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See WR, Yousefi M, Ooi YS. A review of virus host factor discovery using CRISPR screening. mBio 2024:e0320523. [PMID: 39422472 DOI: 10.1128/mbio.03205-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2024] Open
Abstract
The emergence of genome-scale forward genetic screening techniques, such as Haploid Genetic screen and clustered regularly interspaced short palindromic repeats (CRISPR) knockout screen has opened new horizons in our understanding of virus infection biology. CRISPR screening has become a popular tool for the discovery of novel host factors for several viruses due to its specificity and efficiency in genome editing. Here, we review how CRISPR screening has revolutionized our understanding of virus-host interactions from scientific and technological viewpoints. A summary of the published screens conducted thus far to uncover virus host factors is presented, highlighting their experimental design and significant findings. We will outline relevant methods for customizing the CRISPR screening process to answer more specific hypotheses and compile a glossary of conducted CRISPR screens to show their design aspects. Furthermore, using flaviviruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as examples, we hope to offer a broad-based perspective on the capabilities of CRISPR screening to serve as a reference point to guide future unbiased discovery of virus host factors.
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Affiliation(s)
- Wayne Ren See
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Meisam Yousefi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Yaw Shin Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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2
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Yousefi M, See WR, Aw-Yong KL, Lee WS, Yong CL, Fanusi F, Smith GJD, Ooi EE, Li S, Ghosh S, Ooi YS. GeneRaMeN enables integration, comparison, and meta-analysis of multiple ranked gene lists to identify consensus, unique, and correlated genes. Brief Bioinform 2024; 25:bbae452. [PMID: 39293806 PMCID: PMC11410378 DOI: 10.1093/bib/bbae452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/15/2024] [Accepted: 08/30/2024] [Indexed: 09/20/2024] Open
Abstract
High-throughput experiments often produce ranked gene outputs, with forward genetic screening being a notable example. While there are various tools for analyzing individual datasets, those that perform comparative and meta-analytical examination of such ranked gene lists remain scarce. Here, we introduce Gene Rank Meta Analyzer (GeneRaMeN), an R Shiny tool utilizing rank statistics to facilitate the identification of consensus, unique, and correlated genes across multiple hit lists. We focused on two key topics to showcase GeneRaMeN: virus host factors and cancer dependencies. Using GeneRaMeN 'Rank Aggregation', we integrated 24 published and new flavivirus genetic screening datasets, including dengue, Japanese encephalitis, and Zika viruses. This meta-analysis yielded a consensus list of flavivirus host factors, elucidating the significant influence of cell line selection on screening outcomes. Similar analysis on 13 SARS-CoV-2 CRISPR screening datasets highlighted the pivotal role of meta-analysis in revealing redundant biological pathways exploited by the virus to enter human cells. Such redundancy was further underscored using GeneRaMeN's 'Rank Correlation', where a strong negative correlation was observed for host factors implicated in one entry pathway versus the alternate route. Utilizing GeneRaMeN's 'Rank Uniqueness', we analyzed human coronaviruses 229E, OC43, and SARS-CoV-2 datasets, identifying host factors uniquely associated with a defined subset of the screening datasets. Similar analyses were performed on over 1000 Cancer Dependency Map (DepMap) datasets spanning 19 human cancer types to reveal unique cancer vulnerabilities for each organ/tissue. GeneRaMeN, an efficient tool to integrate and maximize the usability of genetic screening datasets, is freely accessible via https://ysolab.shinyapps.io/GeneRaMeN.
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Affiliation(s)
- Meisam Yousefi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Wayne Ren See
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Kam Leng Aw-Yong
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Wai Suet Lee
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Cythia Lingli Yong
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Felic Fanusi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Gavin J D Smith
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Shang Li
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Sujoy Ghosh
- Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- Laboratory of Computational Biology, Pennington Biomedical Research Center, 6400 Perkins Road, Baton Rouge, LA 70808, United States
| | - Yaw Shin Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- A*STAR Infectious Diseases Laboratories (ID Labs), Agency for Science and Technology Research (A*STAR), 8A Biomedical Grove, #05-13 Immunos, Singapore 138648, Singapore
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3
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Cao Y, Li X, Pan Y, Wang H, Yang S, Hong L, Ye L. CRISPR-based genetic screens advance cancer immunology. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2571-0. [PMID: 39048715 DOI: 10.1007/s11427-023-2571-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/18/2024] [Indexed: 07/27/2024]
Abstract
CRISPR technologies have revolutionized research areas ranging from fundamental science to translational medicine. CRISPR-based genetic screens offer a powerful platform for unbiased screening in various fields, such as cancer immunology. Immune checkpoint blockade (ICB) therapy has been shown to strongly affect cancer treatment. However, the currently available ICBs are limited and do not work in all cancer patients. Pooled CRISPR screens enable the identification of previously unknown immune regulators that can regulate T-cell activation, cytotoxicity, persistence, infiltration into tumors, cytokine secretion, memory formation, T-cell metabolism, and CD4+ T-cell differentiation. These novel targets can be developed as new immunotherapies or used with the current ICBs as new combination therapies that may yield synergistic efficacy. Here, we review the progress made in the development of CRISPR technologies, particularly technological advances in CRISPR screens and their application in novel target identification for immunotherapy.
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Affiliation(s)
- Yuanfang Cao
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Xueting Li
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Yumu Pan
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Huahe Wang
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Siyu Yang
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Lingjuan Hong
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China
| | - Lupeng Ye
- Institute of Modern Biology, Nanjing University, Nanjing, 210008, China.
