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Lin CP, Levy PL, Alflen A, Apriamashvili G, Ligtenberg MA, Vredevoogd DW, Bleijerveld OB, Alkan F, Malka Y, Hoekman L, Markovits E, George A, Traets JJH, Krijgsman O, van Vliet A, Poźniak J, Pulido-Vicuña CA, de Bruijn B, van Hal-van Veen SE, Boshuizen J, van der Helm PW, Díaz-Gómez J, Warda H, Behrens LM, Mardesic P, Dehni B, Visser NL, Marine JC, Markel G, Faller WJ, Altelaar M, Agami R, Besser MJ, Peeper DS. Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness. Cancer Cell 2024; 42:623-645.e10. [PMID: 38490212 PMCID: PMC11003465 DOI: 10.1016/j.ccell.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/03/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
Genes limiting T cell antitumor activity may serve as therapeutic targets. It has not been systematically studied whether there are regulators that uniquely or broadly contribute to T cell fitness. We perform genome-scale CRISPR-Cas9 knockout screens in primary CD8 T cells to uncover genes negatively impacting fitness upon three modes of stimulation: (1) intense, triggering activation-induced cell death (AICD); (2) acute, triggering expansion; (3) chronic, causing dysfunction. Besides established regulators, we uncover genes controlling T cell fitness either specifically or commonly upon differential stimulation. Dap5 ablation, ranking highly in all three screens, increases translation while enhancing tumor killing. Loss of Icam1-mediated homotypic T cell clustering amplifies cell expansion and effector functions after both acute and intense stimulation. Lastly, Ctbp1 inactivation induces functional T cell persistence exclusively upon chronic stimulation. Our results functionally annotate fitness regulators based on their unique or shared contribution to traits limiting T cell antitumor activity.
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Affiliation(s)
- Chun-Pu Lin
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pierre L Levy
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Tumor Immunology and Immunotherapy Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Astrid Alflen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Hematology and Medical Oncology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany; Research Center for Immunotherapy (FZI), University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany
| | - Georgi Apriamashvili
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten A Ligtenberg
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ferhat Alkan
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Yuval Malka
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ettai Markovits
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Austin George
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joleen J H Traets
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alex van Vliet
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joanna Poźniak
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Carlos Ariel Pulido-Vicuña
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Beaunelle de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Susan E van Hal-van Veen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Julia Boshuizen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pim W van der Helm
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Judit Díaz-Gómez
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Hamdy Warda
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Leonie M Behrens
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Paula Mardesic
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bilal Dehni
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Nils L Visser
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Gal Markel
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel
| | - William J Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Michal J Besser
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel; Felsenstein Medical Research Center, Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Pathology, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands.
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2
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Ho P, Melms JC, Rogava M, Frangieh CJ, Poźniak J, Shah SB, Walsh Z, Kyrysyuk O, Amin AD, Caprio L, Fullerton BT, Soni RK, Ager CR, Biermann J, Wang Y, Khosravi-Maharlooei M, Zanetti G, Mu M, Fatima H, Moore EK, Vasan N, Bakhoum SF, Reiner SL, Bernatchez C, Sykes M, Mace EM, Wucherpfennig KW, Schadendorf D, Bechter O, Shah P, Schwartz GK, Marine JC, Izar B. The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity. Cancer Cell 2023; 41:1207-1221.e12. [PMID: 37327789 PMCID: PMC10524902 DOI: 10.1016/j.ccell.2023.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2023] [Accepted: 05/22/2023] [Indexed: 06/18/2023]
Abstract
The cell-autonomous balance of immune-inhibitory and -stimulatory signals is a critical process in cancer immune evasion. Using patient-derived co-cultures, humanized mouse models, and single-cell RNA-sequencing of patient melanomas biopsied before and on immune checkpoint blockade, we find that intact cancer cell-intrinsic expression of CD58 and ligation to CD2 is required for anti-tumor immunity and is predictive of treatment response. Defects in this axis promote immune evasion through diminished T cell activation, impaired intratumoral T cell infiltration and proliferation, and concurrently increased PD-L1 protein stabilization. Through CRISPR-Cas9 and proteomics screens, we identify and validate CMTM6 as critical for CD58 stability and upregulation of PD-L1 upon CD58 loss. Competition between CD58 and PD-L1 for CMTM6 binding determines their rate of endosomal recycling over lysosomal degradation. Overall, we describe an underappreciated yet critical axis of cancer immunity and provide a molecular basis for how cancer cells balance immune inhibitory and stimulatory cues.
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Affiliation(s)
- Patricia Ho
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Johannes C Melms
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Meri Rogava
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Chris J Frangieh
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Klarman Cell Observatory, the Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joanna Poźniak
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Shivem B Shah
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Zachary Walsh
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Oleksandr Kyrysyuk
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amit Dipak Amin
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Lindsay Caprio
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Benjamin T Fullerton
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY 10032, USA
| | - Casey R Ager
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Jana Biermann
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Yiping Wang
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Mohsen Khosravi-Maharlooei
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Immunology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Giorgia Zanetti
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Michael Mu
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Hijab Fatima
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Emily K Moore
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Medicine, Division of Rheumatology, Columbia University, New York, NY 10032, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Samuel F Bakhoum
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Steven L Reiner
- Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA
| | - Chantale Bernatchez
- Department of Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA; Department of Surgery, Columbia University, New York, NY 10032, USA
| | - Emily M Mace
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site, 45147 Essen, Germany
| | | | - Parin Shah
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA
| | - Gary K Schwartz
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Benjamin Izar
- Department of Medicine, Division of Hematology and Oncology, Columbia University, New York, NY 10032, USA; Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Program for Mathematical Genomics, Department of Systems Biology, Columbia University, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.
