: 36991128 PMCID: PMC10569211 DOI: 10.1038/s41586-023-05880-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/22/2023] [Indexed: 03/31/2023]
Abstract
Metastasis frequently develops from disseminated cancer cells that remain dormant after the apparently successful treatment of a primary tumour. These cells fluctuate between an immune-evasive quiescent state and a proliferative state liable to immune-mediated elimination1-6. Little is known about the clearing of reawakened metastatic cells and how this process could be therapeutically activated to eliminate residual disease in patients. Here we use models of indolent lung adenocarcinoma metastasis to identify cancer cell-intrinsic determinants of immune reactivity during exit from dormancy. Genetic screens of tumour-intrinsic immune regulators identified the stimulator of interferon genes (STING) pathway as a suppressor of metastatic outbreak. STING activity increases in metastatic progenitors that re-enter the cell cycle and is dampened by hypermethylation of the STING promoter and enhancer in breakthrough metastases or by chromatin repression in cells re-entering dormancy in response to TGFβ. STING expression in cancer cells derived from spontaneous metastases suppresses their outgrowth. Systemic treatment of mice with STING agonists eliminates dormant metastasis and prevents spontaneous outbreaks in a T cell- and natural killer cell-dependent manner-these effects require cancer cell STING function. Thus, STING provides a checkpoint against the progression of dormant metastasis and a therapeutically actionable strategy for the prevention of disease relapse.
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Affiliation(s)
- Jing Hu
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco J Sánchez-Rivera
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhenghan Wang
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gabriela N Johnson
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu-Jui Ho
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karuna Ganesh
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shigeaki Umeda
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Siting Gan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adriana M Mujal
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca B Delconte
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica P Hampton
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Huiyong Zhao
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sanjay Kottapalli
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- The Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph C Sun
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joan Massagué
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- The Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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16
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Scinicariello S, Soderholm A, Schäfer M, Shulkina A, Schwartz I, Hacker K, Gogova R, Kalis R, Froussios K, Budroni V, Bestehorn A, Clausen T, Kovarik P, Zuber J, Versteeg GA. HUWE1 controls tristetraprolin proteasomal degradation by regulating its phosphorylation. eLife 2023; 12:e83159. [PMID: 36961408 PMCID: PMC10038661 DOI: 10.7554/elife.83159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/26/2023] [Indexed: 03/25/2023] Open
Abstract
Tristetraprolin (TTP) is a critical negative immune regulator. It binds AU-rich elements in the untranslated-regions of many mRNAs encoding pro-inflammatory mediators, thereby accelerating their decay. A key but poorly understood mechanism of TTP regulation is its timely proteolytic removal: TTP is degraded by the proteasome through yet unidentified phosphorylation-controlled drivers. In this study, we set out to identify factors controlling TTP stability. Cellular assays showed that TTP is strongly lysine-ubiquitinated, which is required for its turnover. A genetic screen identified the ubiquitin E3 ligase HUWE1 as a strong regulator of TTP proteasomal degradation, which we found to control TTP stability indirectly by regulating its phosphorylation. Pharmacological assessment of multiple kinases revealed that HUWE1-regulated TTP phosphorylation and stability was independent of the previously characterized effects of MAPK-mediated S52/S178 phosphorylation. HUWE1 function was dependent on phosphatase and E3 ligase binding sites identified in the TTP C-terminus. Our findings indicate that while phosphorylation of S52/S178 is critical for TTP stabilization at earlier times after pro-inflammatory stimulation, phosphorylation of the TTP C-terminus controls its stability at later stages.
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Affiliation(s)
- Sara Scinicariello
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Adrian Soderholm
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Markus Schäfer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Alexandra Shulkina
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Irene Schwartz
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Kathrin Hacker
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Rebeca Gogova
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Robert Kalis
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Kimon Froussios
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Valentina Budroni
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Annika Bestehorn
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
- Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Pavel Kovarik
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
- Medical University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Gijs A Versteeg
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
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17
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Wong CH, Wingett SW, Qian C, Taliaferro JM, Ross-Thriepland D, Bullock SL. Genome-scale requirements for dynein-based trafficking revealed by a high-content arrayed CRISPR screen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530592. [PMID: 36909483 PMCID: PMC10002790 DOI: 10.1101/2023.03.01.530592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The cytoplasmic dynein-1 (dynein) motor plays a key role in cellular organisation by transporting a wide variety of cellular constituents towards the minus ends of microtubules. However, relatively little is known about how the biosynthesis, assembly and functional diversity of the motor is orchestrated. To address this issue, we have conducted an arrayed CRISPR loss-of-function screen in human cells using the distribution of dynein-tethered peroxisomes and early endosomes as readouts. From a guide RNA library targeting 18,253 genes, 195 validated hits were recovered and parsed into those impacting multiple dynein cargoes and those whose effects are restricted to a subset of cargoes. Clustering of high-dimensional phenotypic fingerprints generated from multiplexed images revealed co-functional genes involved in many cellular processes, including several candidate novel regulators of core dynein functions. Mechanistic analysis of one of these proteins, the RNA-binding protein SUGP1, provides evidence that it promotes cargo trafficking by sustaining functional expression of the dynein activator LIS1. Our dataset represents a rich source of new hypotheses for investigating microtubule-based transport, as well as several other aspects of cellular organisation that were captured by our high-content imaging.
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Affiliation(s)
- Chun Hao Wong
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Discovery Biology, Discovery Sciences, AstraZeneca, R&D, Cambridge, CB4 0WG, UK
- Current address: Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Steven W. Wingett
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Chen Qian
- Quantitative Biology, Discovery Sciences, AstraZeneca, R&D, Cambridge, CB4 0WG, UK
| | - J. Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Simon L. Bullock
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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18
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EVI1 drives leukemogenesis through aberrant ERG activation. Blood 2023; 141:453-466. [PMID: 36095844 DOI: 10.1182/blood.2022016592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/10/2022] [Accepted: 08/28/2022] [Indexed: 02/07/2023] Open
Abstract
Chromosomal rearrangements involving the MDS1 and EVI1 complex locus (MECOM) on chromosome 3q26 define an aggressive subtype of acute myeloid leukemia (AML) that is associated with chemotherapy resistance and dismal prognosis. Established treatment regimens commonly fail in these patients, therefore, there is an urgent need for new therapeutic concepts that will require a better understanding of the molecular and cellular functions of the ecotropic viral integration site 1 (EVI1) oncogene. To characterize gene regulatory functions of EVI1 and associated dependencies in AML, we developed experimentally tractable human and murine disease models, investigated the transcriptional consequences of EVI1 withdrawal in vitro and in vivo, and performed the first genome-wide CRISPR screens in EVI1-dependent AML. By integrating conserved transcriptional targets with genetic dependency data, we identified and characterized the ETS transcription factor ERG as a direct transcriptional target of EVI1 that is aberrantly expressed and selectively required in both human and murine EVI1-driven AML. EVI1 controls the expression of ERG and occupies a conserved intragenic enhancer region in AML cell lines and samples from patients with primary AML. Suppression of ERG induces terminal differentiation of EVI1-driven AML cells, whereas ectopic expression of ERG abrogates their dependence on EVI1, indicating that the major oncogenic functions of EVI1 are mediated through aberrant transcriptional activation of ERG. Interfering with this regulatory axis may provide entry points for the development of rational targeted therapies.
