1
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Papakyriacou I, Kutkaite G, Rúbies Bedós M, Nagarajan D, Alford LP, Menden MP, Mao Y. Loss of NEDD8 in cancer cells causes vulnerability to immune checkpoint blockade in triple-negative breast cancer. Nat Commun 2024; 15:3581. [PMID: 38678024 PMCID: PMC11055868 DOI: 10.1038/s41467-024-47987-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
Immune checkpoint blockade therapy aims to activate the immune system to eliminate cancer cells. However, clinical benefits are only recorded in a subset of patients. Here, we leverage genome-wide CRISPR/Cas9 screens in a Tumor-Immune co-Culture System focusing on triple-negative breast cancer (TNBC). We reveal that NEDD8 loss in cancer cells causes a vulnerability to nivolumab (anti-PD-1). Genetic deletion of NEDD8 only delays cell division initially but cell proliferation is unaffected after recovery. Since the NEDD8 gene is commonly essential, we validate this observation with additional CRISPR screens and uncover enhanced immunogenicity in NEDD8 deficient cells using proteomics. In female immunocompetent mice, PD-1 blockade lacks efficacy against established EO771 breast cancer tumors. In contrast, we observe tumor regression mediated by CD8+ T cells against Nedd8 deficient EO771 tumors after PD-1 blockade. In essence, we provide evidence that NEDD8 is conditionally essential in TNBC and presents as a synergistic drug target for PD-1/L1 blockade therapy.
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Affiliation(s)
- Irineos Papakyriacou
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ginte Kutkaite
- Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, Martinsried, Germany
| | - Marta Rúbies Bedós
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Divya Nagarajan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Liam P Alford
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Michael P Menden
- Computational Health Center, Helmholtz Munich, Neuherberg, Germany
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Yumeng Mao
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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2
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Kristenson L, Badami C, Ljungberg A, Islamagic E, Tian Y, Xie G, Hussein BA, Pesce S, Tang KW, Thorén FB. Deletion of the TMEM30A gene enables leukemic cell evasion of NK cell cytotoxicity. Proc Natl Acad Sci U S A 2024; 121:e2316447121. [PMID: 38557174 PMCID: PMC11009675 DOI: 10.1073/pnas.2316447121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
Natural killer (NK) cell immunotherapy has gained attention as a promising strategy for treatment of various malignancies. In this study, we used a genome-wide CRISPR screen to identify genes that provide protection or susceptibility to NK cell cytotoxicity. The screen confirmed the role of several genes in NK cell regulation, such as genes involved in interferon-γ signaling and antigen presentation, as well as genes encoding the NK cell receptor ligands B7-H6 and CD58. Notably, the gene TMEM30A, encoding CDC50A-beta-subunit of the flippase shuttling phospholipids in the plasma membrane, emerged as crucial for NK cell killing. Accordingly, a broad range of TMEM30A knock-out (KO) leukemia and lymphoma cells displayed increased surface levels of phosphatidylserine (PtdSer). TMEM30A KO cells triggered less NK cell degranulation, cytokine production and displayed lower susceptibility to NK cell cytotoxicity. Blockade of PtdSer or the inhibitory receptor TIM-3, restored the NK cell ability to eliminate TMEM30A-mutated cells. The key role of the TIM-3 - PtdSer interaction for NK cell regulation was further substantiated by disruption of the receptor gene in primary NK cells, which significantly reduced the impact of elevated PtdSer in TMEM30A KO leukemic cells. Our study underscores the potential significance of agents targeting the interaction between PtdSer and TIM-3 in the realm of cancer immunotherapy.
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Affiliation(s)
- Linnea Kristenson
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 90, Sweden
| | - Chiara Badami
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 90, Sweden
| | - Angelica Ljungberg
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
| | - Erna Islamagic
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 90, Sweden
| | - Yarong Tian
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 46, Sweden
| | - Guojiang Xie
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 46, Sweden
| | - Brwa Ali Hussein
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 90, Sweden
| | - Silvia Pesce
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Dipartimento di Medicina Sperimentale, Università di Genova, Genoa16132, Italy
| | - Ka-Wei Tang
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 46, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg413 46, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg413 90, Sweden
| | - Fredrik B. Thorén
- Tumor Immunology (TIMM) Laboratory at Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg413 90, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg413 90, Sweden
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3
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Zhao YQ, Jin HR, Kim D, Jung SH, Liu S, Wan J, Lo HY, Fu XQ, Wang Q, Hao C, Bellail AC. SUMO1 degrader induces ER stress and ROS accumulation through deSUMOylation of TCF4 and inhibition of its transcription of StarD7 in colon cancer. Mol Carcinog 2023; 62:1249-1262. [PMID: 37191369 PMCID: PMC10524896 DOI: 10.1002/mc.23560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/09/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
Small molecule degraders of small ubiquitin-related modifier 1 (SUMO1) induce SUMO1 degradation in colon cancer cells and inhibits the cancer cell growth; however, it is unclear how SUMO1 degradation leads to the anticancer activity of the degraders. Genome-wide CRISPR-Cas9 knockout screen has identified StAR-related lipid transfer domain containing 7 (StarD7) as a critical gene for the degrader's anticancer activity. Here, we show that both StarD7 mRNA and protein are overexpressed in human colon cancer and its knockout significantly reduces colon cancer cell growth and xenograft progression. The treatment with the SUMO1 degrader lead compound HB007 reduces StarD7 mRNA and protein levels and increases endoplasmic reticulum (ER) stress and reactive oxygen species (ROS) production in colon cancer cells and three-dimensional (3D) organoids. The study further provides a novel mechanism of the compound anticancer activity that SUMO1 degrader-induced decrease of StarD7 occur through degradation of SUMO1, deSUMOylation and degradation of T cell-specific transcription 4 (TCF4) and thereby inhibition of its transcription of StarD7 in colon cancer cells, 3D organoids and patient-derived xenografts (PDX).