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3
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Baxter AE, Huang H, Giles JR, Chen Z, Wu JE, Drury S, Dalton K, Park SL, Torres L, Simone BW, Klapholz M, Ngiow SF, Freilich E, Manne S, Alcalde V, Ekshyyan V, Berger SL, Shi J, Jordan MS, Wherry EJ. The SWI/SNF chromatin remodeling complexes BAF and PBAF differentially regulate epigenetic transitions in exhausted CD8 + T cells. Immunity 2023; 56:1320-1340.e10. [PMID: 37315535 DOI: 10.1016/j.immuni.2023.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/28/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023]
Abstract
CD8+ T cell exhaustion (Tex) limits disease control during chronic viral infections and cancer. Here, we investigated the epigenetic factors mediating major chromatin-remodeling events in Tex-cell development. A protein-domain-focused in vivo CRISPR screen identified distinct functions for two versions of the SWI/SNF chromatin-remodeling complex in Tex-cell differentiation. Depletion of the canonical SWI/SNF form, BAF, impaired initial CD8+ T cell responses in acute and chronic infection. In contrast, disruption of PBAF enhanced Tex-cell proliferation and survival. Mechanistically, PBAF regulated the epigenetic and transcriptional transition from TCF-1+ progenitor Tex cells to more differentiated TCF-1- Tex subsets. Whereas PBAF acted to preserve Tex progenitor biology, BAF was required to generate effector-like Tex cells, suggesting that the balance of these factors coordinates Tex-cell subset differentiation. Targeting PBAF improved tumor control both alone and in combination with anti-PD-L1 immunotherapy. Thus, PBAF may present a therapeutic target in cancer immunotherapy.
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Affiliation(s)
- Amy E Baxter
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hua Huang
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Josephine R Giles
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Zeyu Chen
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jennifer E Wu
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sydney Drury
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Katherine Dalton
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Simone L Park
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Leonel Torres
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brandon W Simone
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Max Klapholz
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Radiation Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shin Foong Ngiow
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Elizabeth Freilich
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sasikanth Manne
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Victor Alcalde
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Viktoriya Ekshyyan
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Junwei Shi
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Martha S Jordan
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - E John Wherry
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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4
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Wells MF, Nemesh J, Ghosh S, Mitchell JM, Salick MR, Mello CJ, Meyer D, Pietilainen O, Piccioni F, Guss EJ, Raghunathan K, Tegtmeyer M, Hawes D, Neumann A, Worringer KA, Ho D, Kommineni S, Chan K, Peterson BK, Raymond JJ, Gold JT, Siekmann MT, Zuccaro E, Nehme R, Kaykas A, Eggan K, McCarroll SA. Natural variation in gene expression and viral susceptibility revealed by neural progenitor cell villages. Cell Stem Cell 2023; 30:312-332.e13. [PMID: 36796362 PMCID: PMC10581885 DOI: 10.1016/j.stem.2023.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023]
Abstract
Human genome variation contributes to diversity in neurodevelopmental outcomes and vulnerabilities; recognizing the underlying molecular and cellular mechanisms will require scalable approaches. Here, we describe a "cell village" experimental platform we used to analyze genetic, molecular, and phenotypic heterogeneity across neural progenitor cells from 44 human donors cultured in a shared in vitro environment using algorithms (Dropulation and Census-seq) to assign cells and phenotypes to individual donors. Through rapid induction of human stem cell-derived neural progenitor cells, measurements of natural genetic variation, and CRISPR-Cas9 genetic perturbations, we identified a common variant that regulates antiviral IFITM3 expression and explains most inter-individual variation in susceptibility to the Zika virus. We also detected expression QTLs corresponding to GWAS loci for brain traits and discovered novel disease-relevant regulators of progenitor proliferation and differentiation such as CACHD1. This approach provides scalable ways to elucidate the effects of genes and genetic variation on cellular phenotypes.
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Affiliation(s)
- Michael F Wells
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jana M Mitchell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Insitro, South San Francisco, CA 94080, USA
| | | | - Curtis J Mello
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Olli Pietilainen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Federica Piccioni
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Ellen J Guss
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kavya Raghunathan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Derek Hawes
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Anna Neumann
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Kathleen A Worringer
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Daniel Ho
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Sravya Kommineni
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Karrie Chan
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Brant K Peterson
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Joseph J Raymond
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - John T Gold
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Biology, Davidson College, Davidson, NC 28035, USA
| | - Marco T Siekmann
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Emanuela Zuccaro
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | | | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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5
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Maranda V, Zhang Y, Vizeacoumar FS, Freywald A, Vizeacoumar FJ. A CRISPR Platform for Targeted In Vivo Screens. Methods Mol Biol 2023; 2614:397-409. [PMID: 36587138 DOI: 10.1007/978-1-0716-2914-7_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Large-scale genetic screens are becoming increasingly used as powerful tools to query the genome to identify therapeutic targets in cancer. The advent of the CRISPR technology has revolutionized the effectiveness of these screens and has made it possible to carry out loss-of-function screens to identify cancer-specific genetic interactions. Such loss-of-function screens can be performed in silico, in vitro, and in vivo, depending on the scale of the screen, as well as research questions to be answered. Performing screens in vivo has its challenges but also advantages, providing opportunities to study the tumor microenvironment and cancer immunity. In this chapter, we present a procedural framework and associated notes for conducting in vivo CRISPR knockout screens in cancer models to study cancer biology, anti-tumor immune responses, tumor microenvironment, and predicting treatment responses.
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Affiliation(s)
- Vincent Maranda
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Yue Zhang
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | | | - Andrew Freywald
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, Canada.
| | - Franco J Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada.
- Cancer Research Department, Saskatchewan Cancer Agency, Saskatoon, Canada.
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6
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Vinceti A, Perron U, Trastulla L, Iorio F. Reduced gene templates for supervised analysis of scale-limited CRISPR-Cas9 fitness screens. Cell Rep 2022; 40:111145. [PMID: 35905712 DOI: 10.1016/j.celrep.2022.111145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/26/2022] [Accepted: 07/07/2022] [Indexed: 12/21/2022] Open
Abstract
Pooled genome-wide CRISPR-Cas9 screens are furthering our mechanistic understanding of human biology and have allowed us to identify new oncology therapeutic targets. Scale-limited CRISPR-Cas9 screens-typically employing guide RNA libraries targeting subsets of functionally related genes, biological pathways, or portions of the druggable genome-constitute an optimal setting for investigating narrow hypotheses and are easier to execute on complex models, such as organoids and in vivo models. Different supervised methods are used for computational analysis of genome-wide CRISPR-Cas9 screens; most are not well suited for scale-limited screens, as they require large sets of positive/negative control genes (gene templates) to be included among the screened ones. Here, we develop a computational framework identifying optimal subsets of known essential and nonessential genes (at different subsampling percentages) that can be used as templates for supervised analyses of scale-limited CRISPR-Cas9 screens, while having a reduced impact on the size of the employed library.