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Morgens DW, Gulyas L, Rivera-Madera A, Souza AS, Glaunsinger BA. From enhancers to genome conformation: complex transcriptional control underlies expression of a single herpesviral gene. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.08.548212. [PMID: 37461644 PMCID: PMC10350069 DOI: 10.1101/2023.07.08.548212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Complex transcriptional control is a conserved feature of both eukaryotes and the viruses that infect them. Here, we illustrate this by combining high-density functional genomics, expression profiling, and viral-specific chromosome conformation capture to define with unprecedented detail the transcriptional regulation of a single gene, ORF68, from Kaposi's sarcoma-associated herpesvirus (KSHV). We first identified seven cis-regulatory regions by densely tiling the ~154 kb KSHV genome with CRISPRi. A parallel Cas9 nuclease screen indicated that three of these regions act as promoters of genes that regulate ORF68. RNA expression profiling demonstrated that three more of these regions act by either repressing or enhancing other distal viral genes involved in ORF68 transcriptional regulation. Finally, we tracked how the 3D structure of the viral genome changes during its lifecycle, revealing that these enhancing regulatory elements are physically closer to their targets when active, and that disrupting some elements caused large-scale changes to the 3D genome. These data enable us to construct a complete model revealing that the mechanistic diversity of this essential regulatory circuit matches that of human genes.
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Affiliation(s)
- David W Morgens
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
| | - Leah Gulyas
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
| | | | | | - Britt A Glaunsinger
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, UC Berkeley, CA, USA
- Howard Hughes Medical Institute, UC Berkeley, CA, USA
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5
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Maes A, Botzki A, Mathys J, Impens F, Saelens X. Systematic review and meta-analysis of genome-wide pooled CRISPR screens to identify host factors involved in influenza A virus infection. J Virol 2024; 98:e0185723. [PMID: 38567969 PMCID: PMC11257101 DOI: 10.1128/jvi.01857-23] [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: 12/01/2023] [Accepted: 03/14/2024] [Indexed: 05/15/2024] Open
Abstract
The host-virus interactome is increasingly recognized as an important research field to discover new therapeutic targets to treat influenza. Multiple pooled genome-wide CRISPR-Cas screens have been reported to identify new pro- and antiviral host factors of the influenza A virus. However, at present, a comprehensive summary of the results is lacking. We performed a systematic review of all reported CRISPR studies in this field in combination with a meta-analysis using the algorithm of meta-analysis by information content (MAIC). Two ranked gene lists were generated based on evidence in 15 proviral and 4 antiviral screens. Enriched pathways in the proviral MAIC results were compared to those of a prior array-based RNA interference (RNAi) meta-analysis. The top 50 proviral MAIC list contained genes whose role requires further elucidation, such as the endosomal ion channel TPCN1 and the kinase WEE1. Moreover, MAIC indicated that ALYREF, a component of the transcription export complex, has antiviral properties, whereas former knockdown experiments attributed a proviral role to this host factor. CRISPR-Cas-pooled screens displayed a bias toward early-replication events, whereas the prior RNAi meta-analysis covered early and late-stage events. RNAi screens led to the identification of a larger fraction of essential genes than CRISPR screens. In summary, the MAIC algorithm points toward the importance of several less well-known pathways in host-influenza virus interactions that merit further investigation. The results from this meta-analysis of CRISPR screens in influenza A virus infection may help guide future research efforts to develop host-directed anti-influenza drugs. IMPORTANCE Viruses rely on host factors for their replication, whereas the host cell has evolved virus restriction factors. These factors represent potential targets for host-oriented antiviral therapies. Multiple pooled genome-wide CRISPR-Cas screens have been reported to identify pro- and antiviral host factors in the context of influenza virus infection. We performed a comprehensive analysis of the outcome of these screens based on the publicly available gene lists, using the recently developed algorithm meta-analysis by information content (MAIC). MAIC allows the systematic integration of ranked and unranked gene lists into a final ranked gene list. This approach highlighted poorly characterized host factors and pathways with evidence from multiple screens, such as the vesicle docking and lipid metabolism pathways, which merit further exploration.
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Affiliation(s)
- Annabel Maes
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Janssen Pharmaceutica NV, Beerse, Belgium
| | | | | | - Francis Impens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Xavier Saelens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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6
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Mouysset B, Le Grand M, Camoin L, Pasquier E. Poly-pharmacology of existing drugs: How to crack the code? Cancer Lett 2024; 588:216800. [PMID: 38492768 DOI: 10.1016/j.canlet.2024.216800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/15/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Drug development in oncology is highly challenging, with less than 5% success rate in clinical trials. This alarming figure points out the need to study in more details the multiple biological effects of drugs in specific contexts. Indeed, the comprehensive assessment of drug poly-pharmacology can provide insights into their therapeutic and adverse effects, to optimize their utilization and maximize the success rate of clinical trials. Recent technological advances have made possible in-depth investigation of drug poly-pharmacology. This review first highlights high-throughput methodologies that have been used to unveil new mechanisms of action of existing drugs. Then, we discuss how emerging chemo-proteomics strategies allow effectively dissecting the poly-pharmacology of drugs in an unsupervised manner.
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Affiliation(s)
- Baptiste Mouysset
- Centre de Recherche en Cancérologie de Marseille Inserm U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France.
| | - Marion Le Grand
- Centre de Recherche en Cancérologie de Marseille Inserm U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France.
| | - Luc Camoin
- Centre de Recherche en Cancérologie de Marseille Inserm U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France.
| | - Eddy Pasquier
- Centre de Recherche en Cancérologie de Marseille Inserm U1068, CNRS UMR7258, Aix-Marseille University U105, Marseille, France.