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Affiliation(s)
- Yin Quan Zhao
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin Province, 130021, China
- School of Life Sciences, Jilin University, Changchun, Jilin Province, 130012, China
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hong Ri Jin
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Daeho Kim
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sung Han Jung
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ho-Yin Lo
- Synovel Laboratory LLC, Danbury, CT 06811, USA
| | - Xue Qi Fu
- School of Life Sciences, Jilin University, Changchun, Jilin Province, 130012, China
| | - Quan Wang
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin Province, 130021, China
| | - Chunhai Hao
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anita C. Bellail
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- HB Therapeutics Inc. Indianapolis, IN 46202, USA
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4
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Moretton A, Kourtis S, Gañez Zapater A, Calabrò C, Espinar Calvo ML, Fontaine F, Darai E, Abad Cortel E, Block S, Pascual‐Reguant L, Pardo‐Lorente N, Ghose R, Vander Heiden MG, Janic A, Müller AC, Loizou JI, Sdelci S. A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability. Mol Syst Biol 2023; 19:e11267. [PMID: 37259925 PMCID: PMC10333845 DOI: 10.15252/msb.202211267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Abstract
While cellular metabolism impacts the DNA damage response, a systematic understanding of the metabolic requirements that are crucial for DNA damage repair has yet to be achieved. Here, we investigate the metabolic enzymes and processes that are essential for the resolution of DNA damage. By integrating functional genomics with chromatin proteomics and metabolomics, we provide a detailed description of the interplay between cellular metabolism and the DNA damage response. Further analysis identified that Peroxiredoxin 1, PRDX1, contributes to the DNA damage repair. During the DNA damage response, PRDX1 translocates to the nucleus where it reduces DNA damage-induced nuclear reactive oxygen species. Moreover, PRDX1 loss lowers aspartate availability, which is required for the DNA damage-induced upregulation of de novo nucleotide synthesis. In the absence of PRDX1, cells accumulate replication stress and DNA damage, leading to proliferation defects that are exacerbated in the presence of etoposide, thus revealing a role for PRDX1 as a DNA damage surveillance factor.
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Affiliation(s)
- Amandine Moretton
- Center for Cancer Research, Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Savvas Kourtis
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Antoni Gañez Zapater
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Chiara Calabrò
- Center for Cancer Research, Comprehensive Cancer CenterMedical University of ViennaViennaAustria
| | | | - Frédéric Fontaine
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Evangelia Darai
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Etna Abad Cortel
- Department of Medicine and Life SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - Samuel Block
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Laura Pascual‐Reguant
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Natalia Pardo‐Lorente
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Ritobrata Ghose
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Dana‐Farber Cancer InstituteBostonMAUSA
| | - Ana Janic
- Department of Medicine and Life SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Joanna I Loizou
- Center for Cancer Research, Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Sara Sdelci
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
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5
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Colicchia V, Häggblad M, Sirozh O, Porebski B, Balan M, Li X, Lidemalm L, Carreras‐Puigvert J, Hühn D, Fernandez‐Capetillo O. New regulators of the tetracycline-inducible gene expression system identified by chemical and genetic screens. FEBS Open Bio 2022; 12:1896-1908. [PMID: 36062323 PMCID: PMC9527584 DOI: 10.1002/2211-5463.13482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/01/2022] [Accepted: 09/02/2022] [Indexed: 12/14/2022] Open
Abstract
The tetracycline repressor (tetR)-regulated system is a widely used tool to specifically control gene expression in mammalian cells. Based on this system, we generated a human osteosarcoma cell line, which allows for the inducible expression of an EGFP fusion of the TAR DNA-binding protein 43 (TDP-43), which has been linked to neurodegenerative diseases. Consistent with previous findings, TDP-43 overexpression led to the accumulation of aggregates and limited the viability of U2OS. Using this inducible system, we conducted a chemical screen with a library that included FDA-approved drugs. While the primary screen identified several compounds that prevented TDP-43 toxicity, further experiments revealed that these chemicals abrogated the doxycycline-dependent TDP-43 expression. This antagonistic effect was observed with both doxycycline and tetracycline, and in several Tet-On cell lines expressing different genes, confirming the general effect of these compounds as inhibitors of the tetR system. Using the same cell line, a genome-wide CRISPR/Cas9 screen identified epigenetic regulators such as the G9a methyltransferase and TRIM28 as potential modifiers of TDP-43 toxicity. Yet again, further experiments revealed that G9a inhibition or TRIM28 loss prevented doxycycline-dependent expression of TDP-43. In summary, we have identified new chemical and genetic regulators of the tetR system, thereby raising awareness of the limitations of this approach to conduct chemical or genetic screening in mammalian cells.