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19
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Lehmann J, Caduff N, Krzywińska E, Stierli S, Salas-Bastos A, Loos B, Levesque MP, Dummer R, Stockmann C, Münz C, Diener J, Sommer L. Escape from NK cell tumor surveillance by NGFR-induced lipid remodeling in melanoma. SCIENCE ADVANCES 2023; 9:eadc8825. [PMID: 36638181 PMCID: PMC9839334 DOI: 10.1126/sciadv.adc8825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/09/2022] [Indexed: 05/27/2023]
Abstract
Metastatic disease is a major cause of death for patients with melanoma. Melanoma cells can become metastatic not only due to cell-intrinsic plasticity but also due to cancer-induced protumorigenic remodeling of the immune microenvironment. Here, we report that innate immune surveillance by natural killer (NK) cells is bypassed by human melanoma cells expressing the stem cell marker NGFR. Using in vitro and in vivo cytotoxic assays, we show that NGFR protects melanoma cells from NK cell-mediated killing and, furthermore, boosts metastasis formation in a mouse model with adoptively transferred human NK cells. Mechanistically, NGFR leads to down-regulation of NK cell activating ligands and simultaneous up-regulation of the fatty acid stearoyl-coenzyme A desaturase (SCD) in melanoma cells. Notably, pharmacological and small interfering RNA-mediated inhibition of SCD reverted NGFR-induced NK cell evasion in vitro and in vivo. Hence, NGFR orchestrates immune control antagonizing pathways to protect melanoma cells from NK cell clearance, which ultimately favors metastatic disease.
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Affiliation(s)
- Julia Lehmann
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Nicole Caduff
- University of Zurich, Institute of Experimental Immunology, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Ewelina Krzywińska
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Salome Stierli
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Adrian Salas-Bastos
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Benjamin Loos
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Mitchell P. Levesque
- University of Zurich Hospital, Department of Dermatology, Gloriastrasse 31, 8091 Zürich, Switzerland
| | - Reinhard Dummer
- University of Zurich Hospital, Department of Dermatology, Gloriastrasse 31, 8091 Zürich, Switzerland
| | - Christian Stockmann
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Christian Münz
- University of Zurich, Institute of Experimental Immunology, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Johanna Diener
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lukas Sommer
- University of Zurich, Institute of Anatomy, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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20
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Wessels HH, Méndez-Mancilla A, Hao Y, Papalexi E, Mauck WM, Lu L, Morris JA, Mimitou EP, Smibert P, Sanjana NE, Satija R. Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq. Nat Methods 2023; 20:86-94. [PMID: 36550277 PMCID: PMC10030154 DOI: 10.1038/s41592-022-01705-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
Abstract
Pooled CRISPR screens coupled with single-cell RNA-sequencing have enabled systematic interrogation of gene function and regulatory networks. Here, we introduce Cas13 RNA Perturb-seq (CaRPool-seq), which leverages the RNA-targeting CRISPR-Cas13d system and enables efficient combinatorial perturbations alongside multimodal single-cell profiling. CaRPool-seq encodes multiple perturbations on a cleavable CRISPR array that is associated with a detectable barcode sequence, allowing for the simultaneous targeting of multiple genes. We compared CaRPool-seq to existing Cas9-based methods, highlighting its unique strength to efficiently profile combinatorially perturbed cells. Finally, we apply CaRPool-seq to perform multiplexed combinatorial perturbations of myeloid differentiation regulators in an acute myeloid leukemia (AML) model system and identify extensive interactions between different chromatin regulators that can enhance or suppress AML differentiation phenotypes.
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Affiliation(s)
- Hans-Hermann Wessels
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Alejandro Méndez-Mancilla
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Yuhan Hao
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Efthymia Papalexi
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - William M Mauck
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Lu Lu
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - John A Morris
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Eleni P Mimitou
- New York Genome Center, New York, NY, USA
- Technology Innovation Laboratory, New York Genome Center, New York, NY, USA
| | - Peter Smibert
- New York Genome Center, New York, NY, USA
- Technology Innovation Laboratory, New York Genome Center, New York, NY, USA
| | - Neville E Sanjana
- New York Genome Center, New York, NY, USA.
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.
| | - Rahul Satija
- New York Genome Center, New York, NY, USA.
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.
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21
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Schrempf A, Bernardo S, Arasa Verge EA, Ramirez Otero MA, Wilson J, Kirchhofer D, Timelthaler G, Ambros AM, Kaya A, Wieder M, Ecker GF, Winter GE, Costanzo V, Loizou JI. POLθ processes ssDNA gaps and promotes replication fork progression in BRCA1-deficient cells. Cell Rep 2022; 41:111716. [PMID: 36400033 DOI: 10.1016/j.celrep.2022.111716] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/21/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
Polymerase theta (POLθ) is an error-prone DNA polymerase whose loss is synthetically lethal in cancer cells bearing breast cancer susceptibility proteins 1 and 2 (BRCA1/2) mutations. To investigate the basis of this genetic interaction, we utilized a small-molecule inhibitor targeting the POLθ polymerase domain. We found that POLθ processes single-stranded DNA (ssDNA) gaps that emerge in the absence of BRCA1, thus promoting unperturbed replication fork progression and survival of BRCA1 mutant cells. A genome-scale CRISPR-Cas9 knockout screen uncovered suppressors of the functional interaction between POLθ and BRCA1, including NBN, a component of the MRN complex, and cell-cycle regulators such as CDK6. While the MRN complex nucleolytically processes ssDNA gaps, CDK6 promotes cell-cycle progression, thereby exacerbating replication stress, a feature of BRCA1-deficient cells that lack POLθ activity. Thus, ssDNA gap formation, modulated by cell-cycle regulators and MRN complex activity, underlies the synthetic lethality between POLθ and BRCA1, an important insight for clinical trials with POLθ inhibitors.
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Affiliation(s)
- Anna Schrempf
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sara Bernardo
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria
| | - Emili A Arasa Verge
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria
| | - Miguel A Ramirez Otero
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, 20139 Milan, Italy
| | - Jordan Wilson
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Dominik Kirchhofer
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria
| | - Gerald Timelthaler
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria
| | - Anna M Ambros
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Atilla Kaya
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Marcus Wieder
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Georg E Winter
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, 20139 Milan, Italy
| | - Joanna I Loizou
- Center for Cancer Research, Comprehensive Cancer Centre, Medical University of Vienna, 1090 Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
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22
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Walton RT, Singh A, Blainey PC. Pooled genetic screens with image‐based profiling. Mol Syst Biol 2022; 18:e10768. [PMID: 36366905 PMCID: PMC9650298 DOI: 10.15252/msb.202110768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Spatial structure in biology, spanning molecular, organellular, cellular, tissue, and organismal scales, is encoded through a combination of genetic and epigenetic factors in individual cells. Microscopy remains the most direct approach to exploring the intricate spatial complexity defining biological systems and the structured dynamic responses of these systems to perturbations. Genetic screens with deep single‐cell profiling via image features or gene expression programs have the capacity to show how biological systems work in detail by cataloging many cellular phenotypes with one experimental assay. Microscopy‐based cellular profiling provides information complementary to next‐generation sequencing (NGS) profiling and has only recently become compatible with large‐scale genetic screens. Optical screening now offers the scale needed for systematic characterization and is poised for further scale‐up. We discuss how these methodologies, together with emerging technologies for genetic perturbation and microscopy‐based multiplexed molecular phenotyping, are powering new approaches to reveal genotype–phenotype relationships.