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Elgamal OA, Fobare S, Vibhute S, Mehmood A, Vroom DC, Johnson ML, Stearns B, Lerma JR, Truxall J, Stahl E, Carmichael B, Orwick SJ, Mims AS, Curran E, Santhanam R, Tridandapani S, Phelps MA, Xie Z, Coss CC, Baker SD, Patrick J, Ezzell JK, Rai J, Pan J, Rai SN, Stillwell C, Wunderlich M, Abdulrahim M, Goodwin TE, Hilinski G, Bennett CE, Hertlein E, Byrd JC. Pyrimidine depletion enhances targeted and immune therapy combinations in acute myeloid leukemia. JCI Insight 2024; 9:e173646. [PMID: 38646934 PMCID: PMC11141866 DOI: 10.1172/jci.insight.173646] [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: 07/12/2023] [Accepted: 03/05/2024] [Indexed: 04/25/2024] Open
Abstract
Acute myeloid leukemia (AML) is a fatal disease characterized by the accumulation of undifferentiated myeloblasts, and agents that promote differentiation have been effective in this disease but are not curative. Dihydroorotate dehydrogenase inhibitors (DHODHi) have the ability to promote AML differentiation and target aberrant malignant myelopoiesis. We introduce HOSU-53, a DHODHi with significant monotherapy activity, which is further enhanced when combined with other standard-of-care therapeutics. We further discovered that DHODHi modulated surface expression of CD38 and CD47, prompting the evaluation of HOSU-53 combined with anti-CD38 and anti-CD47 therapies, where we identified a compelling curative potential in an aggressive AML model with CD47 targeting. Finally, we explored using plasma dihydroorotate (DHO) levels to monitor HOSU-53 safety and found that the level of DHO accumulation could predict HOSU-53 intolerability, suggesting the clinical use of plasma DHO to determine safe DHODHi doses. Collectively, our data support the clinical translation of HOSU-53 in AML, particularly to augment immune therapies. Potent DHODHi to date have been limited by their therapeutic index; however, we introduce pharmacodynamic monitoring to predict tolerability while preserving antitumor activity. We additionally suggest that DHODHi is effective at lower doses with select immune therapies, widening the therapeutic index.
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Affiliation(s)
- Ola A. Elgamal
- Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Hematology, Department of Internal Medicine, College of Medicine
| | - Sydney Fobare
- Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Hematology, Department of Internal Medicine, College of Medicine
| | - Sandip Vibhute
- Medicinal Chemistry Shared Resource, Comprehensive Cancer Center
| | - Abeera Mehmood
- Division of Hematology, Department of Internal Medicine, College of Medicine
| | - Dennis C. Vroom
- Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Mariah L. Johnson
- Division of Hematology, Department of Internal Medicine, College of Medicine
| | - Blaise Stearns
- Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - James R. Lerma
- Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Jean Truxall
- Division of Hematology, Department of Internal Medicine, College of Medicine
| | - Emily Stahl
- Division of Hematology, Department of Internal Medicine, College of Medicine
| | - Bridget Carmichael
- Division of Hematology, Department of Internal Medicine, College of Medicine
| | - Shelley J. Orwick
- Division of Hematology, Department of Internal Medicine, College of Medicine
| | - Alice S. Mims
- Division of Hematology, Department of Internal Medicine, College of Medicine
| | - Emily Curran
- Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Ramasamy Santhanam
- Division of Hematology, Department of Internal Medicine, College of Medicine
| | | | | | - Zhiliang Xie
- College of Pharmacy and Comprehensive Cancer Center; and
| | - Christopher C. Coss
- Drug Development Institute, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | | | - Jeffrey Patrick
- Drug Development Institute, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Janel K. Ezzell
- Drug Development Institute, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Jayesh Rai
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine
- Cancer Data Science Center, College of Medicine; and
- Biostatistics and Informatics Shared Resource, University of Cincinnati Cancer Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Jianmin Pan
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine
- Cancer Data Science Center, College of Medicine; and
- Biostatistics and Informatics Shared Resource, University of Cincinnati Cancer Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Shesh N. Rai
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine
- Cancer Data Science Center, College of Medicine; and
- Biostatistics and Informatics Shared Resource, University of Cincinnati Cancer Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Cody Stillwell
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | | | | | - Gerard Hilinski
- Drug Development Institute, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Chad E. Bennett
- Medicinal Chemistry Shared Resource, Comprehensive Cancer Center
- Drug Development Institute, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Erin Hertlein
- Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Hematology, Department of Internal Medicine, College of Medicine
| | - John C. Byrd
- Division of Hematology and Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Hematology, Department of Internal Medicine, College of Medicine
- College of Pharmacy and Comprehensive Cancer Center; and
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8
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He Y, Zhou J, Gao H, Liu C, Zhan P, Liu X. Broad-spectrum antiviral strategy: Host-targeting antivirals against emerging and re-emerging viruses. Eur J Med Chem 2024; 265:116069. [PMID: 38160620 DOI: 10.1016/j.ejmech.2023.116069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/06/2023] [Accepted: 12/16/2023] [Indexed: 01/03/2024]
Abstract
Viral infections are amongst the most prevalent diseases that pose a significant threat to human health. Targeting viral proteins or host factors represents two primary strategies for the development of antiviral drugs. In contrast to virus-targeting antivirals (VTAs), host-targeting antivirals (HTAs) offer advantages in terms of overcoming drug resistance and effectively combating a wide range of viruses, including newly emerging ones. Therefore, targeting host factors emerges as an extremely promising strategy with the potential to address critical challenges faced by VTAs. In recent years, extensive research has been conducted on the discovery and development of HTAs, leading to the approval of maraviroc, a chemokine receptor type 5 (CCR5) antagonist used for the treatment of HIV-1 infected individuals, with several other potential treatments in various stages of development for different viral infections. This review systematically summarizes advancements made in medicinal chemistry regarding various host targets and classifies them into four distinct catagories based on their involvement in the viral life cycle: virus attachment and entry, biosynthesis, nuclear import and export, and viral release.
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Affiliation(s)
- Yong He
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Jiahui Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Huizhan Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Chuanfeng Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, 250012, Shandong Province, PR China.
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9
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Ryan CJ, Devakumar LPS, Pettitt SJ, Lord CJ. Complex synthetic lethality in cancer. Nat Genet 2023; 55:2039-2048. [PMID: 38036785 DOI: 10.1038/s41588-023-01557-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/04/2023] [Indexed: 12/02/2023]
Abstract
The concept of synthetic lethality has been widely applied to identify therapeutic targets in cancer, with varying degrees of success. The standard approach normally involves identifying genetic interactions between two genes, a driver and a target. In reality, however, most cancer synthetic lethal effects are likely complex and also polygenic, being influenced by the environment in addition to involving contributions from multiple genes. By acknowledging and delineating this complexity, we describe in this article how the success rate in cancer drug discovery and development could be improved.