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Affiliation(s)
- Alessandro Vinceti
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy
| | - Umberto Perron
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy
| | - Lucia Trastulla
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy
| | - Francesco Iorio
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini, 1 - 20157 Milano, Italy; Cancer Dependency Map Analytics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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7
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Michl J, Wang Y, Monterisi S, Blaszczak W, Beveridge R, Bridges EM, Koth J, Bodmer WF, Swietach P. CRISPR-Cas9 screen identifies oxidative phosphorylation as essential for cancer cell survival at low extracellular pH. Cell Rep 2022; 38:110493. [PMID: 35263578 PMCID: PMC8924371 DOI: 10.1016/j.celrep.2022.110493] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/05/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
Unlike most cell types, many cancer cells survive at low extracellular pH (pHe), a chemical signature of tumors. Genes that facilitate survival under acid stress are therefore potential targets for cancer therapies. We performed a genome-wide CRISPR-Cas9 cell viability screen at physiological and acidic conditions to systematically identify gene knockouts associated with pH-related fitness defects in colorectal cancer cells. Knockouts of genes involved in oxidative phosphorylation (NDUFS1) and iron-sulfur cluster biogenesis (IBA57, NFU1) grew well at physiological pHe, but underwent profound cell death under acidic conditions. We identified several small-molecule inhibitors of mitochondrial metabolism that can kill cancer cells at low pHe only. Xenografts established from NDUFS1-/- cells grew considerably slower than their wild-type controls, but growth could be stimulated with systemic bicarbonate therapy that lessens the tumoral acid stress. These findings raise the possibility of therapeutically targeting mitochondrial metabolism in combination with acid stress as a cancer treatment option.
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Affiliation(s)
- Johanna Michl
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK.
| | - Yunyi Wang
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Stefania Monterisi
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Wiktoria Blaszczak
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK
| | - Ryan Beveridge
- Virus Screening Facility, MRC Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Esther M Bridges
- Department of NDM Experimental Medicine, MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, JR Hospital, Headington, Oxford OX3 9DS, UK
| | - Jana Koth
- MRC Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Walter F Bodmer
- MRC Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics, Parks Road, Oxford OX1 3PT, UK.
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8
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Mennuni M, Filograna R, Felser A, Bonekamp NA, Giavalisco P, Lytovchenko O, Larsson N. Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen. EMBO Rep 2022; 23:e53054. [PMID: 34779571 PMCID: PMC8728608 DOI: 10.15252/embr.202153054] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 12/20/2022] Open
Abstract
Cancer cells depend on mitochondria to sustain their increased metabolic need and mitochondria therefore constitute possible targets for cancer treatment. We recently developed small-molecule inhibitors of mitochondrial transcription (IMTs) that selectively impair mitochondrial gene expression. IMTs have potent antitumor properties in vitro and in vivo, without affecting normal tissues. Because therapy-induced resistance is a major constraint to successful cancer therapy, we investigated mechanisms conferring resistance to IMTs. We employed a CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats)-(CRISP-associated protein 9) whole-genome screen to determine pathways conferring resistance to acute IMT1 treatment. Loss of genes belonging to von Hippel-Lindau (VHL) and mammalian target of rapamycin complex 1 (mTORC1) pathways caused resistance to acute IMT1 treatment and the relevance of these pathways was confirmed by chemical modulation. We also generated cells resistant to chronic IMT treatment to understand responses to persistent mitochondrial gene expression impairment. We report that IMT1-acquired resistance occurs through a compensatory increase of mitochondrial DNA (mtDNA) expression and cellular metabolites. We found that mitochondrial transcription factor A (TFAM) downregulation and inhibition of mitochondrial translation impaired survival of resistant cells. The identified susceptibility and resistance mechanisms to IMTs may be relevant for different types of mitochondria-targeted therapies.
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Affiliation(s)
- Mara Mennuni
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Roberta Filograna
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Andrea Felser
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- University Institute of Clinical ChemistryBern University HospitalBernSwitzerland
| | - Nina A Bonekamp
- Mitochondrial Biology GroupMax Planck Institute for Biology of AgeingCologneGermany
- Department of NeuroanatomyMannheim Center for Translational Neuroscience (MCTN)Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Patrick Giavalisco
- Metabolomics Core FacilityMax Planck Institute for Biology of AgeingCologneGermany
| | - Oleksandr Lytovchenko
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Nils‐Göran Larsson
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
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9
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Abstract
The maintenance of genome stability requires dedicated DNA repair processes and pathways that are essential for the faithful duplication and propagation of chromosomes. These DNA repair mechanisms counteract the potentially deleterious impact of the frequent genotoxic challenges faced by cells from both exogenous and endogenous agents. Intrinsic to these mechanisms, cells have an arsenal of protein factors that can be utilised to promote repair processes in response to DNA lesions. Orchestration of the protein factors within the various cellular DNA repair pathways is performed, in part, by post-translational modifications, such as phosphorylation, ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs). In this review, we firstly explore recent advances in the tools for identifying factors involved in both DNA repair and ubiquitin signaling pathways. We then expand on this by evaluating the growing repertoire of proteomic, biochemical and structural techniques available to further understand the mechanistic basis by which these complex modifications regulate DNA repair. Together, we provide a snapshot of the range of methods now available to investigate and decode how ubiquitin signaling can promote DNA repair and maintain genome stability in mammalian cells.