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Affiliation(s)
- Russell T Walton
- Broad Institute of MIT and Harvard Cambridge MA USA
- Department of Biological Engineering MIT Cambridge MA USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard Cambridge MA USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard Cambridge MA USA
- Department of Biological Engineering MIT Cambridge MA USA
- Koch Institute for Integrative Cancer Research MIT Cambridge MA USA
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23
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Differential trafficking of ligands trogocytosed via CD28 versus CTLA4 promotes collective cellular control of co-stimulation. Nat Commun 2022; 13:6459. [PMID: 36309492 PMCID: PMC9617924 DOI: 10.1038/s41467-022-34156-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
Intercellular communication is crucial for collective regulation of cellular behaviors. While clustering T cells have been shown to mutually control the production of key communication signals, it is unclear whether they also jointly regulate their availability and degradation. Here we use newly developed reporter systems, bioinformatic analyses, protein structure modeling and genetic perturbations to assess this. We find that T cells utilize trogocytosis by competing antagonistic receptors to differentially control the abundance of immunoregulatory ligands. Specifically, ligands trogocytosed via CD28 are shuttled to the T cell surface, enabling them to co-stimulate neighboring T cells. In contrast, CTLA4-mediated trogocytosis targets ligands for degradation. Mechanistically, this fate separation is controlled by different acid-sensitivities of receptor-ligand interactions and by the receptor intracellular domains. The ability of CD28 and CTLA4 to confer different fates to trogocytosed ligands reveals an additional layer of collective regulation of cellular behaviors and promotes the robustness of population dynamics.
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24
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Tang S, Wu X, Liu J, Zhang Q, Wang X, Shao S, Gokbag B, Fan K, Liu X, Li F, Cheng L, Li L. Generation of dual-gRNA library for combinatorial CRISPR screening of synthetic lethal gene pairs. STAR Protoc 2022; 3:101556. [PMID: 36060092 PMCID: PMC9428847 DOI: 10.1016/j.xpro.2022.101556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Combinatorial CRISPR screening is useful for investigating synthetic lethality (SL) gene pairs. Here, we detail the steps for dual-gRNA library construction, with the introduction of two backbones, LentiGuide_DKO and LentiCRISPR_DKO. We describe steps for in vitro screening with 22Rv1-Cas9 and SaOS2-Cas9 cells followed by sequencing and data analysis. By introducing two backbones, we optimized the library construction process, facilitated standard pair-end sequencing, and provided options of screening on cells with or without modification of Cas9 expression.
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Affiliation(s)
- Shan Tang
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA.
| | - Xue Wu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Jinghui Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Qiongsi Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Xinyi Wang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Shuai Shao
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Birkan Gokbag
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Kunjie Fan
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Fuhai Li
- Institute for Informatics and Department of Pediatrics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Lijun Cheng
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
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25
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Pinter T, Fischer M, Schäfer M, Fellner M, Jude J, Zuber J, Busslinger M, Wöhner M. Comprehensive CRISPR-Cas9 screen identifies factors which are important for plasmablast development. Front Immunol 2022; 13:979606. [PMID: 36189249 PMCID: PMC9521597 DOI: 10.3389/fimmu.2022.979606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Plasma cells (PCs) and their progenitors plasmablasts (PBs) are essential for the acute and long-term protection of the host against infections by providing vast levels of highly specific antibodies. Several transcription factors, like Blimp1 and Irf4, are already known to be essential for PC and PB differentiation and survival. We set out to identify additional genes, that are essential for PB development by CRISPR-Cas9 screening of 3,000 genes for the loss of PBs by employing the in vitro-inducible germinal center B cell (iGB) culture system and Rosa26Cas9/+ mice. Identified hits in the screen were Mau2 and Nipbl, which are known to contribute to the loop extrusion function of the cohesin complex. Other examples of promising hits were Taf6, Stat3, Ppp6c and Pgs1. We thus provide a new set of genes, which are important for PB development.
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26
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Pechincha C, Groessl S, Kalis R, de Almeida M, Zanotti A, Wittmann M, Schneider M, de Campos RP, Rieser S, Brandstetter M, Schleiffer A, Müller-Decker K, Helm D, Jabs S, Haselbach D, Lemberg MK, Zuber J, Palm W. Lysosomal enzyme trafficking factor LYSET enables nutritional usage of extracellular proteins. Science 2022; 378:eabn5637. [PMID: 36074822 DOI: 10.1126/science.abn5637] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Mammalian cells can generate amino acids through macropinocytosis and lysosomal breakdown of extracellular proteins, which is exploited by cancer cells to grow in nutrient-poor tumors. Here, through genetic screens in defined nutrient conditions we characterized LYSET, a transmembrane protein (TMEM251) selectively required when cells consume extracellular proteins. LYSET was found to associate in the Golgi with GlcNAc-1-phosphotransferase, which targets catabolic enzymes to lysosomes through mannose-6-phosphate modification. Without LYSET, GlcNAc-1-phosphotransferase was unstable owing to a hydrophilic transmembrane domain. Consequently, LYSET-deficient cells were depleted of lysosomal enzymes and impaired in turnover of macropinocytic and autophagic cargoes. Thus, LYSET represents a core component of the lysosomal enzyme trafficking pathway, underlies the pathomechanism for hereditary lysosomal storage disorders, and may represent a target to suppress metabolic adaptations in cancer.
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Affiliation(s)
- Catarina Pechincha
- Cell Signaling and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Sven Groessl
- Cell Signaling and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Robert Kalis
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Melanie de Almeida
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Andrea Zanotti
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Marten Wittmann
- Cell Signaling and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- MS-based Protein Analysis Unit, Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rafael P de Campos
- Cell Signaling and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Sarah Rieser
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Marlene Brandstetter
- Electron Microscopy Facility, Vienna BioCenter Core Facilities GmbH, Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Karin Müller-Decker
- Core Facility Tumor Models, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Helm
- MS-based Protein Analysis Unit, Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sabrina Jabs
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Marius K Lemberg
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.,Center for Biochemistry and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Wilhelm Palm
- Cell Signaling and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
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27
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Accounting for small variations in the tracrRNA sequence improves sgRNA activity predictions for CRISPR screening. Nat Commun 2022; 13:5255. [PMID: 36068235 PMCID: PMC9448816 DOI: 10.1038/s41467-022-33024-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/30/2022] [Indexed: 12/17/2022] Open
Abstract
CRISPR technology is a powerful tool for studying genome function. To aid in picking sgRNAs that have maximal efficacy against a target of interest from many possible options, several groups have developed models that predict sgRNA on-target activity. Although multiple tracrRNA variants are commonly used for screening, no existing models account for this feature when nominating sgRNAs. Here we develop an on-target model, Rule Set 3, that makes optimal predictions for multiple tracrRNA variants. We validate Rule Set 3 on a new dataset of sgRNAs tiling essential and non-essential genes, demonstrating substantial improvement over prior prediction models. By analyzing the differences in sgRNA activity between tracrRNA variants, we show that Pol III transcription termination is a strong determinant of sgRNA activity. We expect these results to improve the performance of CRISPR screening and inform future research on tracrRNA engineering and sgRNA modeling.