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Affiliation(s)
- Colm J Ryan
- Conway Institute and School of Computer Science, University College Dublin, Dublin, Ireland.
| | - Lovely Paul Solomon Devakumar
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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10
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Gao A, Bai P, Zhang M, Yao Y, Herman JG, Guo M. RASSF1A promotes ATM signaling and RASSF1A methylation is a synthetic lethal marker for ATR inhibitors. Epigenomics 2023; 15:1205-1220. [PMID: 38093706 DOI: 10.2217/epi-2023-0306] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Abstract
Aim: The mechanism of RASSF1A in DNA damage repair remains to be further clarified for applying to synthetic lethal strategy. Materials & methods: Eight esophageal cancer cell lines, 181 cases of esophageal dysplasia and 1066 cases of primary esophageal squamous cell carcinoma (ESCC) were employed. Methylation-specific PCR, the CRISPR/Cas9 technique, immunoprecipitation assay and a xenograft mouse model were used. Results: RASSF1A was methylated in 2.21% of esophageal dysplasia and 11.73% of ESCC. RASSF1A was also involved in DNA damage repair through activating Hippo signaling. Loss of RASSF1A expression sensitized esophageal cancer cell lines to ataxia telangiectasia mutated and rad3-related (ATR) inhibitor (VE-822) both in vitro and in vivo. Conclusion: RASSF1A methylation is a synthetic lethal marker for ATR inhibitors.
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Affiliation(s)
- Aiai Gao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Panpan Bai
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
- Henan Advanced Technology Research Institute, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Meiying Zhang
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yuanxin Yao
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
- National Key Laboratory of Kidney Diseases, Beijing, 100853, China
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11
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Heydari N, Mahdizadeh M, Jafari SM. The evolving landscape of involvement of DTYMK enzymes in cancer. Med Oncol 2023; 40:213. [PMID: 37358701 DOI: 10.1007/s12032-023-02086-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/13/2023] [Indexed: 06/27/2023]
Abstract
Cancer cells require continuous synthesis of nucleotides for their uncontrolled proliferation. Deoxy thymidylate kinase (DTYMK) belongs to the thymidylate kinase family and is concerned with pyrimidine metabolism. DTYMK catalyzes the ATP-based conversion of deoxy-TMP to deoxy-TDP in both de novo and salvage pathways. Different studies demonstrated that DTYMK was increased in various types of cancers such as hepatocellular carcinoma, colon cancer, lung cancer, etc. Increased level of DTYMK was associated with poorer survival and prognosis, stage, grade and size of tumor, cell proliferation, colony formation, enhanced sensitivity to chemotherapy drugs, migration. Some studies were showed that knockdown of DTYMK reduced the signaling pathway of PI3K/AKT and downregulated expression of CART, MAPKAPK2, AKT1 and NRF1. Moreover, some microRNAs could suppress DTYMK expressions. On the other hand based on the TIMER database, the infiltration of macrophages, dendritic cells, neutrophils, B cells, CD4+ T cell and CD8+ T cell is affected by DTYMK. In the present review, we describe the genomic location, protein structure and isoforms of DTYMK and focus on its role in cancer development.
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Affiliation(s)
- Nadia Heydari
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Islamic Republic of Iran
- Department of Biochemistry and Biophysics, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Islamic Republic of Iran
| | - Mahsa Mahdizadeh
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Islamic Republic of Iran
- Department of Biochemistry and Biophysics, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Islamic Republic of Iran
| | - Seyyed Mehdi Jafari
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Islamic Republic of Iran.
- Department of Biochemistry and Biophysics, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Islamic Republic of Iran.
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12
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Spencley AL, Bar S, Swigut T, Flynn RA, Lee CH, Chen LF, Bassik MC, Wysocka J. Co-transcriptional genome surveillance by HUSH is coupled to termination machinery. Mol Cell 2023; 83:1623-1639.e8. [PMID: 37164018 PMCID: PMC10915761 DOI: 10.1016/j.molcel.2023.04.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/12/2023]
Abstract
The HUSH complex recognizes and silences foreign DNA such as viruses, transposons, and transgenes without prior exposure to its targets. Here, we show that endogenous targets of the HUSH complex fall into two distinct classes based on the presence or absence of H3K9me3. These classes are further distinguished by their transposon content and differential response to the loss of HUSH. A de novo genomic rearrangement at the Sox2 locus induces a switch from H3K9me3-independent to H3K9me3-associated HUSH targeting, resulting in silencing. We further demonstrate that HUSH interacts with the termination factor WDR82 and-via its component MPP8-with nascent RNA. HUSH accumulates at sites of high RNAPII occupancy including long exons and transcription termination sites in a manner dependent on WDR82 and CPSF. Together, our results uncover the functional diversity of HUSH targets and show that this vertebrate-specific complex exploits evolutionarily ancient transcription termination machinery for co-transcriptional chromatin targeting and genome surveillance.
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Affiliation(s)
- Andrew L Spencley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Shiran Bar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Cameron H Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Liang-Fu Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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13
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Proof-of-principle studies on a strategy to enhance nucleotide imbalance specifically in cancer cells. Cell Death Dis 2022; 8:464. [PMID: 36424385 PMCID: PMC9691752 DOI: 10.1038/s41420-022-01254-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 11/26/2022]
Abstract
Highly specific and potent inhibitors of dihydroorotate dehydrogenase (DHODH), an essential enzyme of the de novo pyrimidine ribonucleotide synthesis pathway, are in clinical trials for autoimmune diseases, viral infections and cancer. However, because DHODH inhibitors (DHODHi) are immunosuppressants they may reduce the anticancer activity of the immune system. Therefore, there may be a need to improve the therapeutic index of DHODHi in cancer patients. The aim of this study was to find strategies to protect activated T cells from DHODHi and to identify cancer types hypersensitive to these inhibitors. First, we observed that like uridine supplementation, adding cytidine to the culture medium protects T cells from DHODH blockage. Next, we identified tumor types with altered expression of pyrimidine ribonucleotide synthesis enzymes. In this regard, we detected that the expression of cytidine deaminase (CDA), which converts cytidine into uridine, is low in an important proportion of cancer cell lines and consistently low in neuroblastoma samples and in cell lines from neuroblastoma and small cell lung carcinoma. This suggested that in the presence of a DHODHi, an excess of cytidine would be deleterious for low CDA expressing cancer cell lines. We show that this was the case (as could be seen almost immediately after treatment) when cells were cultured with fetal bovine serum but, was significantly less evident when cultures contained human serum. One interesting feature of CDA is that aside from acting intracellularly, it is also present in human plasma/serum. Altogether, experiments using recombinant CDA, human serum, pharmacologic inhibition of CDA and T cell/cancer cell co-cultures suggest that the therapeutic index of DHODHi could be improved by selecting patients with low-CDA expressing cancers in combination with strategies to increase cytidine or the cytidine/uridine ratio in the extracellular environment. Collectively, this proof-of-principle study warrants the discovery of agents to deplete extracellular CDA.