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Affiliation(s)
| | | | - Ian Gibbs-Seymour
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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10
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Luo Y, Tan CW, Xie SZ, Chen Y, Yao YL, Zhao K, Zhu Y, Wang Q, Liu MQ, Yang XL, Wang LF, Shi ZL. Identification of ZDHHC17 as a Potential Drug Target for Swine Acute Diarrhea Syndrome Coronavirus Infection. mBio 2021; 12:e0234221. [PMID: 34700373 DOI: 10.1128/mBio.02342-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The recent emergence and spread of zoonotic viruses highlights that animal-sourced viruses are the biggest threat to global public health. Swine acute diarrhea syndrome coronavirus (SADS-CoV) is an HKU2-related bat coronavirus that was spilled over from Rhinolophus bats to swine, causing large-scale outbreaks of severe diarrhea disease in piglets in China. Unlike other porcine coronaviruses, SADS-CoV possesses broad species tissue tropism, including primary human cells, implying a significant risk of cross-species spillover. To explore host dependency factors for SADS-CoV as therapeutic targets, we employed genome-wide CRISPR knockout library screening in HeLa cells. Consistent with two independent screens, we identified the zinc finger DHHC-type palmitoyltransferase 17 (ZDHHC17 or ZD17) as an important host factor for SADS-CoV infection. Through truncation mutagenesis, we demonstrated that the DHHC domain of ZD17 that is involved in palmitoylation is important for SADS-CoV infection. Mechanistic studies revealed that ZD17 is required for SADS-CoV genomic RNA replication. Treatment of infected cells with the palmitoylation inhibitor 2-bromopalmitate (2-BP) significantly suppressed SADS-CoV infection. Our findings provide insight on SADS-CoV-host interactions and a potential therapeutic application.
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11
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Kinowaki Y, Taguchi T, Onishi I, Kirimura S, Kitagawa M, Yamamoto K. Overview of Ferroptosis and Synthetic Lethality Strategies. Int J Mol Sci 2021; 22:ijms22179271. [PMID: 34502181 PMCID: PMC8430824 DOI: 10.3390/ijms22179271] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 12/31/2022] Open
Abstract
Ferroptosis, a term first proposed in 2012, is iron-dependent, non-apoptotic regulatory cell death induced by erastin. Ferroptosis was originally discovered during synthetic lethal screening for drugs sensitive to RAS mutant cells, and is closely related to synthetic lethality. Ferroptosis sensitizes cancer stem cells and tumors that undergo epithelial−mesenchymal transition and are resistant to anticancer drugs or targeted therapy. Therefore, ferroptosis-inducing molecules are attractive new research targets. In contrast, synthetic lethal strategies approach mechanisms and genetic abnormalities that cannot be directly targeted by conventional therapeutic strategies, such as RAS mutations, hypoxia, and abnormalities in the metabolic environment. They also target the environment and conditions specific to malignant cells, have a low toxicity to normal cells, and can be used in combination with known drugs to produce new ones. However, the concept of synthetic lethality has not been widely adopted with ferroptosis. In this review, we surveyed the literature on ferroptosis-related factors and synthetic lethality to examine the potential therapeutic targets in ferroptosis-related molecules, focusing on factors related to synthetic lethality, discovery methods, clinical application stages, and issues in drug discovery.
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Affiliation(s)
- Yuko Kinowaki
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan; (T.T.); (M.K.)
- Correspondence: (Y.K.); (K.Y.); Tel.: +81-3-5803-5175 (Y.K.); Fax: +81-3-5803-0123 (K.Y.)
| | - Towako Taguchi
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan; (T.T.); (M.K.)
| | - Iichiroh Onishi
- Division of Surgical Pathology, Tokyo Medical and Dental University Hospital, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan; (I.O.); (S.K.)
| | - Susumu Kirimura
- Division of Surgical Pathology, Tokyo Medical and Dental University Hospital, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan; (I.O.); (S.K.)
| | - Masanobu Kitagawa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan; (T.T.); (M.K.)
| | - Kouhei Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan; (T.T.); (M.K.)
- Correspondence: (Y.K.); (K.Y.); Tel.: +81-3-5803-5175 (Y.K.); Fax: +81-3-5803-0123 (K.Y.)
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12
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Vervoort SJ, Welsh SA, Devlin JR, Barbieri E, Knight DA, Offley S, Bjelosevic S, Costacurta M, Todorovski I, Kearney CJ, Sandow JJ, Fan Z, Blyth B, McLeod V, Vissers JHA, Pavic K, Martin BP, Gregory G, Demosthenous E, Zethoven M, Kong IY, Hawkins ED, Hogg SJ, Kelly MJ, Newbold A, Simpson KJ, Kauko O, Harvey KF, Ohlmeyer M, Westermarck J, Gray N, Gardini A, Johnstone RW. The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer. Cell 2021; 184:3143-3162.e32. [PMID: 34004147 PMCID: PMC8567840 DOI: 10.1016/j.cell.2021.04.022] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/27/2020] [Accepted: 04/14/2021] [Indexed: 12/18/2022]
Abstract
Gene expression by RNA polymerase II (RNAPII) is tightly controlled by cyclin-dependent kinases (CDKs) at discrete checkpoints during the transcription cycle. The pausing checkpoint following transcription initiation is primarily controlled by CDK9. We discovered that CDK9-mediated, RNAPII-driven transcription is functionally opposed by a protein phosphatase 2A (PP2A) complex that is recruited to transcription sites by the Integrator complex subunit INTS6. PP2A dynamically antagonizes phosphorylation of key CDK9 substrates including DSIF and RNAPII-CTD. Loss of INTS6 results in resistance to tumor cell death mediated by CDK9 inhibition, decreased turnover of CDK9 phospho-substrates, and amplification of acute oncogenic transcriptional responses. Pharmacological PP2A activation synergizes with CDK9 inhibition to kill both leukemic and solid tumor cells, providing therapeutic benefit in vivo. These data demonstrate that fine control of gene expression relies on the balance between kinase and phosphatase activity throughout the transcription cycle, a process dysregulated in cancer that can be exploited therapeutically.