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28
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Hanscom T, Woodward N, Batorsky R, Brown AJ, Roberts SA, McVey M. Characterization of sequence contexts that favor alternative end joining at Cas9-induced double-strand breaks. Nucleic Acids Res 2022; 50:7465-7478. [PMID: 35819195 PMCID: PMC9303309 DOI: 10.1093/nar/gkac575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative end joining (alt-EJ) mechanisms, such as polymerase theta-mediated end joining, are increasingly recognized as important contributors to inaccurate double-strand break repair. We previously proposed an alt-EJ model whereby short DNA repeats near a double-strand break anneal to form secondary structures that prime limited DNA synthesis. The nascent DNA then pairs with microhomologous sequences on the other break end. This synthesis-dependent microhomology-mediated end joining (SD-MMEJ) explains many of the alt-EJ repair products recovered following I-SceI nuclease cutting in Drosophila. However, sequence-specific factors that influence SD-MMEJ repair remain to be fully characterized. Here, we expand the utility of the SD-MMEJ model through computational analysis of repair products at Cas9-induced double-strand breaks for 1100 different sequence contexts. We find evidence at single nucleotide resolution for sequence characteristics that drive successful SD-MMEJ repair. These include optimal primer repeat length, distance of repeats from the break, flexibility of DNA sequence between primer repeats, and positioning of microhomology templates relative to preferred primer repeats. In addition, we show that DNA polymerase theta is necessary for most SD-MMEJ repair at Cas9 breaks. The analysis described here includes a computational pipeline that can be utilized to characterize preferred mechanisms of alt-EJ repair in any sequence context.
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Affiliation(s)
- Terrence Hanscom
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Nicholas Woodward
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Rebecca Batorsky
- Data Intensive Studies Center, Tufts University, 177 College Ave, Medford, MA 02155, USA
| | - Alexander J Brown
- School of Molecular Biosciences, Washington State University, P100 Dairy Road, Pullman, WA 99164, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, P100 Dairy Road, Pullman, WA 99164, USA
| | - Mitch McVey
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
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29
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Nguyen T, Ramachandran H, Martins S, Krutmann J, Rossi A. Identification of genome edited cells using CRISPRnano. Nucleic Acids Res 2022; 50:W199-W203. [PMID: 35640601 PMCID: PMC9252781 DOI: 10.1093/nar/gkac440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 12/30/2022] Open
Abstract
Genome engineering-induced cleavage sites can be resolved by non-homologous end joining (NHEJ) or homology-directed repair (HDR). Identifying genetically modified clones at the target locus remains an intensive and laborious task. Different workflows and software that rely on deep sequencing data have been developed to detect and quantify targeted mutagenesis. Nevertheless, these pipelines require high-quality reads generated by Next Generation Sequencing (NGS) platforms. Here, we have developed a robust, versatile, and easy-to-use computational webserver named CRISPRnano (www.CRISPRnano.de) that enables the analysis of low-quality reads generated by affordable and portable sequencers including Oxford Nanopore Technologies (ONT) devices. CRISPRnano allows fast and accurate identification, quantification, and visualization of genetically modified cell lines, it is compatible with NGS and ONT sequencing reads, and it can be used without an internet connection.
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Affiliation(s)
- Thach Nguyen
- IUF - Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | | | - Soraia Martins
- IUF - Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Jean Krutmann
- IUF - Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Andrea Rossi
- IUF - Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
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30
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Li R, Klingbeil O, Monducci D, Young MJ, Rodriguez DJ, Bayyat Z, Dempster JM, Kesar D, Yang X, Zamanighomi M, Vakoc CR, Ito T, Sellers WR. Comparative optimization of combinatorial CRISPR screens. Nat Commun 2022; 13:2469. [PMID: 35513429 PMCID: PMC9072436 DOI: 10.1038/s41467-022-30196-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/21/2022] [Indexed: 12/14/2022] Open
Abstract
Combinatorial CRISPR technologies have emerged as a transformative approach to systematically probe genetic interactions and dependencies of redundant gene pairs. However, the performance of different functional genomic tools for multiplexing sgRNAs vary widely. Here, we generate and benchmark ten distinct pooled combinatorial CRISPR libraries targeting paralog pairs to optimize digenic knockout screens. Libraries composed of dual Streptococcus pyogenes Cas9 (spCas9), orthogonal spCas9 and Staphylococcus aureus (saCas9), and enhanced Cas12a from Acidaminococcus were evaluated. We demonstrate a combination of alternative tracrRNA sequences from spCas9 consistently show superior effect size and positional balance between the sgRNAs as a robust combinatorial approach to profile genetic interactions of multiple genes.
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Affiliation(s)
- Ruitong Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | - Zaid Bayyat
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Devishi Kesar
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xiaoping Yang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | - Takahiro Ito
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Scorpion Therapeutics, Boston, MA, USA.
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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31
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Abstract
Over the past decade, CRISPR has become as much a verb as it is an acronym, transforming biomedical research and providing entirely new approaches for dissecting all facets of cell biology. In cancer research, CRISPR and related tools have offered a window into previously intractable problems in our understanding of cancer genetics, the noncoding genome and tumour heterogeneity, and provided new insights into therapeutic vulnerabilities. Here, we review the progress made in the development of CRISPR systems as a tool to study cancer, and the emerging adaptation of these technologies to improve diagnosis and treatment.
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Affiliation(s)
- Alyna Katti
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Bianca J Diaz
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Christina M Caragine
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Neville E Sanjana
- Department of Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
| | - Lukas E Dow
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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32
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Köferle A, Schlattl A, Hörmann A, Thatikonda V, Popa A, Spreitzer F, Ravichandran MC, Supper V, Oberndorfer S, Puchner T, Wieshofer C, Corcokovic M, Reiser C, Wöhrle S, Popow J, Pearson M, Martinez J, Weitzer S, Mair B, Neumüller RA. Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes. Cell Rep 2022; 39:110636. [PMID: 35417719 DOI: 10.1016/j.celrep.2022.110636] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023] Open
Abstract
Genetic networks are characterized by extensive buffering. During tumor evolution, disruption of functional redundancies can create de novo vulnerabilities that are specific to cancer cells. Here, we systematically search for cancer-relevant paralog interactions using CRISPR screens and publicly available loss-of-function datasets. Our analysis reveals >2,000 candidate dependencies, several of which we validate experimentally, including CSTF2-CSTF2T, DNAJC15-DNAJC19, FAM50A-FAM50B, and RPP25-RPP25L. We provide evidence that RPP25L can physically and functionally compensate for the absence of RPP25 as a member of the RNase P/MRP complexes in tRNA processing. Our analysis also reveals unexpected redundancies between sex chromosome genes. We show that chrX- and chrY-encoded paralogs, such as ZFX-ZFY, DDX3X-DDX3Y, and EIF1AX-EIF1AY, are functionally linked. Tumor cell lines from male patients with loss of chromosome Y become dependent on the chrX-encoded gene. We propose targeting of chrX-encoded paralogs as a general therapeutic strategy for human tumors that have lost the Y chromosome.