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14
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Kim JH, Ofori S, Tagmount A, Vulpe CD, Awuah SG. Genome-wide CRISPR Screen Reveal Targets of Chiral Gold(I) Anticancer Compound in Mammalian Cells. ACS OMEGA 2022; 7:39197-39205. [PMID: 36340096 PMCID: PMC9631916 DOI: 10.1021/acsomega.2c05166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/06/2022] [Indexed: 06/09/2023]
Abstract
Metal-based drugs, such as cisplatin and auranofin, are used for the treatment of cancer and rheumatoid arthritis, respectively. Auranofin and other gold-derived compounds have been shown to possess anticancer, anti-inflammatory, antimicrobial, and antiparasitic activity in preclinical and clinical trials. Unlike platinum agents which are known to target DNA, the target of gold is not well elucidated. To better understand the targets and effects of gold agents in mammalian cells, we used a targeted CRISPR (ToxCRISPR) screen in K562 cancer cells to identify genes that modulate cellular sensitivity to gold. We synthesized a novel chiral gold(I) compound, JHK-21, with potent anticancer activity. Among the most sensitizing hits were proteins involved in mitochondrial carriers, mitochondrial metabolism, and oxidative phosphorylation. Further analysis revealed that JHK-21 induced inner mitochondria membrane dysfunction and modulated ATP-binding cassette subfamily member C (ABCC1) function in a manner distinct from auranofin. Characterizing the therapeutic effects and toxicities of metallodrugs in mammalian cells is of growing interest to guide future drug discovery, and cellular and preclinical/clinical studies.
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Affiliation(s)
- Jong Hyun Kim
- Department
of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Samuel Ofori
- Department
of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Abderrahmane Tagmount
- Department
of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32611, United States
| | - Chris D. Vulpe
- Department
of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32611, United States
| | - Samuel G. Awuah
- Department
of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Markey
Cancer Center, University of Kentucky, Lexington, Kentucky 40536, United States
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15
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Yoshinaga M, Han K, Morgens DW, Horii T, Kobayashi R, Tsuruyama T, Hia F, Yasukura S, Kajiya A, Cai T, Cruz PHC, Vandenbon A, Suzuki Y, Kawahara Y, Hatada I, Bassik MC, Takeuchi O. The N 6-methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity. Nat Commun 2022; 13:6435. [PMID: 36307435 PMCID: PMC9616860 DOI: 10.1038/s41467-022-34078-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/12/2022] [Indexed: 02/07/2023] Open
Abstract
During erythroid differentiation, the maintenance of genome integrity is key for the success of multiple rounds of cell division. However, molecular mechanisms coordinating the expression of DNA repair machinery in erythroid progenitors are poorly understood. Here, we discover that an RNA N6-methyladenosine (m6A) methyltransferase, METTL16, plays an essential role in proper erythropoiesis by safeguarding genome integrity via the control of DNA-repair-related genes. METTL16-deficient erythroblasts exhibit defective differentiation capacity, DNA damage and activation of the apoptotic program. Mechanistically, METTL16 controls m6A deposition at the structured motifs in DNA-repair-related transcripts including Brca2 and Fancm mRNAs, thereby upregulating their expression. Furthermore, a pairwise CRISPRi screen revealed that the MTR4-nuclear RNA exosome complex is involved in the regulation of METTL16 substrate mRNAs in erythroblasts. Collectively, our study uncovers that METTL16 and the MTR4-nuclear RNA exosome act as essential regulatory machinery to maintain genome integrity and erythropoiesis.
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Affiliation(s)
- Masanori Yoshinaga
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Kyuho Han
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - David W. Morgens
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Takuro Horii
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan
| | - Ryosuke Kobayashi
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan
| | - Tatsuaki Tsuruyama
- grid.258799.80000 0004 0372 2033Department of Drug and Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Fabian Hia
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Shota Yasukura
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Asako Kajiya
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Ting Cai
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
| | - Pedro H. C. Cruz
- grid.136593.b0000 0004 0373 3971Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Alexis Vandenbon
- grid.258799.80000 0004 0372 2033Laboratory of Tissue Homeostasis, Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507 Japan
| | - Yutaka Suzuki
- grid.26999.3d0000 0001 2151 536XLaboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Yukio Kawahara
- grid.136593.b0000 0004 0373 3971Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
| | - Izuho Hatada
- grid.256642.10000 0000 9269 4097Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, 371-8512 Japan ,grid.256642.10000 0000 9269 4097Viral Vector Core, Gunma University Initiative for Advanced Research (GIAR), Gunma, 371-8512 Japan
| | - Michael C. Bassik
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Osamu Takeuchi
- grid.258799.80000 0004 0372 2033Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501 Japan
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16
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Mashayekh S, Stunkard LM, Kienle M, Mathews II, Khosla C. Structure-Based Prototyping of Allosteric Inhibitors of Human Uridine/Cytidine Kinase 2 (UCK2). Biochemistry 2022; 61:2261-2266. [PMID: 36190114 DOI: 10.1021/acs.biochem.2c00451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyrimidine nucleotide biosynthesis in humans is a promising chemotherapeutic target for infectious diseases caused by RNA viruses. Because mammalian cells derive pyrimidine ribonucleotides through a combination of de novo biosynthesis and salvage, combined inhibition of dihydroorotate dehydrogenase (DHODH; the first committed step in de novo pyrimidine nucleotide biosynthesis) and uridine/cytidine kinase 2 (UCK2; the first step in salvage of exogenous nucleosides) strongly attenuates viral replication in infected cells. However, while several pharmacologically promising inhibitors of human DHODH are known, to date there are no reports of medicinally viable leads against UCK2. Here, we use structure-based drug prototyping to identify two classes of promising leads that noncompetitively inhibit UCK2 activity. In the process, we have identified a hitherto unknown allosteric site at the intersubunit interface of this homotetrameric enzyme. By reducing the kcat of human UCK2 without altering its KM, these new inhibitors have the potential to enable systematic dialing of the fractional inhibition of pyrimidine salvage to achieve the desired antiviral effect with minimal host toxicity.