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Affiliation(s)
- Stephin J Vervoort
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia.
| | - Sarah A Welsh
- The Wistar Institute, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer R Devlin
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | | | - Deborah A Knight
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Sarah Offley
- The Wistar Institute, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stefan Bjelosevic
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Matteo Costacurta
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Izabela Todorovski
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Conor J Kearney
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute, Parkville 3010, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Zheng Fan
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Benjamin Blyth
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia
| | - Victoria McLeod
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia
| | - Joseph H A Vissers
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia; Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Karolina Pavic
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku FI-20014, Finland; Institute of Biomedicine, University of Turku, Turku FI-20014, Finland
| | - Ben P Martin
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Gareth Gregory
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton 3168, VIC, Australia
| | | | - Magnus Zethoven
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia
| | - Isabella Y Kong
- The Walter and Eliza Hall Institute, Parkville 3010, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Edwin D Hawkins
- The Walter and Eliza Hall Institute, Parkville 3010, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Simon J Hogg
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Madison J Kelly
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Andrea Newbold
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | | | - Otto Kauko
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku FI-20014, Finland; Institute of Biomedicine, University of Turku, Turku FI-20014, Finland
| | - Kieran F Harvey
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia; Department of Anatomy and Developmental Biology, and Biomedicine Discovery Institute, Monash University, Clayton 3168, VIC, Australia
| | - Michael Ohlmeyer
- Mount Sinai School of Medicine, New York, NY 10029, USA; Atux Iskay LLC, Plainsboro, NJ 08536, USA
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku FI-20014, Finland; Institute of Biomedicine, University of Turku, Turku FI-20014, Finland
| | | | | | - Ricky W Johnstone
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia.
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13
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Baumgarten N, Schmidt F, Wegner M, Hebel M, Kaulich M, Schulz MH. Computational prediction of CRISPR-impaired non-coding regulatory regions. Biol Chem 2021; 402:973-982. [PMID: 33660495 DOI: 10.1515/hsz-2020-0392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/18/2021] [Indexed: 12/14/2022]
Abstract
Genome-wide CRISPR screens are becoming more widespread and allow the simultaneous interrogation of thousands of genomic regions. Although recent progress has been made in the analysis of CRISPR screens, it is still an open problem how to interpret CRISPR mutations in non-coding regions of the genome. Most of the tools concentrate on the interpretation of mutations introduced in gene coding regions. We introduce a computational pipeline that uses epigenomic information about regulatory elements for the interpretation of CRISPR mutations in non-coding regions. We illustrate our analysis protocol on the analysis of a genome-wide CRISPR screen in hTERT-RPE1 cells and reveal novel regulatory elements that mediate chemoresistance against doxorubicin in these cells. We infer links to established and to novel chemoresistance genes. Our analysis protocol is general and can be applied on any cell type and with different CRISPR enzymes.
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Affiliation(s)
- Nina Baumgarten
- Institute for Cardiovascular Regeneration, Goethe University, 60590Frankfurt am Main, Germany.,German Center for Cardiovascular Research, Partner site Rhein-Main, 60590Frankfurt am Main, Germany.,Cluster of Excellence MMCI, Saarland University, and Max Planck Institute for Informatics, Saarland Informatics Campus, 66123Saarbrücken, Germany.,Cardiopulmonary Institute (CPI), Goethe University, 60590 Frankfurt am Main, Germany
| | - Florian Schmidt
- Institute for Cardiovascular Regeneration, Goethe University, 60590Frankfurt am Main, Germany.,German Center for Cardiovascular Research, Partner site Rhein-Main, 60590Frankfurt am Main, Germany.,Cluster of Excellence MMCI, Saarland University, and Max Planck Institute for Informatics, Saarland Informatics Campus, 66123Saarbrücken, Germany.,Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore, Singapore
| | - Martin Wegner
- Institute of Biochemistry II, Goethe University - Medical Faculty, University Hospital, 60590Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, 60590Frankfurt am Main, Germany
| | - Marie Hebel
- Institute of Biochemistry II, Goethe University - Medical Faculty, University Hospital, 60590Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, 60590Frankfurt am Main, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University - Medical Faculty, University Hospital, 60590Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, 60590Frankfurt am Main, Germany
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe University, 60590Frankfurt am Main, Germany.,German Center for Cardiovascular Research, Partner site Rhein-Main, 60590Frankfurt am Main, Germany.,Cluster of Excellence MMCI, Saarland University, and Max Planck Institute for Informatics, Saarland Informatics Campus, 66123Saarbrücken, Germany.,Cardiopulmonary Institute (CPI), Goethe University, 60590 Frankfurt am Main, Germany
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14
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Hundley FV, Sanvisens Delgado N, Marin HC, Carr KL, Tian R, Toczyski DP. A comprehensive phenotypic CRISPR-Cas9 screen of the ubiquitin pathway uncovers roles of ubiquitin ligases in mitosis. Mol Cell 2021; 81:1319-1336.e9. [PMID: 33539788 DOI: 10.1016/j.molcel.2021.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 10/20/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
Abstract
The human ubiquitin proteasome system, composed of over 700 ubiquitin ligases (E3s) and deubiquitinases (DUBs), has been difficult to characterize systematically and phenotypically. We performed chemical-genetic CRISPR-Cas9 screens to identify E3s/DUBs whose loss renders cells sensitive or resistant to 41 compounds targeting a broad range of biological processes, including cell cycle progression, genome stability, metabolism, and vesicular transport. Genes and compounds clustered functionally, with inhibitors of related pathways interacting similarly with E3s/DUBs. Some genes, such as FBXW7, showed interactions with many of the compounds. Others, such as RNF25 and FBXO42, showed interactions primarily with a single compound (methyl methanesulfonate for RNF25) or a set of related compounds (the mitotic cluster for FBXO42). Mutation of several E3s with sensitivity to mitotic inhibitors led to increased aberrant mitoses, suggesting a role for these genes in cell cycle regulation. Our comprehensive CRISPR-Cas9 screen uncovered 466 gene-compound interactions covering 25% of the interrogated E3s/DUBs.