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Affiliation(s)
- Valeria Colicchia
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and BiophysicsKarolinska InstituteStockholmSweden,Present address:
Department of BiologyUniversity of Rome Tor VergataItaly
| | - Maria Häggblad
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and BiophysicsKarolinska InstituteStockholmSweden
| | - Oleksandra Sirozh
- Genomic Instability GroupSpanish National Cancer Research Centre (CNIO)MadridSpain
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and BiophysicsKarolinska InstituteStockholmSweden
| | - Mirela Balan
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and BiophysicsKarolinska InstituteStockholmSweden
| | - Xuexin Li
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and BiophysicsKarolinska InstituteStockholmSweden
| | - Louise Lidemalm
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and BiophysicsKarolinska InstituteStockholmSweden
| | - Jordi Carreras‐Puigvert
- Present address:
Department of BiologyUniversity of Rome Tor VergataItaly,Present address:
Department of Pharmaceutical Biosciences and Science for Life LaboratoryUppsala UniversitySweden
| | - Daniela Hühn
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and BiophysicsKarolinska InstituteStockholmSweden
| | - Oscar Fernandez‐Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and BiophysicsKarolinska InstituteStockholmSweden,Genomic Instability GroupSpanish National Cancer Research Centre (CNIO)MadridSpain
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6
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Gubat J, Selvaraju K, Sjöstrand L, Kumar Singh D, Turkina MV, Schmierer B, Sabatier P, Zubarev RA, Linder S, D’Arcy P. Comprehensive Target Screening and Cellular Profiling of the Cancer-Active Compound b-AP15 Indicate Abrogation of Protein Homeostasis and Organelle Dysfunction as the Primary Mechanism of Action. Front Oncol 2022; 12:852980. [PMID: 35530310 PMCID: PMC9076133 DOI: 10.3389/fonc.2022.852980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/17/2022] [Indexed: 12/11/2022] Open
Abstract
Dienone compounds have been demonstrated to display tumor-selective anti-cancer activity independently of the mutational status of TP53. Previous studies have shown that cell death elicited by this class of compounds is associated with inhibition of the ubiquitin-proteasome system (UPS). Here we extend previous findings by showing that the dienone compound b-AP15 inhibits proteasomal degradation of long-lived proteins. We show that exposure to b-AP15 results in increased association of the chaperones VCP/p97/Cdc48 and BAG6 with proteasomes. Comparisons between the gene expression profile generated by b-AP15 to those elicited by siRNA showed that knock-down of the proteasome-associated deubiquitinase (DUB) USP14 is the closest related to drug response. USP14 is a validated target for b-AP15 and we show that b-AP15 binds covalently to two cysteines, Cys203 and Cys257, in the ubiquitin-binding pocket of the enzyme. Consistent with this, deletion of USP14 resulted in decreased sensitivity to b-AP15. Targeting of USP14 was, however, found to not fully account for the observed proteasome inhibition. In search for additional targets, we utilized genome-wide CRISPR/Cas9 library screening and Proteome Integral Solubility Alteration (PISA) to identify mechanistically essential genes and b-AP15 interacting proteins respectively. Deletion of genes encoding mitochondrial proteins decreased the sensitivity to b-AP15, suggesting that mitochondrial dysfunction is coupled to cell death induced by b-AP15. Enzymes known to be involved in Phase II detoxification such as aldo-ketoreductases and glutathione-S-transferases were identified as b-AP15-targets using PISA. The finding that different exploratory approaches yielded different results may be explained in terms of a “target” not necessarily connected to the “mechanism of action” thus highlighting the importance of a holistic approach in the identification of drug targets. We conclude that b-AP15, and likely also other dienone compounds of the same class, affect protein degradation and proteasome function at more than one level.
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Affiliation(s)
- Johannes Gubat
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Karthik Selvaraju
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Linda Sjöstrand
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Dhananjay Kumar Singh
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Pharmacy, Central University of South Bihar, Gaya, India
| | - Maria V. Turkina
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Bernhard Schmierer
- Department of Medical Biochemistry and Biophysics, Division of Chemical Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pierre Sabatier
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry I, Karolinska Institutet, Stockholm, Sweden
| | - Roman A. Zubarev
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry I, Karolinska Institutet, Stockholm, Sweden
- Department of Pharmacological and Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Stig Linder
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Pádraig D’Arcy
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- *Correspondence: Pádraig D’Arcy,
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7
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DeHart L, Yockey OP, Bakke J. Identification of Essential Genes Using Sequential CRISPR and siRNA Screens. Methods Mol Biol 2022; 2377:89-107. [PMID: 34709612 DOI: 10.1007/978-1-0716-1720-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Genome-wide CRISPR and siRNA screening methodologies are powerful tools that are aptly suited to the discovery of essential genes. In this chapter, we outline our methods to conduct sequential CRISPR and siRNA screens to quickly and efficiently identify essential genes within a collection of cell lines. The utilization of both screening methodologies provides a pipeline that minimizes costs and time while enabling the robust detection of candidate genes.
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Affiliation(s)
- Luke DeHart
- Department of Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, MI, USA
| | - Oliver P Yockey
- Department of Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, MI, USA
| | - Jesse Bakke
- Department of Foundational Sciences, College of Medicine, Central Michigan University, Mount Pleasant, MI, USA.