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Affiliation(s)
- Anna Köferle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Andreas Schlattl
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Hörmann
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Fiona Spreitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | | | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Sarah Oberndorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Corinna Wieshofer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Maja Corcokovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Christoph Reiser
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
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33
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Herman JA, Arora S, Carter L, Zhu J, Biggins S, Paddison PJ. Functional dissection of human mitotic genes using CRISPR-Cas9 tiling screens. Genes Dev 2022; 36:495-510. [PMID: 35483740 PMCID: PMC9067404 DOI: 10.1101/gad.349319.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/12/2022] [Indexed: 12/03/2022]
Abstract
In this Resource/Methodology, Herman et al. developed a method that leverages CRISPR–Cas9-induced mutations across protein-coding genes for the a priori identification of functional regions at the sequence level. As a test case, they applied this method to 48 human mitotic genes, revealing hundreds of regions required for cell proliferation, including domains that were experimentally characterized, ones that were predicted based on homology, and novel ones. The identity of human protein-coding genes is well known, yet our in-depth knowledge of their molecular functions and domain architecture remains limited by shortcomings in homology-based predictions and experimental approaches focused on whole-gene depletion. To bridge this knowledge gap, we developed a method that leverages CRISPR–Cas9-induced mutations across protein-coding genes for the a priori identification of functional regions at the sequence level. As a test case, we applied this method to 48 human mitotic genes, revealing hundreds of regions required for cell proliferation, including domains that were experimentally characterized, ones that were predicted based on homology, and novel ones. We validated screen outcomes for 15 regions, including amino acids 387–402 of Mad1, which were previously uncharacterized but contribute to Mad1 kinetochore localization and chromosome segregation fidelity. Altogether, we demonstrate that CRISPR–Cas9-based tiling mutagenesis identifies key functional domains in protein-coding genes de novo, which elucidates separation of function mutants and allows functional annotation across the human proteome.
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Affiliation(s)
- Jacob A Herman
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Lucas Carter
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Sue Biggins
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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34
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Fiore A, Zeitler L, Russier M, Groß A, Hiller MK, Parker JL, Stier L, Köcher T, Newstead S, Murray PJ. Kynurenine importation by SLC7A11 propagates anti-ferroptotic signaling. Mol Cell 2022; 82:920-932.e7. [PMID: 35245456 DOI: 10.1016/j.molcel.2022.02.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 11/17/2021] [Accepted: 02/02/2022] [Indexed: 12/19/2022]
Abstract
IDO1 oxidizes tryptophan (TRP) to generate kynurenine (KYN), the substrate for 1-carbon and NAD metabolism, and is implicated in pro-cancer pathophysiology and infection biology. However, the mechanistic relationships between IDO1 in amino acid depletion versus product generation have remained a longstanding mystery. We found an unrecognized link between IDO1 and cell survival mediated by KYN that serves as the source for molecules that inhibit ferroptotic cell death. We show that this effect requires KYN export from IDO1-expressing cells, which is then available for non-IDO1-expressing cells via SLC7A11, the central transporter involved in ferroptosis suppression. Whether inside the "producer" IDO1+ cell or the "receiver" cell, KYN is converted into downstream metabolites, suppressing ferroptosis by ROS scavenging and activating an NRF2-dependent, AHR-independent cell-protective pathway, including SLC7A11, propagating anti-ferroptotic signaling. IDO1, therefore, controls a multi-pronged protection pathway from ferroptotic cell death, underscoring the need to re-evaluate the use of IDO1 inhibitors in cancer treatment.
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Affiliation(s)
- Alessandra Fiore
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Leonie Zeitler
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Marion Russier
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Annette Groß
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Luca Stier
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Thomas Köcher
- Vienna BioCenter Core Facilities GmbH, Vienna, Austria
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Peter J Murray
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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35
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Prime editing efficiency and fidelity are enhanced in the absence of mismatch repair. Nat Commun 2022; 13:760. [PMID: 35140211 PMCID: PMC8828784 DOI: 10.1038/s41467-022-28442-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/26/2022] [Indexed: 02/07/2023] Open
Abstract
Prime editing (PE) is a powerful genome engineering approach that enables the introduction of base substitutions, insertions and deletions into any given genomic locus. However, the efficiency of PE varies widely and depends not only on the genomic region targeted, but also on the genetic background of the edited cell. Here, to determine which cellular factors affect PE efficiency, we carry out a focused genetic screen targeting 32 DNA repair factors, spanning all reported repair pathways. We show that, depending on cell line and type of edit, ablation of mismatch repair (MMR) affords a 2–17 fold increase in PE efficiency, across several human cell lines, types of edits and genomic loci. The accumulation of the key MMR factors MLH1 and MSH2 at PE sites argues for direct involvement of MMR in PE control. Our results shed new light on the mechanism of PE and suggest how its efficiency might be optimised. Prime Editing is a versatile genome engineering tool. Here, the authors identify the DNA repair pathway known as mismatch repair as inhibitory for Prime Editing, thus, loss of mismatch repair enhances the efficiency of Prime Editing.
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36
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Port F, Boutros M. Tissue-Specific CRISPR-Cas9 Screening in Drosophila. Methods Mol Biol 2022; 2540:157-176. [PMID: 35980577 DOI: 10.1007/978-1-0716-2541-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last century research in Drosophila has resulted in many fundamental contributions to our understanding of the biology of multicellular organisms. Many of these breakthroughs have been based on the identification of novel gene functions in large-scale genetic screens. However, conventional forward-genetic screens have been limited by the random nature of mutagenesis and difficulties in mapping causal mutations, while reverse-genetic RNAi screens suffer from incomplete knockdown of gene expression. Recently developed large-scale CRISPR-Cas9 libraries promise to address these limitations by allowing the induction of targeted mutations in genes with spatial and temporal control. Here, we provide a guide for tissue-specific CRISPR screening in Drosophila, including the characterization of Gal4 UAS-Cas9 lines, selection of sgRNA libraries, and various quality control measures. We also discuss confounding factors that can give rise to false-positive and false-negative results in such experiments and suggest strategies on how to detect and avoid them. Conditional CRISPR screening represents an exciting new approach for functional genomics in vivo and is set to further expand our knowledge of the molecular underpinning of development, homeostasis, and disease.
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Affiliation(s)
- Fillip Port
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Michael Boutros
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany.
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37
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Butz S, Schmolka N, Karemaker ID, Villaseñor R, Schwarz I, Domcke S, Uijttewaal ECH, Jude J, Lienert F, Krebs AR, de Wagenaar NP, Bao X, Zuber J, Elling U, Schübeler D, Baubec T. DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions. Nat Genet 2022; 54:1702-1710. [PMID: 36333500 PMCID: PMC9649441 DOI: 10.1038/s41588-022-01210-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
Abstract
Genomic imprinting is regulated by parental-specific DNA methylation of imprinting control regions (ICRs). Despite an identical DNA sequence, ICRs can exist in two distinct epigenetic states that are memorized throughout unlimited cell divisions and reset during germline formation. Here, we systematically study the genetic and epigenetic determinants of this epigenetic bistability. By iterative integration of ICRs and related DNA sequences to an ectopic location in the mouse genome, we first identify the DNA sequence features required for maintenance of epigenetic states in embryonic stem cells. The autonomous regulatory properties of ICRs further enabled us to create DNA-methylation-sensitive reporters and to screen for key components involved in regulating their epigenetic memory. Besides DNMT1, UHRF1 and ZFP57, we identify factors that prevent switching from methylated to unmethylated states and show that two of these candidates, ATF7IP and ZMYM2, are important for the stability of DNA and H3K9 methylation at ICRs in embryonic stem cells.
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Affiliation(s)
- Stefan Butz
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Nina Schmolka
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Present Address: Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Ino D. Karemaker
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Rodrigo Villaseñor
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.5252.00000 0004 1936 973XPresent Address: Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Isabel Schwarz
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Silvia Domcke
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland ,grid.34477.330000000122986657Present Address: Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Esther C. H. Uijttewaal
- grid.473822.80000 0005 0375 3232Institute of Molecular Biotechnology Austria (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julian Jude
- grid.14826.390000 0000 9799 657XResearch Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Florian Lienert
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland
| | - Arnaud R. Krebs
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.4709.a0000 0004 0495 846XPresent Address: European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Nathalie P. de Wagenaar
- grid.5477.10000000120346234Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Xue Bao
- grid.5477.10000000120346234Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Johannes Zuber
- grid.14826.390000 0000 9799 657XResearch Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Ulrich Elling
- grid.473822.80000 0005 0375 3232Institute of Molecular Biotechnology Austria (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dirk Schübeler
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland. .,Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands.