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Affiliation(s)
- Siavash Mashayekh
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Lee M Stunkard
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Maryline Kienle
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, California 94305, United States.,Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States.,Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
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17
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Siepe DH, Henneberg LT, Wilson SC, Hess GT, Bassik MC, Zinn K, Garcia KC. Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform. eLife 2022; 11:e81398. [PMID: 36178190 PMCID: PMC9578707 DOI: 10.7554/elife.81398] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022] Open
Abstract
Secreted proteins, which include cytokines, hormones, and growth factors, are extracellular ligands that control key signaling pathways mediating cell-cell communication within and between tissues and organs. Many drugs target secreted ligands and their cell surface receptors. Still, there are hundreds of secreted human proteins that either have no identified receptors ('orphans') or are likely to act through cell surface receptors that have not yet been characterized. Discovery of secreted ligand-receptor interactions by high-throughput screening has been problematic, because the most commonly used high-throughput methods for protein-protein interaction (PPI) screening are not optimized for extracellular interactions. Cell-based screening is a promising technology for the deorphanization of ligand-receptor interactions, because multimerized ligands can enrich for cells expressing low affinity cell surface receptors, and such methods do not require purification of receptor extracellular domains. Here, we present a proteo-genomic cell-based CRISPR activation (CRISPRa) enrichment screening platform employing customized pooled cell surface receptor sgRNA libraries in combination with a magnetic bead selection-based enrichment workflow for rapid, parallel ligand-receptor deorphanization. We curated 80 potentially high-value orphan secreted proteins and ultimately screened 20 secreted ligands against two cell sgRNA libraries with targeted expression of all single-pass (TM1) or multi-pass transmembrane (TM2+) receptors by CRISPRa. We identified previously unknown interactions in 12 of these screens, and validated several of them using surface plasmon resonance and/or cell binding assays. The newly deorphanized ligands include three receptor protein tyrosine phosphatase (RPTP) ligands and a chemokine-like protein that binds to killer immunoglobulin-like receptors (KIRs). These new interactions provide a resource for future investigations of interactions between the human-secreted and membrane proteomes.
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Affiliation(s)
- Dirk H Siepe
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Lukas T Henneberg
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Steven C Wilson
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Gaelen T Hess
- Stanford ChEM-H, Department of Genetics, Stanford UniversityStanfordUnited States
| | - Michael C Bassik
- Stanford ChEM-H, Department of Genetics, Stanford UniversityStanfordUnited States
| | - Kai Zinn
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
- Department of Structural Biology, Stanford University School of MedicineStanfordUnited States
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18
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Khurana A, Sayed N, Singh V, Khurana I, Allawadhi P, Rawat PS, Navik U, Pasumarthi SK, Bharani KK, Weiskirchen R. A comprehensive overview of CRISPR/Cas 9 technology and application thereof in drug discovery. J Cell Biochem 2022; 123:1674-1698. [PMID: 36128934 DOI: 10.1002/jcb.30329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/13/2022] [Accepted: 09/01/2022] [Indexed: 11/07/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas technology possesses revolutionary potential to positively affect various domains of drug discovery. It has initiated a rise in the area of genetic engineering and its advantages range from classical science to translational medicine. These genome editing systems have given a new dimension to our capabilities to alter, detect and annotate specified gene sequences. Moreover, the ease, robustness and adaptability of the CRISPR/Cas9 technology have led to its extensive utilization in research areas in such a short period of time. The applications include the development of model cell lines, understanding disease mechanisms, discovering disease targets, developing transgenic animals and plants, and transcriptional modulation. Further, the technology is rapidly growing; hence, an overlook of progressive success is crucial. This review presents the current status of the CRISPR-Cas technology in a tailor-made format from its discovery to several advancements for drug discovery alongwith future trends associated with possibilities and hurdles including ethical concerns.