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8
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Bellail AC, Jin HR, Lo HY, Jung SH, Hamdouchi C, Kim D, Higgins RK, Blanck M, le Sage C, Cross BCS, Li J, Mosley AL, Wijeratne AB, Jiang W, Ghosh M, Zhao YQ, Hauck PM, Shekhar A, Hao C. Ubiquitination and degradation of SUMO1 by small-molecule degraders extends survival of mice with patient-derived tumors. Sci Transl Med 2021; 13:eabh1486. [PMID: 34644148 DOI: 10.1126/scitranslmed.abh1486] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Anita C Bellail
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA.,HB Therapeutics Inc., Indianapolis, IN 46202, USA
| | - Hong Ri Jin
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ho-Yin Lo
- Synovel Laboratory LLC, Danbury, CT 06811, USA
| | - Sung Han Jung
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Chafiq Hamdouchi
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Daeho Kim
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ryan K Higgins
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | | | | | - Jing Li
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Amber L Mosley
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Aruna B Wijeratne
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wen Jiang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Manali Ghosh
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Yin Quan Zhao
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Paula M Hauck
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anantha Shekhar
- Department of Psychiatry and Indiana Clinical and Translational Sciences Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Chunhai Hao
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA.,Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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9
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Giovannucci TA, Salomons FA, Haraldsson M, Elfman LHM, Wickström M, Young P, Lundbäck T, Eirich J, Altun M, Jafari R, Gustavsson AL, Johnsen JI, Dantuma NP. Inhibition of the ubiquitin-proteasome system by an NQO1-activatable compound. Cell Death Dis 2021; 12:914. [PMID: 34615851 PMCID: PMC8494907 DOI: 10.1038/s41419-021-04191-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 11/10/2022]
Abstract
Malignant cells display an increased sensitivity towards drugs that reduce the function of the ubiquitin-proteasome system (UPS), which is the primary proteolytic system for destruction of aberrant proteins. Here, we report on the discovery of the bioactivatable compound CBK77, which causes an irreversible collapse of the UPS, accompanied by a general accumulation of ubiquitylated proteins and caspase-dependent cell death. CBK77 caused accumulation of ubiquitin-dependent, but not ubiquitin-independent, reporter substrates of the UPS, suggesting a selective effect on ubiquitin-dependent proteolysis. In a genome-wide CRISPR interference screen, we identified the redox enzyme NAD(P)H:quinone oxidoreductase 1 (NQO1) as a critical mediator of CBK77 activity, and further demonstrated its role as the compound bioactivator. Through affinity-based proteomics, we found that CBK77 covalently interacts with ubiquitin. In vitro experiments showed that CBK77-treated ubiquitin conjugates were less susceptible to disassembly by deubiquitylating enzymes. In vivo efficacy of CBK77 was validated by reduced growth of NQO1-proficient human adenocarcinoma cells in nude mice treated with CBK77. This first-in-class NQO1-activatable UPS inhibitor suggests that it may be possible to exploit the intracellular environment in malignant cells for leveraging the impact of compounds that impair the UPS.
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Affiliation(s)
- Tatiana A Giovannucci
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Florian A Salomons
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Martin Haraldsson
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Lotta H M Elfman
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Malin Wickström
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Patrick Young
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Stockholm, Sweden
- Mechanistic & Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Jürgen Eirich
- Science for Life Laboratory, Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Solna, Stockholm, Sweden
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Solna, Stockholm, Sweden
- Institute of Plant Biology and Biotechnology, University of Muenster, 48143, Muenster, Germany
| | - Mikael Altun
- Science for Life Laboratory, Department of Laboratory Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Rozbeh Jafari
- Science for Life Laboratory, Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Stockholm, Sweden
| | - John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Nico P Dantuma
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden.
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10
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Gozgit JM, Vasbinder MM, Abo RP, Kunii K, Kuplast-Barr KG, Gui B, Lu AZ, Molina JR, Minissale E, Swinger KK, Wigle TJ, Blackwell DJ, Majer CR, Ren Y, Niepel M, Varsamis ZA, Nayak SP, Bamberg E, Mo JR, Church WD, Mady ASA, Song J, Utley L, Rao PE, Mitchison TJ, Kuntz KW, Richon VM, Keilhack H. PARP7 negatively regulates the type I interferon response in cancer cells and its inhibition triggers antitumor immunity. Cancer Cell 2021; 39:1214-1226.e10. [PMID: 34375612 DOI: 10.1016/j.ccell.2021.06.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 05/25/2021] [Accepted: 06/25/2021] [Indexed: 01/07/2023]
Abstract
PARP7 is a monoPARP that catalyzes the transfer of single units of ADP-ribose onto substrates to change their function. Here, we identify PARP7 as a negative regulator of nucleic acid sensing in tumor cells. Inhibition of PARP7 restores type I interferon (IFN) signaling responses to nucleic acids in tumor models. Restored signaling can directly inhibit cell proliferation and activate the immune system, both of which contribute to tumor regression. Oral dosing of the PARP7 small-molecule inhibitor, RBN-2397, results in complete tumor regression in a lung cancer xenograft and induces tumor-specific adaptive immune memory in an immunocompetent mouse cancer model, dependent on inducing type I IFN signaling in tumor cells. PARP7 is a therapeutic target whose inhibition induces both cancer cell-autonomous and immune stimulatory effects via enhanced IFN signaling. These data support the targeting of a monoPARP in cancer and introduce a potent and selective PARP7 inhibitor to enter clinical development.
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Affiliation(s)
- Joseph M Gozgit
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA.
| | - Melissa M Vasbinder
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Ryan P Abo
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Kaiko Kunii
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | | | - Bin Gui
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Alvin Z Lu
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Jennifer R Molina
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Elena Minissale
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Kerren K Swinger
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Tim J Wigle
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | | | - Christina R Majer
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Yue Ren
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Mario Niepel
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | | | - Sunaina P Nayak
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Ellen Bamberg
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Jan-Rung Mo
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - W David Church
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Ahmed S A Mady
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Jeff Song
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Luke Utley
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | | | - Timothy J Mitchison
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert 536, Boston, MA 02115, USA
| | - Kevin W Kuntz
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Victoria M Richon
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Heike Keilhack
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA.