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15
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Condon KJ, Orozco JM, Adelmann CH, Spinelli JB, van der Helm PW, Roberts JM, Kunchok T, Sabatini DM. Genome-wide CRISPR screens reveal multitiered mechanisms through which mTORC1 senses mitochondrial dysfunction. Proc Natl Acad Sci U S A 2021; 118:e2022120118. [PMID: 33483422 PMCID: PMC7848693 DOI: 10.1073/pnas.2022120118] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In mammalian cells, nutrients and growth factors signal through an array of upstream proteins to regulate the mTORC1 growth control pathway. Because the full complement of these proteins has not been systematically identified, we developed a FACS-based CRISPR-Cas9 genetic screening strategy to pinpoint genes that regulate mTORC1 activity. Along with almost all known positive components of the mTORC1 pathway, we identified many genes that impact mTORC1 activity, including DCAF7, CSNK2B, SRSF2, IRS4, CCDC43, and HSD17B10 Using the genome-wide screening data, we generated a focused sublibrary containing single guide RNAs (sgRNAs) targeting hundreds of genes and carried out epistasis screens in cells lacking nutrient- and stress-responsive mTORC1 modulators, including GATOR1, AMPK, GCN2, and ATF4. From these data, we pinpointed mitochondrial function as a particularly important input into mTORC1 signaling. While it is well appreciated that mitochondria signal to mTORC1, the mechanisms are not completely clear. We find that the kinases AMPK and HRI signal, with varying kinetics, mitochondrial distress to mTORC1, and that HRI acts through the ATF4-dependent up-regulation of both Sestrin2 and Redd1. Loss of both AMPK and HRI is sufficient to render mTORC1 signaling largely resistant to mitochondrial dysfunction induced by the ATP synthase inhibitor oligomycin as well as the electron transport chain inhibitors piericidin and antimycin. Taken together, our data reveal a catalog of genes that impact the mTORC1 pathway and clarify the multifaceted ways in which mTORC1 senses mitochondrial dysfunction.
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Affiliation(s)
- Kendall J Condon
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Jose M Orozco
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Charles H Adelmann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Jessica B Spinelli
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Pim W van der Helm
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Justin M Roberts
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Tenzin Kunchok
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142;
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
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16
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Christodoulou E, Rashid M, Pacini C, Droop A, Robertson H, van Groningen T, Teunisse AFAS, Iorio F, Jochemsen AG, Adams DJ, van Doorn R. Analysis of CRISPR-Cas9 screens identifies genetic dependencies in melanoma. Pigment Cell Melanoma Res 2021; 34:122-131. [PMID: 32767816 PMCID: PMC7818247 DOI: 10.1111/pcmr.12919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/03/2020] [Accepted: 07/29/2020] [Indexed: 12/13/2022]
Abstract
Targeting the MAPK signaling pathway has transformed the treatment of metastatic melanoma. CRISPR-Cas9 genetic screens provide a genome-wide approach to uncover novel genetic dependencies that might serve as therapeutic targets. Here, we analyzed recently reported CRISPR-Cas9 screens comparing data from 28 melanoma cell lines and 313 cell lines of other tumor types in order to identify fitness genes related to melanoma. We found an average of 1,494 fitness genes in each melanoma cell line. We identified 33 genes, inactivation of which specifically reduced the fitness of melanoma. This set of tumor type-specific genes includes established melanoma fitness genes as well as many genes that have not previously been associated with melanoma growth. Several genes encode proteins that can be targeted using available inhibitors. We verified that genetic inactivation of DUSP4 and PPP2R2A reduces the proliferation of melanoma cells. DUSP4 encodes an inhibitor of ERK, suggesting that further activation of MAPK signaling activity through its loss is selectively deleterious to melanoma cells. Collectively, these data present a resource of genetic dependencies in melanoma that may be explored as potential therapeutic targets.
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Affiliation(s)
| | - Mamunur Rashid
- Experimental Cancer Genetics GroupWellcome Trust Sanger InstituteCambridgeUK
| | - Clare Pacini
- Cancer Dependency Map AnalyticsWellcome Trust Sanger InstituteCambridgeUK
| | - Alastair Droop
- Experimental Cancer Genetics GroupWellcome Trust Sanger InstituteCambridgeUK
| | - Holly Robertson
- Experimental Cancer Genetics GroupWellcome Trust Sanger InstituteCambridgeUK
| | - Tim van Groningen
- Department of DermatologyLeiden University Medical CenterLeidenThe Netherlands
| | - Amina F. A. S. Teunisse
- Department of Cell and Chemical BiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Francesco Iorio
- Cancer Dependency Map AnalyticsWellcome Trust Sanger InstituteCambridgeUK
- Centre for Computational BiologyHuman TechnopoleMilanoItaly
| | - Aart G. Jochemsen
- Department of Cell and Chemical BiologyLeiden University Medical CenterLeidenThe Netherlands
| | - David J. Adams
- Experimental Cancer Genetics GroupWellcome Trust Sanger InstituteCambridgeUK
| | - Remco van Doorn
- Department of DermatologyLeiden University Medical CenterLeidenThe Netherlands
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17
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Petitjean O, Girardi E, Ngondo RP, Lupashin V, Pfeffer S. Genome-Wide CRISPR-Cas9 Screen Reveals the Importance of the Heparan Sulfate Pathway and the Conserved Oligomeric Golgi Complex for Synthetic Double-Stranded RNA Uptake and Sindbis Virus Infection. mSphere 2020; 5:e00914-20. [PMID: 33177215 DOI: 10.1128/mSphere.00914-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
When facing a viral infection, the organism has to put in place a number of defense mechanisms in order to clear the pathogen from the cell. At the early phase of this preparation for fighting against the invader, the innate immune response is triggered by the sensing of danger signals. Among those molecular cues, double-stranded RNA (dsRNA) is a very potent inducer of different reactions at the cellular level that can ultimately lead to cell death. Using a genome-wide screening approach, we set to identify genes involved in dsRNA entry, sensing, and apoptosis induction in human cells. This allowed us to determine that the heparan sulfate pathway and the conserved oligomeric Golgi complex are key determinants allowing entry of both dsRNA and viral nucleic acid leading to cell death. Double-stranded RNA (dsRNA) is the hallmark of many viral infections. dsRNA is produced either by RNA viruses during replication or by DNA viruses upon convergent transcription. Synthetic dsRNA is also able to mimic viral-induced activation of innate immune response and cell death. In this study, we employed a genome-wide CRISPR-Cas9 loss-of-function screen based on cell survival in order to identify genes implicated in the host response to dsRNA. By challenging HCT116 human cells with either synthetic dsRNA or Sindbis virus (SINV), we identified the heparan sulfate (HS) pathway as a crucial factor for dsRNA entry, and we validated SINV dependency on HS. Interestingly, we uncovered a novel role for COG4, a component of the conserved oligomeric Golgi (COG) complex, as a factor involved in cell survival to both dsRNA and SINV in human cells. We showed that COG4 knockout led to a decrease of extracellular HS that specifically affected dsRNA transfection efficiency and reduced viral production, which explains the increased cell survival of these mutants. IMPORTANCE When facing a viral infection, the organism has to put in place a number of defense mechanisms in order to clear the pathogen from the cell. At the early phase of this preparation for fighting against the invader, the innate immune response is triggered by the sensing of danger signals. Among those molecular cues, double-stranded RNA (dsRNA) is a very potent inducer of different reactions at the cellular level that can ultimately lead to cell death. Using a genome-wide screening approach, we set to identify genes involved in dsRNA entry, sensing, and apoptosis induction in human cells. This allowed us to determine that the heparan sulfate pathway and the conserved oligomeric Golgi complex are key determinants allowing entry of both dsRNA and viral nucleic acid leading to cell death.