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38
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Dempster JM, Boyle I, Vazquez F, Root DE, Boehm JS, Hahn WC, Tsherniak A, McFarland JM. Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects. Genome Biol 2021; 22:343. [PMID: 34930405 PMCID: PMC8686573 DOI: 10.1186/s13059-021-02540-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 11/03/2021] [Indexed: 12/13/2022] Open
Abstract
CRISPR loss of function screens are powerful tools to interrogate biology but exhibit a number of biases and artifacts that can confound the results. Here, we introduce Chronos, an algorithm for inferring gene knockout fitness effects based on an explicit model of cell proliferation dynamics after CRISPR gene knockout. We test Chronos on two pan-cancer CRISPR datasets and one longitudinal CRISPR screen. Chronos generally outperforms competitors in separation of controls and strength of biomarker associations, particularly when longitudinal data is available. Additionally, Chronos exhibits the lowest copy number and screen quality bias of evaluated methods. Chronos is available at https://github.com/broadinstitute/chronos .
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Affiliation(s)
- Joshua M Dempster
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Isabella Boyle
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Francisca Vazquez
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jesse S Boehm
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - William C Hahn
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Aviad Tsherniak
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - James M McFarland
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
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39
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CRISPR-SID: Identifying EZH2 as a druggable target for desmoid tumors via in vivo dependency mapping. Proc Natl Acad Sci U S A 2021; 118:2115116118. [PMID: 34789568 DOI: 10.1073/pnas.2115116118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer precision medicine implies identification of tumor-specific vulnerabilities associated with defined oncogenic pathways. Desmoid tumors are soft-tissue neoplasms strictly driven by Wnt signaling network hyperactivation. Despite this clearly defined genetic etiology and the strict and unique implication of the Wnt/β-catenin pathway, no specific molecular targets for these tumors have been identified. To address this caveat, we developed fast, efficient, and penetrant genetic Xenopus tropicalis desmoid tumor models to identify and characterize drug targets. We used multiplexed CRISPR/Cas9 genome editing in these models to simultaneously target a tumor suppressor gene (apc) and candidate dependency genes. Our methodology CRISPR/Cas9 selection-mediated identification of dependencies (CRISPR-SID) uses calculated deviations between experimentally observed gene editing outcomes and deep-learning-predicted double-strand break repair patterns to identify genes under negative selection during tumorigenesis. This revealed EZH2 and SUZ12, both encoding polycomb repressive complex 2 components, and the transcription factor CREB3L1 as genetic dependencies for desmoid tumors. In vivo EZH2 inhibition by Tazemetostat induced partial regression of established autochthonous tumors. In vitro models of patient desmoid tumor cells revealed a direct effect of Tazemetostat on Wnt pathway activity. CRISPR-SID represents a potent approach for in vivo mapping of tumor vulnerabilities and drug target identification.
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40
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Vinceti A, Karakoc E, Pacini C, Perron U, De Lucia RR, Garnett MJ, Iorio F. CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens. BMC Genomics 2021; 22:828. [PMID: 34789150 PMCID: PMC8597285 DOI: 10.1186/s12864-021-08129-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 10/28/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND CRISPR-Cas9 genome-wide screens are being increasingly performed, allowing systematic explorations of cancer dependencies at unprecedented accuracy and scale. One of the major computational challenges when analysing data derived from such screens is to identify genes that are essential for cell survival invariantly across tissues, conditions, and genomic-contexts (core-fitness genes), and to distinguish them from context-specific essential genes. This is of paramount importance to assess the safety profile of candidate therapeutic targets and for elucidating mechanisms involved in tissue-specific genetic diseases. RESULTS We have developed CoRe: an R package implementing existing and novel methods for the identification of core-fitness genes (at two different level of stringency) from joint analyses of multiple CRISPR-Cas9 screens. We demonstrate, through a fully reproducible benchmarking pipeline, that CoRe outperforms state-of-the-art tools, yielding more reliable and biologically relevant sets of core-fitness genes. CONCLUSIONS CoRe offers a flexible pipeline, compatible with many pre-processing methods for the analysis of CRISPR data, which can be tailored onto different use-cases. The CoRe package can be used for the identification of high-confidence novel core-fitness genes, as well as a means to filter out potentially cytotoxic hits while analysing cancer dependency datasets for identifying and prioritising novel selective therapeutic targets.
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Affiliation(s)
| | - Emre Karakoc
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Clare Pacini
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | | | - Mathew J Garnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Francesco Iorio
- Human Technopole, Milan, Italy.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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41
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AKIRIN2 controls the nuclear import of proteasomes in vertebrates. Nature 2021; 599:491-496. [PMID: 34711951 DOI: 10.1038/s41586-021-04035-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/16/2021] [Indexed: 02/08/2023]
Abstract
Protein expression and turnover are controlled through a complex interplay of transcriptional, post-transcriptional and post-translational mechanisms to enable spatial and temporal regulation of cellular processes. To systematically elucidate such gene regulatory networks, we developed a CRISPR screening assay based on time-controlled Cas9 mutagenesis, intracellular immunostaining and fluorescence-activated cell sorting that enables the identification of regulatory factors independent of their effects on cellular fitness. We pioneered this approach by systematically probing the regulation of the transcription factor MYC, a master regulator of cell growth1-3. Our screens uncover a highly conserved protein, AKIRIN2, that is essentially required for nuclear protein degradation. We found that AKIRIN2 forms homodimers that directly bind to fully assembled 20S proteasomes to mediate their nuclear import. During mitosis, proteasomes are excluded from condensing chromatin and re-imported into newly formed daughter nuclei in a highly dynamic, AKIRIN2-dependent process. Cells undergoing mitosis in the absence of AKIRIN2 become devoid of nuclear proteasomes, rapidly causing accumulation of MYC and other nuclear proteins. Collectively, our study reveals a dedicated pathway controlling the nuclear import of proteasomes in vertebrates and establishes a scalable approach to decipher regulators in essential cellular processes.
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42
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Sorafenib fails to trigger ferroptosis across a wide range of cancer cell lines. Cell Death Dis 2021; 12:698. [PMID: 34257282 PMCID: PMC8277867 DOI: 10.1038/s41419-021-03998-w] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023]
Abstract
Sorafenib, a protein kinase inhibitor approved for the treatment of hepatocellular carcinoma and advanced renal cell carcinoma, has been repeatedly reported to induce ferroptosis by possibly involving inhibition of the cystine/glutamate antiporter, known as system xc-. Using a combination of well-defined genetically engineered tumor cell lines and canonical small molecule ferroptosis inhibitors, we now provide unequivocal evidence that sorafenib does not induce ferroptosis in a series of tumor cell lines unlike the cognate system xc- inhibitors sulfasalazine and erastin. We further show that only a subset of tumor cells dies by ferroptosis upon sulfasalazine and erastin treatment, implying that certain cell lines appear to be resistant to system xc- inhibition, while others undergo ferroptosis-independent cell death. From these findings, we conclude that sorafenib does not qualify as a bona fide ferroptosis inducer and that ferroptosis induced by system xc- inhibitors can only be achieved in a fraction of tumor cell lines despite robust expression of SLC7A11, the substrate-specific subunit of system xc-.