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11
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Diehl V, Wegner M, Grumati P, Husnjak K, Schaubeck S, Gubas A, Shah V, Polat I, Langschied F, Prieto-Garcia C, Müller K, Kalousi A, Ebersberger I, Brandts C, Dikic I, Kaulich M. Minimized combinatorial CRISPR screens identify genetic interactions in autophagy. Nucleic Acids Res 2021; 49:5684-5704. [PMID: 33956155 PMCID: PMC8191801 DOI: 10.1093/nar/gkab309] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/01/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Combinatorial CRISPR-Cas screens have advanced the mapping of genetic interactions, but their experimental scale limits the number of targetable gene combinations. Here, we describe 3Cs multiplexing, a rapid and scalable method to generate highly diverse and uniformly distributed combinatorial CRISPR libraries. We demonstrate that the library distribution skew is the critical determinant of its required screening coverage. By circumventing iterative cloning of PCR-amplified oligonucleotides, 3Cs multiplexing facilitates the generation of combinatorial CRISPR libraries with low distribution skews. We show that combinatorial 3Cs libraries can be screened with minimal coverages, reducing associated efforts and costs at least 10-fold. We apply a 3Cs multiplexing library targeting 12,736 autophagy gene combinations with 247,032 paired gRNAs in viability and reporter-based enrichment screens. In the viability screen, we identify, among others, the synthetic lethal WDR45B-PIK3R4 and the proliferation-enhancing ATG7-KEAP1 genetic interactions. In the reporter-based screen, we identify over 1,570 essential genetic interactions for autophagy flux, including interactions among paralogous genes, namely ATG2A-ATG2B, GABARAP-MAP1LC3B and GABARAP-GABARAPL2. However, we only observe few genetic interactions within paralogous gene families of more than two members, indicating functional compensation between them. This work establishes 3Cs multiplexing as a platform for genetic interaction screens at scale.
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Affiliation(s)
- Valentina Diehl
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Martin Wegner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Paolo Grumati
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Simone Schaubeck
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Andrea Gubas
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Varun Jayeshkumar Shah
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ibrahim H Polat
- Department of Medicine, Hematology/Oncology, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
| | - Felix Langschied
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Cristian Prieto-Garcia
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Konstantin Müller
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alkmini Kalousi
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Christian H Brandts
- Department of Medicine, Hematology/Oncology, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- University Cancer Center Frankfurt (UCT), University Hospital, Goethe University, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
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12
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Li KC, Girardi E, Kartnig F, Grosche S, Pemovska T, Bigenzahn JW, Goldmann U, Sedlyarov V, Bensimon A, Schick S, Lin JMG, Gürtl B, Reil D, Klavins K, Kubicek S, Sdelci S, Superti-Furga G. Cell-surface SLC nucleoside transporters and purine levels modulate BRD4-dependent chromatin states. Nat Metab 2021; 3:651-664. [PMID: 33972798 PMCID: PMC7612075 DOI: 10.1038/s42255-021-00386-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023]
Abstract
Metabolism negotiates cell-endogenous requirements of energy, nutrients and building blocks with the immediate environment to enable various processes, including growth and differentiation. While there is an increasing number of examples of crosstalk between metabolism and chromatin, few involve uptake of exogenous metabolites. Solute carriers (SLCs) represent the largest group of transporters in the human genome and are responsible for the transport of a wide variety of substrates, including nutrients and metabolites. We aimed to investigate the possible involvement of SLC-mediated solutes uptake and cellular metabolism in regulating cellular epigenetic states. Here, we perform a CRISPR-Cas9 transporter-focused genetic screen and a metabolic compound library screen for the regulation of BRD4-dependent chromatin states in human myeloid leukaemia cells. Intersection of the two orthogonal approaches reveal that loss of transporters involved with purine transport or inhibition of de novo purine synthesis lead to dysfunction of BRD4-dependent transcriptional regulation. Through mechanistic characterization of the metabolic circuitry, we elucidate the convergence of SLC-mediated purine uptake and de novo purine synthesis on BRD4-chromatin occupancy. Moreover, adenine-related metabolite supplementation effectively restores BRD4 functionality on purine impairment. Our study highlights the specific role of purine/adenine metabolism in modulating BRD4-dependent epigenetic states.
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Affiliation(s)
- Kai-Chun Li
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Enrico Girardi
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Felix Kartnig
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sarah Grosche
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tea Pemovska
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johannes W Bigenzahn
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Ulrich Goldmann
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ariel Bensimon
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sandra Schick
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jung-Ming G Lin
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Bettina Gürtl
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniela Reil
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kristaps Klavins
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefan Kubicek
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sara Sdelci
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Giulio Superti-Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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13
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Kerek EM, Cromwell CR, Hubbard BP. Identification of Drug Resistance Genes Using a Pooled Lentiviral CRISPR/Cas9 Screening Approach. Methods Mol Biol 2021; 2381:227-242. [PMID: 34590280 DOI: 10.1007/978-1-0716-1740-3_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In addition to advancing the development of gene-editing therapeutics, CRISPR/Cas9 is transforming how functional genetic studies are carried out in the lab. By increasing the ease with which genetic information can be inserted, deleted, or edited in cell and organism models, it facilitates genotype-phenotype analysis. Moreover, CRISPR/Cas9 has revolutionized the speed at which new genes underlying a particular phenotype can be identified through its application in genomic screens. Arrayed high-throughput and pooled lentiviral-based CRISPR/Cas9 screens have now been used in a wide variety of contexts, including the identification of essential genes, genes involved in cancer metastasis and tumor growth, and even genes involved in viral response. This technology has also been successfully used to identify drug targets and drug resistance mechanisms. Here, we provide a detailed protocol for performing a genome-wide pooled lentiviral CRISPR/Cas9 knockout screen to identify genetic modulators of a small-molecule drug. While we exemplify how to identify genes involved in resistance to a cytotoxic histone deacetylase inhibitor, Trichostatin A (TSA), the workflow we present can easily be adapted to different types of selections and other types of exogenous ligands or drugs.
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Affiliation(s)
- Evan M Kerek
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
| | | | - Basil P Hubbard
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada.