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Affiliation(s)
- Amit Khurana
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Aachen, Germany
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Hyderabad, Telangana, India
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal, Telangana, India
| | - Nilofer Sayed
- Department of Pharmacy, Pravara Rural Education Society's (P.R.E.S.'s) College of Pharmacy, Shreemati Nathibai Damodar Thackersey (SNDT) Women's University, Nashik, Maharashtra, India
| | - Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Isha Khurana
- Department of Pharmaceutical Chemistry, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, India
| | - Prince Allawadhi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pushkar Singh Rawat
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | | | - Kala Kumar Bharani
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal, Telangana, India
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Aachen, Germany
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19
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Cohen A, Jeng EE, Voorhies M, Symington J, Ali N, Rodriguez RA, Bassik MC, Sil A. Genome-scale CRISPR screening reveals that C3aR signaling is critical for rapid capture of fungi by macrophages. PLoS Pathog 2022; 18:e1010237. [PMID: 36174103 PMCID: PMC9578593 DOI: 10.1371/journal.ppat.1010237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 10/18/2022] [Accepted: 07/13/2022] [Indexed: 11/18/2022] Open
Abstract
The fungal pathogen Histoplasma capsulatum (Hc) invades, replicates within, and destroys macrophages. To interrogate the molecular mechanisms underlying this interaction, we conducted a host-directed CRISPR-Cas9 screen and identified 361 genes that modify macrophage susceptibility to Hc infection, greatly expanding our understanding of host gene networks targeted by Hc. We identified pathways that have not been previously implicated in Hc interaction with macrophages, including the ragulator complex (involved in nutrient stress sensing), glycosylation enzymes, protein degradation machinery, mitochondrial respiration genes, solute transporters, and the ER membrane complex (EMC). The highest scoring protective hits included the complement C3a receptor (C3aR), a G-protein coupled receptor (GPCR) that recognizes the complement fragment C3a. Although it is known that complement components react with the fungal surface, leading to opsonization and release of small peptide fragments such as C3a, a role for C3aR in macrophage interactions with fungi has not been elucidated. We demonstrated that whereas C3aR is dispensable for macrophage phagocytosis of bacteria and latex beads, it is critical for optimal macrophage capture of pathogenic fungi, including Hc, the ubiquitous fungal pathogen Candida albicans, and the causative agent of Valley Fever Coccidioides posadasii. We showed that C3aR localizes to the early phagosome during Hc infection where it coordinates the formation of actin-rich membrane protrusions that promote Hc capture. We also showed that the EMC promotes surface expression of C3aR, likely explaining its identification in our screen. Taken together, our results provide new insight into host processes that affect Hc-macrophage interactions and uncover a novel and specific role for C3aR in macrophage recognition of fungi.
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Affiliation(s)
- Allison Cohen
- University of California San Francisco, Department of Microbiology and Immunology, San Francisco, California, United States of America
| | - Edwin E. Jeng
- Stanford University, Department of Genetics, Palo Alto, California, United States of America
| | - Mark Voorhies
- University of California San Francisco, Department of Microbiology and Immunology, San Francisco, California, United States of America
| | - Jane Symington
- University of California San Francisco, Department of Microbiology and Immunology, San Francisco, California, United States of America
| | - Nebat Ali
- University of California San Francisco, Department of Microbiology and Immunology, San Francisco, California, United States of America
| | - Rosa A. Rodriguez
- University of California San Francisco, Department of Microbiology and Immunology, San Francisco, California, United States of America
| | - Michael C. Bassik
- Stanford University, Department of Genetics, Palo Alto, California, United States of America
| | - Anita Sil
- University of California San Francisco, Department of Microbiology and Immunology, San Francisco, California, United States of America
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20
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MYCN and Metabolic Reprogramming in Neuroblastoma. Cancers (Basel) 2022; 14:cancers14174113. [PMID: 36077650 PMCID: PMC9455056 DOI: 10.3390/cancers14174113] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Neuroblastoma is a pediatric cancer responsible for approximately 15% of all childhood cancer deaths. Aberrant MYCN activation, as a result of genomic MYCN amplification, is a major driver of high-risk neuroblastoma, which has an overall survival rate of less than 50%, despite the best treatments currently available. Metabolic reprogramming is an integral part of the growth-promoting program driven by MYCN, which fuels cell growth and proliferation by increasing the uptake and catabolism of nutrients, biosynthesis of macromolecules, and production of energy. This reprogramming process also generates metabolic vulnerabilities that can be exploited for therapy. In this review, we present our current understanding of metabolic reprogramming in neuroblastoma, focusing on transcriptional regulation as a key mechanism in driving the reprogramming process. We also highlight some important areas that need to be explored for the successful development of metabolism-based therapy against high-risk neuroblastoma.
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21
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Goel K, Ploski JE. RISC-y Business: Limitations of Short Hairpin RNA-Mediated Gene Silencing in the Brain and a Discussion of CRISPR/Cas-Based Alternatives. Front Mol Neurosci 2022; 15:914430. [PMID: 35959108 PMCID: PMC9362770 DOI: 10.3389/fnmol.2022.914430] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/16/2022] [Indexed: 11/23/2022] Open
Abstract
Manipulating gene expression within and outside the nervous system is useful for interrogating gene function and developing therapeutic interventions for a variety of diseases. Several approaches exist which enable gene manipulation in preclinical models, and some of these have been approved to treat human diseases. For the last couple of decades, RNA interference (RNAi) has been a leading technique to knockdown (i.e., suppress) specific RNA expression. This has been partly due to the technology's simplicity, which has promoted its adoption throughout biomedical science. However, accumulating evidence indicates that this technology can possess significant shortcomings. This review highlights the overwhelming evidence that RNAi can be prone to off-target effects and is capable of inducing cytotoxicity in some cases. With this in mind, we consider alternative CRISPR/Cas-based approaches, which may be safer and more reliable for gene knockdown. We also discuss the pros and cons of each approach.
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Affiliation(s)
- Kanishk Goel
- School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Jonathan E. Ploski
- Department of Neural and Behavioral Sciences, Penn State College of Medicine, Hershey, PA, United States
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22
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The Antifungal Itraconazole Is a Potent Inhibitor of Chikungunya Virus Replication. Viruses 2022; 14:v14071351. [PMID: 35891332 PMCID: PMC9317443 DOI: 10.3390/v14071351] [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: 05/14/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 12/04/2022] Open
Abstract
Chikungunya virus (CHIKV) is the causative agent of chikungunya fever, a disabling disease that can cause long-term severe arthritis. Since the last large CHIKV outbreak in 2015, the reemergence of the virus represents a serious public health concern. The morbidity associated with viral infection emphasizes the need for the development of specific anti-CHIKV drugs. Herein, we describe the development and characterization of a CHIKV reporter replicon cell line and its use in replicon-based screenings. We tested 960 compounds from MMV/DNDi Open Box libraries and identified four candidates with interesting antiviral activities, which were confirmed in viral infection assays employing CHIKV-nanoluc and BHK-21 cells. The most noteworthy compound identified was itraconazole (ITZ), an orally available, safe, and cheap antifungal, that showed high selectivity indexes of >312 and >294 in both replicon-based and viral infection assays, respectively. The antiviral activity of this molecule has been described against positive-sense single stranded RNA viruses (+ssRNA) and was related to cholesterol metabolism that could affect the formation of the replication organelles. Although its precise mechanism of action against CHIKV still needs to be elucidated, our results demonstrate that ITZ is a potent inhibitor of the viral replication that could be repurposed as a broad-spectrum antiviral.