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43
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Lindner B, Martin E, Steininger M, Bundalo A, Lenter M, Zuber J, Schuler M. A genome-wide CRISPR/Cas9 screen to identify phagocytosis modulators in monocytic THP-1 cells. Sci Rep 2021; 11:12973. [PMID: 34155263 PMCID: PMC8217514 DOI: 10.1038/s41598-021-92332-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 06/02/2021] [Indexed: 01/23/2023] Open
Abstract
Phagocytosis of microbial pathogens, dying or dead cells, and cell debris is essential to maintain tissue homeostasis. Impairment of these processes is associated with autoimmunity, developmental defects and toxic protein accumulation. However, the underlying molecular mechanisms of phagocytosis remain incompletely understood. Here, we performed a genome-wide CRISPR knockout screen to systematically identify regulators involved in phagocytosis of Staphylococcus (S.) aureus by human monocytic THP-1 cells. The screen identified 75 hits including known regulators of phagocytosis, e.g. members of the actin cytoskeleton regulation Arp2/3 and WAVE complexes, as well as genes previously not associated with phagocytosis. These novel genes are involved in translational control (EIF5A and DHPS) and the UDP glycosylation pathway (SLC35A2, SLC35A3, UGCG and UXS1) and were further validated by single gene knockout experiments. Whereas the knockout of EIF5A and DHPS impaired phagocytosis, knocking out SLC35A2, SLC35A3, UGCG and UXS1 resulted in increased phagocytosis. In addition to S. aureus phagocytosis, the above described genes also modulate phagocytosis of Escherichia coli and yeast-derived zymosan A. In summary, we identified both known and unknown genetic regulators of phagocytosis, the latter providing a valuable resource for future studies dissecting the underlying molecular and cellular mechanisms and their role in human disease.
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Affiliation(s)
- Benjamin Lindner
- Department of Drug Discovery Science, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstr. 65, 88397, Biberach an der Riss, Germany.
| | - Eva Martin
- Department of Drug Discovery Science, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstr. 65, 88397, Biberach an der Riss, Germany
| | - Monika Steininger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Aleksandra Bundalo
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Martin Lenter
- Department of Drug Discovery Science, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstr. 65, 88397, Biberach an der Riss, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Michael Schuler
- Department of Drug Discovery Science, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstr. 65, 88397, Biberach an der Riss, Germany
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44
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Smeenk L, Ottema S, Mulet-Lazaro R, Ebert A, Havermans M, Arricibita Varea A, Fellner M, Pastoors D, van Herk S, Erpelinck-Verschueren C, Grob T, Hoogenboezem RM, Kavelaars FG, Matson DR, Bresnick EH, Bindels EM, Kentsis A, Zuber J, Delwel R. Selective requirement of MYB for oncogenic hyperactivation of a translocated enhancer in leukemia. Cancer Discov 2021; 11:2868-2883. [PMID: 33980539 DOI: 10.1158/2159-8290.cd-20-1793] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/26/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022]
Abstract
In acute myeloid leukemia (AML) with inv(3)(q21;q26) or t(3;3)(q21;q26), a translocated GATA2 enhancer drives oncogenic expression of EVI1. We generated an EVI1-GFP AML model and applied an unbiased CRISPR/Cas9 enhancer scan to uncover sequence motifs essential for EVI1 transcription. Using this approach, we pinpointed a single regulatory element in the translocated GATA2 enhancer that is critically required for aberrant EVI1 expression. This element contained a DNA binding motif for the transcription factor MYB which specifically occupied this site at the translocated allele and was dispensable for GATA2 expression. MYB knockout as well as peptidomimetic blockade of CBP/p300-dependent MYB functions resulted in downregulation of EVI1 but not of GATA2. Targeting MYB or mutating its DNA-binding motif within the GATA2 enhancer resulted in myeloid differentiation and cell death, suggesting that interference with MYB-driven EVI1 transcription provides a potential entry point for therapy of inv(3)/t(3;3) AMLs.
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Affiliation(s)
- Leonie Smeenk
- Hematology, Erasmus MC Cancer Institute and Oncode Institute
| | - Sophie Ottema
- Hematology, Erasmus MC Cancer Institute and Oncode Institute
| | | | - Anja Ebert
- Department of Molecular Biology and Genetics, Aarhus University
| | | | | | - Michaela Fellner
- Immunology and Cancer, Research Institute of Molecular Pathology
| | - Dorien Pastoors
- Hematology, Erasmus MC Cancer Institute and Oncode Institute
| | | | | | - Tim Grob
- Hematology, Erasmus MC Cancer Institute
| | | | | | - Daniel R Matson
- Cell and Regenerative Biology, Paul Carbone Comprehensive Cancer Center, University of Wisconsin School of Medicine and Public Health
| | - Emery H Bresnick
- Cell and Regenerative Biology, Paul Carbone Comprehensive Cancer Center, University of Wisconsin School of Medicine and Public Health
| | | | - Alex Kentsis
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center
| | - Johannes Zuber
- Immunology and Cancer, Research Institute of Molecular Pathology
| | - Ruud Delwel
- Hematology, Erasmus MC Cancer Institute and Oncode Institute
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45
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He W, Wang H, Wei Y, Jiang Z, Tang Y, Chen Y, Xu H. GuidePro: a multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts. Bioinformatics 2021; 37:134-136. [PMID: 33394026 PMCID: PMC11025339 DOI: 10.1093/bioinformatics/btaa1068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
MOTIVATION The efficiency of CRISPR/Cas9-mediated protein knockout is determined by three factors: sequence-specific sgRNA activity, frameshift probability and the characteristics of targeted amino acids. A number of computational methods have been developed for predicting sgRNA efficiency from different perspectives. However, an integrative method that combines all three factors for rational sgRNA selection is still lacking. RESULTS We developed GuidePro, a two-layer ensemble predictor that enables the integration of multiple factors for the prioritization of sgRNAs in protein knockouts. Tested on independent datasets, GuidePro outperforms existing methods and demonstrates consistent superior performance in predicting phenotypes caused by protein loss-of-function, suggesting its robustness for prioritizing sgRNAs in various applications of CRISPR/Cas9 knockouts. AVAILABILITY AND IMPLEMENTATION GuidePro is available at https://github.com/MDhewei/GuidePro. A web application for prioritizing sgRNAs that target protein-coding genes in human, monkey and mouse genomes is available at https://bioinformatics.mdanderson.org/apps/GuidePro. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wei He
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Helen Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yanjun Wei
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhiyun Jiang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yitao Tang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Han Xu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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46
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Hoffmann HH, Sánchez-Rivera FJ, Schneider WM, Luna JM, Soto-Feliciano YM, Ashbrook AW, Le Pen J, Leal AA, Ricardo-Lax I, Michailidis E, Hao Y, Stenzel AF, Peace A, Zuber J, Allis CD, Lowe SW, MacDonald MR, Poirier JT, Rice CM. Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors. Cell Host Microbe 2021; 29:267-280.e5. [PMID: 33357464 PMCID: PMC7833927 DOI: 10.1016/j.chom.2020.12.009] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/13/2020] [Accepted: 12/09/2020] [Indexed: 12/26/2022]
Abstract
The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has devastated the global economy and claimed more than 1.7 million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a focused high-coverage CRISPR-Cas9 library targeting 332 members of a recently published SARS-CoV-2 protein interactome. We leveraged the compact nature of this library to systematically screen SARS-CoV-2 at two physiologically relevant temperatures along with three related coronaviruses (human coronavirus 229E [HCoV-229E], HCoV-NL63, and HCoV-OC43), allowing us to probe this interactome at a much higher resolution than genome-scale studies. This approach yielded several insights, including potential virus-specific differences in Rab GTPase requirements and glycosylphosphatidylinositol (GPI) anchor biosynthesis, as well as identification of multiple pan-coronavirus factors involved in cholesterol homeostasis. This coronavirus essentiality catalog could inform ongoing drug development efforts aimed at intercepting and treating coronavirus disease 2019 (COVID-19) and help prepare for future coronavirus outbreaks.