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14
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Jimenez-Duran G, Luque-Martin R, Patel M, Koppe E, Bernard S, Sharp C, Buchan N, Rea C, de Winther MPJ, Turan N, Angell D, Wells CA, Cousins R, Mander PK, Masters SL. Pharmacological validation of targets regulating CD14 during macrophage differentiation. EBioMedicine 2020; 61:103039. [PMID: 33038762 PMCID: PMC7648121 DOI: 10.1016/j.ebiom.2020.103039] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/13/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022] Open
Abstract
The signalling receptor for LPS, CD14, is a key marker of, and facilitator for, pro-inflammatory macrophage function. Pro-inflammatory macrophage differentiation remains a process facilitating a broad array of disease pathologies, and has recently emerged as a potential target against cytokine storm in COVID19. Here, we perform a whole-genome CRISPR screen to identify essential nodes regulating CD14 expression in myeloid cells, using the differentiation of THP-1 cells as a starting point. This strategy uncovers many known pathways required for CD14 expression and regulating macrophage differentiation while additionally providing a list of novel targets either promoting or limiting this process. To speed translation of these results, we have then taken the approach of independently validating hits from the screen using well-curated small molecules. In this manner, we identify pharmacologically tractable hits that can either increase CD14 expression on non-differentiated monocytes or prevent CD14 upregulation during macrophage differentiation. An inhibitor for one of these targets, MAP2K3, translates through to studies on primary human monocytes, where it prevents upregulation of CD14 following M-CSF induced differentiation, and pro-inflammatory cytokine production in response to LPS. Therefore, this screening cascade has rapidly identified pharmacologically tractable nodes regulating a critical disease-relevant process.
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Affiliation(s)
- Gisela Jimenez-Duran
- Immunology Catalyst, Immunology Network, Adaptive Immunity Research Unit, GSK, Stevenage, UK; Institute of Infection and Immunity, Medical School, University Hospital of Wales, Cardiff University, Wales, UK
| | - Rosario Luque-Martin
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Meghana Patel
- Immunology Catalyst, Immunology Network, Adaptive Immunity Research Unit, GSK, Stevenage, UK; Cambridge Academy of Therapeutic Sciences (CATS), University of Cambridge, 17 Mill Lane, Cambridge, CB2 1RX
| | - Emma Koppe
- Immunology Catalyst, Immunology Network, Adaptive Immunity Research Unit, GSK, Stevenage, UK
| | - Sharon Bernard
- Immuno-Epigenetics, Adaptive Immunity Research Unit, GSK, Stevenage, UK
| | - Catriona Sharp
- Immuno-Epigenetics, Adaptive Immunity Research Unit, GSK, Stevenage, UK
| | - Natalie Buchan
- Human Genetics Computational Biology, Human Genetics, GSK, Stevenage, UK
| | - Ceara Rea
- Molecular Design, Data and Computational Sciences, GSK, Stevenage, UK
| | - Menno P J de Winther
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Nil Turan
- Immuno-Epigenetics, Adaptive Immunity Research Unit, GSK, Stevenage, UK
| | - Davina Angell
- Immuno-Epigenetics, Adaptive Immunity Research Unit, GSK, Stevenage, UK
| | - Christine A Wells
- Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Rick Cousins
- Immunology Catalyst, Immunology Network, Adaptive Immunity Research Unit, GSK, Stevenage, UK; Cinnabar Consulting Limited, Bedford, UK
| | - Palwinder K Mander
- Immuno-Epigenetics, Adaptive Immunity Research Unit, GSK, Stevenage, UK.
| | - Seth L Masters
- Immunology Catalyst, Immunology Network, Adaptive Immunity Research Unit, GSK, Stevenage, UK; Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Australia.
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15
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Blanck M, Budnik-Zawilska MB, Lenger SR, McGonigle JE, Martin GR, le Sage C, Lawo S, Pemberton HN, Tiwana GS, Sorrell DA, Cross BC. A Flexible, Pooled CRISPR Library for Drug Development Screens. CRISPR J 2020; 3:211-222. [PMID: 33054419 PMCID: PMC7567641 DOI: 10.1089/crispr.2019.0066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Functional genomic screening with CRISPR has provided a powerful and precise new way to interrogate the phenotypic consequences of gene manipulation in high-throughput, unbiased analyses. However, some experimental paradigms prove especially challenging and require carefully and appropriately adapted screening approaches. In particular, negative selection (or sensitivity) screening, often the most experimentally desirable modality of screening, has remained a challenge in drug discovery. Here we assess whether our new, modular genome-wide pooled CRISPR library can improve negative selection CRISPR screening and add utility throughout the drug development pipeline. Our pooled library is split into three parts, allowing it to be scaled to accommodate the experimental challenges encountered during drug development, such as target identification using unlimited cell numbers compared with target identification studies for cell populations where cell numbers are limiting. To test our new library, we chose to look for drug-gene interactions using a well-described small molecule inhibitor targeting poly(ADP-ribose) polymerase 1 (PARP1), and in particular to identify genes which sensitise cells to this drug. We simulate hit identification and performance using each library partition and support these findings through orthogonal drug combination cell panel screening. We also compare our data with a recently published CRISPR sensitivity dataset obtained using the same PARP1 inhibitor. Overall, our data indicate that generating a comprehensive CRISPR knockout screening library where the number of guides can be scaled to suit the biological question being addressed allows a library to have multiple uses throughout the drug development pipeline, and that initial validation of hits can be achieved through high-throughput cell panels screens where clinical grade chemical or biological matter exist.
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Affiliation(s)
| | | | | | | | | | | | - Steffen Lawo
- Max Planck Institute for Biology of Ageing, Cologne, Germany
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16
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Abstract
The discovery of CRISPR-Cas9 systems has fueled a rapid expansion of gene editing
adoption and has impacted pharmaceutical and biotechnology research
substantially. Here, gene editing is used at an industrial scale to identify and
validate new biological targets for precision medicines, with functional genomic
screening having an increasingly important role. Functional genomic strategies
provide a crucial link between observed biological phenomena and the genes that
influence and drive those phenomena. Although such studies are not new, the use
of CRISPR-Cas9 systems in this arena is providing more robust datasets for
target identification and validation. CRISPR-based screening approaches are also
useful later in the drug development pipeline for understanding drug resistance
and sensitivity ahead of entering clinical trials. This review examines the
developing landscape for CRISPR screening technologies within the pharmaceutical
industry and explores the next steps for this constantly evolving screening
platform.