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18
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Sulahian R, Kwon JJ, Walsh KH, Pailler E, Bosse TL, Thaker M, Almanza D, Dempster JM, Pan J, Piccioni F, Dumont N, Gonzalez A, Rennhack J, Nabet B, Bachman JA, Goodale A, Lee Y, Bagul M, Liao R, Navarro A, Yuan TL, Ng RWS, Raghavan S, Gray NS, Tsherniak A, Vazquez F, Root DE, Firestone AJ, Settleman J, Hahn WC, Aguirre AJ. Synthetic Lethal Interaction of SHOC2 Depletion with MEK Inhibition in RAS-Driven Cancers. Cell Rep 2020; 29:118-134.e8. [PMID: 31577942 DOI: 10.1016/j.celrep.2019.08.090] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/22/2019] [Accepted: 08/27/2019] [Indexed: 12/17/2022] Open
Abstract
The mitogen-activated protein kinase (MAPK) pathway is a critical effector of oncogenic RAS signaling, and MAPK pathway inhibition may be an effective combination treatment strategy. We performed genome-scale loss-of-function CRISPR-Cas9 screens in the presence of a MEK1/2 inhibitor (MEKi) in KRAS-mutant pancreatic and lung cancer cell lines and identified genes that cooperate with MEK inhibition. While we observed heterogeneity in genetic modifiers of MEKi sensitivity across cell lines, several recurrent classes of synthetic lethal vulnerabilities emerged at the pathway level. Multiple members of receptor tyrosine kinase (RTK)-RAS-MAPK pathways scored as sensitizers to MEKi. In particular, we demonstrate that knockout, suppression, or degradation of SHOC2, a positive regulator of MAPK signaling, specifically cooperated with MEK inhibition to impair proliferation in RAS-driven cancer cells. The depletion of SHOC2 disrupted survival pathways triggered by feedback RTK signaling in response to MEK inhibition. Thus, these findings nominate SHOC2 as a potential target for combination therapy.
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Affiliation(s)
- Rita Sulahian
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason J Kwon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Emma Pailler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Timothy L Bosse
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maneesha Thaker
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Diego Almanza
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Joshua Pan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Nancy Dumont
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jonathan Rennhack
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - John A Bachman
- Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yenarae Lee
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mukta Bagul
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rosy Liao
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Adrija Navarro
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tina L Yuan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Raymond W S Ng
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Srivatsan Raghavan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Aviad Tsherniak
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jeff Settleman
- Calico Life Sciences, South San Francisco, CA 94080, USA
| | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, MA.
| | - Andrew J Aguirre
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, MA.
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19
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Yuan F, Sun M, Liu H, Qian F. Albumin-conjugated drug is irresistible by single gene mutation of endocytic system: Verification by genome-wide CRISPR-Cas9 loss-of-function screens. J Control Release 2020; 323:311-20. [PMID: 32335155 DOI: 10.1016/j.jconrel.2020.04.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/31/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022]
Abstract
Albumin-conjugated drugs attain KRAS mutant cancer targeting through KRAS-enhanced macropinocytosis and intensified lysosomal degradation due to reduced neonatal Fc receptor (FcRn) expression. The cytosolic delivery of active payloads relies on endocytosis and subsequent intracellular processing of albumin delivery vehicles, wherein complex regulatory mechanisms and molecular machineries are closely involved. Despite the obvious merit of KRAS targeting, could such an endocytic process involving extra molecular regulators also bring about extra vulnerabilities to albumin-conjugated drugs, particularly, unexpected drug resistance? To assess such risks, here we performed an unbiased drug resistance mechanism comparison in pancreatic cancer, between free triptolide (TP, a potent cytotoxin) and albumin-conjugated TP, using genome-wide CRISPR-Cas9 loss-of-function screens. GTF2H5, a subunit of GTF2H transcription factor complex, was the only hit identified regardless of forms of TP treatment. With drug efficacy tests on GTF2H5 knockout clones, we further concluded that GTF2H5 deficiency conferred drug resistance primarily due to the pharmacological mechanism of action (MoA) of TP. In addition, molecules previously considered to be able to affect endocytosis and intracellular processing were not enriched during the screening with albumin-conjugated TP. With the aid of genome-wide CRISPR-Cas9 loss-of-function screens, we conclude that the pharmacological resistance of the active payload, rather than any potential loss-of-function mutations in endocytic molecular machineries, is the solely crucial drug resistance mechanism of albumin-conjugated drugs.