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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
| | - Joseph M Luna
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Yadira M Soto-Feliciano
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Alison W Ashbrook
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Andrew A Leal
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016 USA
| | - Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Yuan Hao
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016 USA
| | - Ansgar F Stenzel
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA; Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Avery Peace
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria; Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - C David Allis
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Scott W Lowe
- Cancer Biology and Genetics, MSKCC New York, NY 10065, USA
| | - Margaret R MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - John T Poirier
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY 10016 USA.
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
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47
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Simpson KE, Venkateshappa R, Pang ZK, Faizi S, Tibbits GF, Claydon TW. Utility of Zebrafish Models of Acquired and Inherited Long QT Syndrome. Front Physiol 2021; 11:624129. [PMID: 33519527 PMCID: PMC7844309 DOI: 10.3389/fphys.2020.624129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/21/2020] [Indexed: 01/12/2023] Open
Abstract
Long-QT Syndrome (LQTS) is a cardiac electrical disorder, distinguished by irregular heart rates and sudden death. Accounting for ∼40% of cases, LQTS Type 2 (LQTS2), is caused by defects in the Kv11.1 (hERG) potassium channel that is critical for cardiac repolarization. Drug block of hERG channels or dysfunctional channel variants can result in acquired or inherited LQTS2, respectively, which are typified by delayed repolarization and predisposition to lethal arrhythmia. As such, there is significant interest in clear identification of drugs and channel variants that produce clinically meaningful perturbation of hERG channel function. While toxicological screening of hERG channels, and phenotypic assessment of inherited channel variants in heterologous systems is now commonplace, affordable, efficient, and insightful whole organ models for acquired and inherited LQTS2 are lacking. Recent work has shown that zebrafish provide a viable in vivo or whole organ model of cardiac electrophysiology. Characterization of cardiac ion currents and toxicological screening work in intact embryos, as well as adult whole hearts, has demonstrated the utility of the zebrafish model to contribute to the development of therapeutics that lack hERG-blocking off-target effects. Moreover, forward and reverse genetic approaches show zebrafish as a tractable model in which LQTS2 can be studied. With the development of new tools and technologies, zebrafish lines carrying precise channel variants associated with LQTS2 have recently begun to be generated and explored. In this review, we discuss the present knowledge and questions raised related to the use of zebrafish as models of acquired and inherited LQTS2. We focus discussion, in particular, on developments in precise gene-editing approaches in zebrafish to create whole heart inherited LQTS2 models and evidence that zebrafish hearts can be used to study arrhythmogenicity and to identify potential anti-arrhythmic compounds.
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Affiliation(s)
- Kyle E. Simpson
- Molecular Cardiac Physiology Group, Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Ravichandra Venkateshappa
- Molecular Cardiac Physiology Group, Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Zhao Kai Pang
- Molecular Cardiac Physiology Group, Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Shoaib Faizi
- Molecular Cardiac Physiology Group, Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Glen F. Tibbits
- Molecular Cardiac Physiology Group, Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- Department of Cardiovascular Science, British Columbia Children’s Hospital, Vancouver, BC, Canada
| | - Tom W. Claydon
- Molecular Cardiac Physiology Group, Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
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Henkel L, Rauscher B, Schmitt B, Winter J, Boutros M. Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library. BMC Biol 2020; 18:174. [PMID: 33228647 PMCID: PMC7686728 DOI: 10.1186/s12915-020-00905-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/20/2020] [Indexed: 12/22/2022] Open
Abstract
Background In recent years, large-scale genetic screens using the CRISPR/Cas9 system have emerged as scalable approaches able to interrogate gene function with unprecedented efficiency and specificity in various biological contexts. By this means, functional dependencies on both the protein-coding and noncoding genome of numerous cell types in different organisms have been interrogated. However, screening designs vary greatly and criteria for optimal experimental implementation and library composition are still emerging. Given their broad utility in functionally annotating genomes, the application and interpretation of genome-scale CRISPR screens would greatly benefit from consistent and optimal design criteria. Results We report advantages of conducting viability screens in selected Cas9 single-cell clones in contrast to Cas9 bulk populations. We further systematically analyzed published CRISPR screens in human cells to identify single-guide (sg) RNAs with consistent high on-target and low off-target activity. Selected guides were collected in a novel genome-scale sgRNA library, which efficiently identifies core and context-dependent essential genes. Conclusion We show how empirically designed libraries in combination with an optimized experimental design increase the dynamic range in gene essentiality screens at reduced library coverage. Supplementary information The online version contains supplementary material available at 10.1186/s12915-020-00905-1.
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Affiliation(s)
- Luisa Henkel
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, D-69120, Heidelberg, Germany
| | - Benedikt Rauscher
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, D-69120, Heidelberg, Germany
| | - Barbara Schmitt
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, D-69120, Heidelberg, Germany
| | - Jan Winter
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, D-69120, Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, D-69120, Heidelberg, Germany.
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Hoffmann HH, Schneider WM, Sánchez-Rivera FJ, Luna JM, Ashbrook AW, Soto-Feliciano YM, Leal AA, Le Pen J, Ricardo-Lax I, Michailidis E, Hao Y, Stenzel AF, Peace A, Allis CD, Lowe SW, MacDonald MR, Poirier JT, Rice CM. Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32935098 DOI: 10.1101/2020.09.11.291716] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ongoing SARS-CoV-2 pandemic has devastated the global economy and claimed nearly one million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a focused high-coverage CRISPR-Cas9 library targeting 332 members of a recently published SARS-CoV-2 protein interactome. We leveraged the compact nature of this library to systematically screen four related coronaviruses (HCoV-229E, HCoV-NL63, HCoV-OC43 and SARS-CoV-2) at two physiologically relevant temperatures (33 °C and 37 °C), allowing us to probe this interactome at a much higher resolution relative to genome scale studies. This approach yielded several new insights, including unexpected virus and temperature specific differences in Rab GTPase requirements and GPI anchor biosynthesis, as well as identification of multiple pan-coronavirus factors involved in cholesterol homeostasis. This coronavirus essentiality catalog could inform ongoing drug development efforts aimed at intercepting and treating COVID-19, and help prepare for future coronavirus outbreaks. HIGHLIGHTS Focused CRISPR screens targeting host factors in the SARS-CoV-2 interactome were performed for SARS-CoV-2, HCoV-229E, HCoV-NL63, and HCoV-OC43 coronaviruses.Focused interactome CRISPR screens achieve higher resolution compared to genome-wide screens, leading to the identification of critical factors missed by the latter.Parallel CRISPR screens against multiple coronaviruses uncover host factors and pathways with pan-coronavirus and virus-specific functional roles.The number of host proteins that interact with a viral bait protein is not proportional to the number of functional interactors.Novel SARS-CoV-2 host factors are expressed in relevant cell types in the human airway.
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