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17
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Moskovskich A, Goldmann U, Kartnig F, Lindinger S, Konecka J, Fiume G, Girardi E, Superti-Furga G. The transporters SLC35A1 and SLC30A1 play opposite roles in cell survival upon VSV virus infection. Sci Rep 2019; 9:10471. [PMID: 31320712 PMCID: PMC6639343 DOI: 10.1038/s41598-019-46952-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/04/2019] [Indexed: 12/19/2022] Open
Abstract
Host factor requirements for different classes of viruses have not been fully unraveled. Replication of the viral genome and synthesis of viral proteins within the human host cell are associated with an increased demand for nutrients and specific metabolites. With more than 400 acknowledged members to date in humans, solute carriers (SLCs) represent the largest family of transmembrane proteins dedicated to the transport of ions and small molecules such as amino acids, sugars and nucleotides. Consistent with their impact on cellular metabolism, several SLCs have been implicated as host factors affecting the viral life cycle and the cellular response to infection. In this study, we aimed at characterizing the role of host SLCs in cell survival upon viral infection by performing unbiased genetic screens using a focused CRISPR knockout library. Genetic screens with the cytolytic vesicular stomatitis virus (VSV) showed that the loss of two SLCs genes, encoding the sialic acid transporter SLC35A1/CST and the zinc transporter SLC30A1/ZnT1, affected cell survival upon infection. Further characterization of these genes suggests a role for both of these transporters in the apoptotic response induced by VSV, offering new insights into the cellular response to oncolytic virus infections.
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Affiliation(s)
- Anna Moskovskich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Ulrich Goldmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Felix Kartnig
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Sabrina Lindinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Justyna Konecka
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Giuseppe Fiume
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Enrico Girardi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria.
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090, Vienna, Austria.
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18
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Ford K, McDonald D, Mali P. Functional Genomics via CRISPR-Cas. J Mol Biol 2019; 431:48-65. [PMID: 29959923 PMCID: PMC6309720 DOI: 10.1016/j.jmb.2018.06.034] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/02/2018] [Accepted: 06/14/2018] [Indexed: 12/22/2022]
Abstract
RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas proteins have recently emerged as versatile tools to investigate and engineer the genome. The programmability of CRISPR-Cas has proven especially useful for probing genomic function in high-throughput. Facile single-guide RNA library synthesis allows CRISPR-Cas screening to rapidly investigate the functional consequences of genomic, transcriptomic, and epigenomic perturbations. Furthermore, by combining CRISPR-Cas perturbations with downstream single-cell analyses (flow cytometry, expression profiling, etc.), forward screens can generate robust data sets linking genotypes to complex cellular phenotypes. In the following review, we highlight recent advances in CRISPR-Cas genomic screening while outlining protocols and pitfalls associated with screen implementation. Finally, we describe current challenges limiting the utility of CRISPR-Cas screening as well as future research needed to resolve these impediments. As CRISPR-Cas technologies develop, so too will their clinical applications. Looking ahead, patient centric functional screening in primary cells will likely play a greater role in disease management and therapeutic development.
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Affiliation(s)
- Kyle Ford
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Daniella McDonald
- Biomedical Sciences Graduate Program, University of California, San Diego, San Diego, CA 92093, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
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19
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Sanson KR, Hanna RE, Hegde M, Donovan KF, Strand C, Sullender ME, Vaimberg EW, Goodale A, Root DE, Piccioni F, Doench JG. Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. Nat Commun 2018; 9:5416. [PMID: 30575746 PMCID: PMC6303322 DOI: 10.1038/s41467-018-07901-8] [Citation(s) in RCA: 463] [Impact Index Per Article: 77.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/05/2018] [Indexed: 12/26/2022] Open
Abstract
The creation of genome-wide libraries for CRISPR knockout (CRISPRko), interference (CRISPRi), and activation (CRISPRa) has enabled the systematic interrogation of gene function. Here, we show that our recently-described CRISPRko library (Brunello) is more effective than previously published libraries at distinguishing essential and non-essential genes, providing approximately the same perturbation-level performance improvement over GeCKO libraries as GeCKO provided over RNAi. Additionally, we present genome-wide libraries for CRISPRi (Dolcetto) and CRISPRa (Calabrese), and show in negative selection screens that Dolcetto, with fewer sgRNAs per gene, outperforms existing CRISPRi libraries and achieves comparable performance to CRISPRko in detecting essential genes. We also perform positive selection CRISPRa screens and demonstrate that Calabrese outperforms the SAM approach at identifying vemurafenib resistance genes. We further compare CRISPRa to genome-scale libraries of open reading frames (ORFs). Together, these libraries represent a suite of genome-wide tools to efficiently interrogate gene function with multiple modalities.
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Affiliation(s)
- Kendall R Sanson
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Ruth E Hanna
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Mudra Hegde
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Katherine F Donovan
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Christine Strand
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Meagan E Sullender
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Emma W Vaimberg
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Amy Goodale
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - David E Root
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Federica Piccioni
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA, 02142, USA.