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20
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Gurusamy D, Henning AN, Yamamoto TN, Yu Z, Zacharakis N, Krishna S, Kishton RJ, Vodnala SK, Eidizadeh A, Jia L, Kariya CM, Black MA, Eil R, Palmer DC, Pan JH, Sukumar M, Patel SJ, Restifo NP. Multi-phenotype CRISPR-Cas9 Screen Identifies p38 Kinase as a Target for Adoptive Immunotherapies. Cancer Cell 2020; 37:818-833.e9. [PMID: 32516591 DOI: 10.1016/j.ccell.2020.05.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 01/11/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022]
Abstract
T cells are central to all currently effective cancer immunotherapies, but the characteristics defining therapeutically effective anti-tumor T cells have not been comprehensively elucidated. Here, we delineate four phenotypic qualities of effective anti-tumor T cells: cell expansion, differentiation, oxidative stress, and genomic stress. Using a CRISPR-Cas9-based genetic screen of primary T cells we measured the multi-phenotypic impact of disrupting 25 T cell receptor-driven kinases. We identified p38 kinase as a central regulator of all four phenotypes and uncovered transcriptional and antioxidant pathways regulated by p38 in T cells. Pharmacological inhibition of p38 improved the efficacy of mouse anti-tumor T cells and enhanced the functionalities of human tumor-reactive and gene-engineered T cells, paving the way for clinically relevant interventions.
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Affiliation(s)
- Devikala Gurusamy
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA.
| | - Amanda N Henning
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Tori N Yamamoto
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhiya Yu
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Nikolaos Zacharakis
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Sri Krishna
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Rigel J Kishton
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Suman K Vodnala
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Arash Eidizadeh
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Li Jia
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Christine M Kariya
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Mary A Black
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Robert Eil
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Douglas C Palmer
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Jenny H Pan
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Madhusudhanan Sukumar
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Shashank J Patel
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA.
| | - Nicholas P Restifo
- Surgery Branch, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Center for Cell-based Therapy, Center for Cancer Research, National Institutes of Health (NIH), Bethesda, MD 20892, USA; Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.
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21
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Krishnan A, Kloehn J, Lunghi M, Chiappino-Pepe A, Waldman BS, Nicolas D, Varesio E, Hehl A, Lourido S, Hatzimanikatis V, Soldati-Favre D. Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism. Cell Host Microbe 2020; 27:290-306.e11. [PMID: 31991093 DOI: 10.1016/j.chom.2020.01.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/02/2019] [Accepted: 01/03/2020] [Indexed: 12/31/2022]
Abstract
To survive and proliferate in diverse host environments with varying nutrient availability, the obligate intracellular parasite Toxoplasma gondii reprograms its metabolism. We have generated and curated a genome-scale metabolic model (iTgo) for the fast-replicating tachyzoite stage, harmonized with experimentally observed phenotypes. To validate the importance of four metabolic pathways predicted by the model, we have performed in-depth in vitro and in vivo phenotyping of mutant parasites including targeted metabolomics and CRISPR-Cas9 fitness screening of all known metabolic genes. This led to unexpected insights into the remarkable flexibility of the parasite, addressing the dependency on biosynthesis or salvage of fatty acids (FAs), purine nucleotides (AMP and GMP), a vitamin (pyridoxal-5P), and a cofactor (heme) in both the acute and latent stages of infection. Taken together, our experimentally validated metabolic network leads to a deeper understanding of the parasite's biology, opening avenues for the development of therapeutic intervention against apicomplexans.
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Affiliation(s)
- Aarti Krishnan
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Joachim Kloehn
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Matteo Lunghi
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Anush Chiappino-Pepe
- Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | | | - Damien Nicolas
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Emmanuel Varesio
- School of Pharmaceutical Sciences Geneva-Lausanne (EPGL), Geneva 1211, Switzerland; Mass Spectrometry Core Facility (MZ 2.0), University of Geneva, Geneva 1211, Switzerland
| | - Adrian Hehl
- Institute of Parasitology, University of Zürich, Zürich 8057, Switzerland
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland.
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22
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Cheng W, Wang S, Zhang Z, Morgens DW, Hayes LR, Lee S, Portz B, Xie Y, Nguyen BV, Haney MS, Yan S, Dong D, Coyne AN, Yang J, Xian F, Cleveland DW, Qiu Z, Rothstein JD, Shorter J, Gao FB, Bassik MC, Sun S. CRISPR-Cas9 Screens Identify the RNA Helicase DDX3X as a Repressor of C9ORF72 (GGGGCC)n Repeat-Associated Non-AUG Translation. Neuron 2019; 104:885-898.e8. [PMID: 31587919 DOI: 10.1016/j.neuron.2019.09.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/16/2019] [Accepted: 09/04/2019] [Indexed: 12/14/2022]
Abstract
Hexanucleotide GGGGCC repeat expansion in C9ORF72 is the most prevalent genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). One pathogenic mechanism is the aberrant accumulation of dipeptide repeat (DPR) proteins produced by the unconventional translation of expanded RNA repeats. Here, we performed genome-wide CRISPR-Cas9 screens for modifiers of DPR protein production in human cells. We found that DDX3X, an RNA helicase, suppresses the repeat-associated non-AUG translation of GGGGCC repeats. DDX3X directly binds to (GGGGCC)n RNAs but not antisense (CCCCGG)n RNAs. Its helicase activity is essential for the translation repression. Reduction of DDX3X increases DPR levels in C9ORF72-ALS/FTD patient cells and enhances (GGGGCC)n-mediated toxicity in Drosophila. Elevating DDX3X expression is sufficient to decrease DPR levels, rescue nucleocytoplasmic transport abnormalities, and improve survival of patient iPSC-differentiated neurons. This work identifies genetic modifiers of DPR protein production and provides potential therapeutic targets for C9ORF72-ALS/FTD.
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Affiliation(s)
- Weiwei Cheng
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaopeng Wang
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhe Zhang
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David W Morgens
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lindsey R Hayes
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Soojin Lee
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yongzhi Xie
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Baotram V Nguyen
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael S Haney
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirui Yan
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daoyuan Dong
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alyssa N Coyne
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Junhua Yang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fengfan Xian
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Don W Cleveland
- Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Zhaozhu Qiu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeffrey D Rothstein
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shuying Sun
- Department of Pathology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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