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20
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le Sage C, Lawo S, Panicker P, Scales TME, Rahman SA, Little AS, McCarthy NJ, Moore JD, Cross BCS. Dual direction CRISPR transcriptional regulation screening uncovers gene networks driving drug resistance. Sci Rep 2017; 7:17693. [PMID: 29255251 PMCID: PMC5735189 DOI: 10.1038/s41598-017-18172-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/07/2017] [Indexed: 01/10/2023] Open
Abstract
Pooled CRISPR–Cas9 knock out screens provide a valuable addition to the methods available for novel drug target identification and validation. However, where gene editing is targeted to amplified loci, the resulting multiple DNA cleavage events can be a cause of false positive hit identification. The generation of nuclease deficient versions of Cas9 has enabled the development of two additional techniques – CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) – that enable the repression or overexpression, respectively, of target genes. Here we report the first direct combination of all three approaches (CRISPRko, CRISPRi and CRISPRa) in the context of genome-wide screens to identify components that influence resistance and sensitivity to the BRAF inhibitor, vemurafenib. The pairing of both loss- and gain-of-function datasets reveals complex gene networks which control drug response and illustrates how such data can add substantial confidence to target identification and validation analyses.
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Affiliation(s)
- Carlos le Sage
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Steffen Lawo
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Prince Panicker
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Tim M E Scales
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Syed Asad Rahman
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Annette S Little
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Nicola J McCarthy
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Jonathan D Moore
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom
| | - Benedict C S Cross
- Horizon Discovery, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, United Kingdom.
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21
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Montalbano A, Canver MC, Sanjana NE. High-Throughput Approaches to Pinpoint Function within the Noncoding Genome. Mol Cell 2017; 68:44-59. [PMID: 28985510 PMCID: PMC5701515 DOI: 10.1016/j.molcel.2017.09.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/13/2017] [Accepted: 09/13/2017] [Indexed: 12/26/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas nuclease system is a powerful tool for genome editing, and its simple programmability has enabled high-throughput genetic and epigenetic studies. These high-throughput approaches offer investigators a toolkit for functional interrogation of not only protein-coding genes but also noncoding DNA. Historically, noncoding DNA has lacked the detailed characterization that has been applied to protein-coding genes in large part because there has not been a robust set of methodologies for perturbing these regions. Although the majority of high-throughput CRISPR screens have focused on the coding genome to date, an increasing number of CRISPR screens targeting noncoding genomic regions continue to emerge. Here, we review high-throughput CRISPR-based approaches to uncover and understand functional elements within the noncoding genome and discuss practical aspects of noncoding library design and screen analysis.
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Affiliation(s)
- Antonino Montalbano
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | | | - Neville E Sanjana
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA.
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22
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Ong SH, Li Y, Koike-Yusa H, Yusa K. Optimised metrics for CRISPR-KO screens with second-generation gRNA libraries. Sci Rep 2017; 7:7384. [PMID: 28785007 PMCID: PMC5547152 DOI: 10.1038/s41598-017-07827-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/03/2017] [Indexed: 12/26/2022] Open
Abstract
Genome-wide CRISPR-based knockout (CRISPR-KO) screening is an emerging technique which enables systematic genetic analysis of a cellular or molecular phenotype in question. Continuous improvements, such as modifications to the guide RNA (gRNA) scaffold and the development of gRNA on-target prediction algorithms, have since been made to increase their screening performance. We compared the performance of three available second-generation human genome-wide CRISPR-KO libraries that included at least one of the improvements, and examined the effect of gRNA scaffold, number of gRNAs per gene and number of replicates on screen performance. We identified duplicated screens using a library with 6 gRNAs per gene as providing the best trade-off. Despite the improvements, we found that each improved library still has library-specific false negatives and, for the first time, estimated the false negative rates of CRISPR-KO screens, which are between 10% and 20%. Our newly-defined optimal screening parameters would be helpful in designing screens and constructing bespoke gRNA libraries.
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Affiliation(s)
- Swee Hoe Ong
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Yilong Li
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Kosuke Yusa
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
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23
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Canver MC, Bauer DE, Orkin SH. Functional interrogation of non-coding DNA through CRISPR genome editing. Methods 2017; 121-122:118-129. [PMID: 28288828 PMCID: PMC5483188 DOI: 10.1016/j.ymeth.2017.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/18/2017] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA.
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Affiliation(s)
| | - Daniel E Bauer
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States.
| | - Stuart H Orkin
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States; Howard Hughes Medical Institute, Boston, MA 02115, United States.
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24
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Martinez E, Sanchez L, Vazquez N, Marks R, Cedillo R, Respondek C, Holguin M, Persans MW, Keniry M. A CRISPR View of Biological Mechanisms. Discoveries (Craiova) 2016; 4:e69. [PMID: 32309588 PMCID: PMC7159838 DOI: 10.15190/d.2016.16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/29/2016] [Accepted: 12/29/2016] [Indexed: 12/26/2022] Open
Abstract
A decade ago, only six manuscripts would be found on a PubMed search for "CRISPR," compared to 2,011 manuscripts in 2016. The purpose of this review is to discuss this emergent technology that has revolutionized molecular biological research in just a few years. Endogenous CRISPR mechanisms are harbored by bacteria and archaea as an adaptive defense system that targets foreign DNA from viruses and plasmids. CRISPR has been adapted as a genome editing tool in a plethora of organisms ranging from yeast to humans. This tool has been employed to create loss of function mutations, gain of function mutations, and tagged alleles in a wide range of settings. CRISPR is now extensively employed for genetic screens. CRISPR has also been adapted to study transcriptional regulation. This versatile and relatively facile technique has, and will be, tremendously impactful in research areas such as biomedical sciences, agriculture, and the basic sciences.
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Affiliation(s)
- Eduardo Martinez
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Lilia Sanchez
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Neftali Vazquez
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Rebecca Marks
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Raechel Cedillo
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Christa Respondek
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Martin Holguin
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Michael W. Persans
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
| | - Megan Keniry
- Department of Biology, University of Texas Rio Grande Valley, 1201 W. University Dr., Edinburg, TX 78539, USA
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