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Phenotypic drug discovery: recent successes, lessons learned and new directions. Nat Rev Drug Discov 2022; 21:899-914. [DOI: 10.1038/s41573-022-00472-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2022] [Indexed: 12/29/2022]
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Vest RT, Chou CC, Zhang H, Haney MS, Li L, Laqtom NN, Chang B, Shuken S, Nguyen A, Yerra L, Yang AC, Green C, Tanga M, Abu-Remaileh M, Bassik MC, Frydman J, Luo J, Wyss-Coray T. Small molecule C381 targets the lysosome to reduce inflammation and ameliorate disease in models of neurodegeneration. Proc Natl Acad Sci U S A 2022; 119:e2121609119. [PMID: 35259016 PMCID: PMC8931323 DOI: 10.1073/pnas.2121609119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/27/2022] [Indexed: 02/07/2023] Open
Abstract
SignificanceNeurodegenerative diseases are poorly understood and difficult to treat. One common hallmark is lysosomal dysfunction leading to the accumulation of aggregates and other undegradable materials, which cause damage to brain resident cells. Lysosomes are acidic organelles responsible for breaking down biomolecules and recycling their constitutive parts. In this work, we find that the antiinflammatory and neuroprotective compound, discovered via a phenotypic screen, imparts its beneficial effects by targeting the lysosome and restoring its function. This is established using a genome-wide CRISPRi target identification screen and then confirmed using a variety of lysosome-targeted studies. The resulting small molecule from this study represents a potential treatment for neurodegenerative diseases as well as a research tool for the study of lysosomes in disease.
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Affiliation(s)
- Ryan T. Vest
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
| | | | - Hui Zhang
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
| | - Michael S. Haney
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Lulin Li
- Palo Alto Veterans Institute for Research, Palo Alto, CA 94304
| | - Nouf N. Laqtom
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Institute for Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA 94305
| | - Betty Chang
- Palo Alto Veterans Institute for Research, Palo Alto, CA 94304
| | - Steven Shuken
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Andy Nguyen
- Palo Alto Veterans Institute for Research, Palo Alto, CA 94304
| | - Lakshmi Yerra
- Palo Alto Veterans Institute for Research, Palo Alto, CA 94304
| | - Andrew C. Yang
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
| | | | | | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Institute for Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA 94305
| | - Michael C. Bassik
- Institute for Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Jian Luo
- Palo Alto Veterans Institute for Research, Palo Alto, CA 94304
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA 94305
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Morgens DW, Nandakumar D, Didychuk AL, Yang KJ, Glaunsinger BA. A Two-tiered functional screen identifies herpesviral transcriptional modifiers and their essential domains. PLoS Pathog 2022; 18:e1010236. [PMID: 35041709 PMCID: PMC8797222 DOI: 10.1371/journal.ppat.1010236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/28/2022] [Accepted: 12/29/2021] [Indexed: 11/19/2022] Open
Abstract
While traditional methods for studying large DNA viruses allow the creation of individual mutants, CRISPR/Cas9 can be used to rapidly create thousands of mutant dsDNA viruses in parallel, enabling the pooled screening of entire viral genomes. Here, we applied this approach to Kaposi’s sarcoma-associated herpesvirus (KSHV) by designing a sgRNA library containing all possible ~22,000 guides targeting the 154 kilobase viral genome, corresponding to one cut site approximately every 8 base pairs. We used the library to profile viral sequences involved in transcriptional activation of late genes, whose regulation involves several well characterized features including dependence on viral DNA replication and a known set of viral transcriptional activators. Upon phenotyping all possible Cas9-targeted viruses for transcription of KSHV late genes we recovered these established regulators and identified a new required factor (ORF46), highlighting the utility of the screening pipeline. By performing targeted deep sequencing of the viral genome to distinguish between knock-out and in-frame alleles created by Cas9, we identify the DNA binding but not catalytic domain of ORF46 to be required for viral DNA replication and thus late gene expression. Our pooled Cas9 tiling screen followed by targeted deep viral sequencing represents a two-tiered screening paradigm that may be widely applicable to dsDNA viruses.
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Affiliation(s)
- David W. Morgens
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, United States of America
- * E-mail: (DM); (BG)
| | - Divya Nandakumar
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, United States of America
| | - Allison L. Didychuk
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, United States of America
| | - Kevin J. Yang
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, California, United States of America
| | - Britt A. Glaunsinger
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, UC Berkeley, Berkeley, California, United States of America
- * E-mail: (DM); (BG)
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Miyake S, Masuda S. Inhibition of mitochondrial complex III or dihydroorotate dehydrogenase (DHODH) triggers formation of poly(A) + RNA foci adjacent to nuclear speckles following activation of ATM (ataxia telangiectasia mutated). RNA Biol 2022; 19:1244-1255. [PMID: 36412986 PMCID: PMC9683070 DOI: 10.1080/15476286.2022.2146919] [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] [Indexed: 11/23/2022] Open
Abstract
Intracellular and intercellular signalling networks play an essential role in optimizing cellular homoeostasis and are thought to be partly reflected in nuclear mRNA dynamics. However, the regulation of nuclear mRNA dynamics by intracellular and intercellular signals remains largely unexplored, and research tools are lacking. Through an original screening based on the mRNA metabolic mechanism, we discovered that eight well-known inhibitors cause significant nuclear poly(A)+ RNA accumulation. Among these inhibitors, we discovered a new mRNA metabolic response in which the addition of antimycin A, an inhibitor of mitochondrial respiratory-chain complex III (complex III), resulted in a marked accumulation of poly(A)+ RNA near the nuclear speckles. Furthermore, dihydroorotate dehydrogenase (DHODH) inhibitors, a rate-limiting enzyme in the intracellular de novo pyrimidine synthesis reaction that specifically exchanges electrons with complex III, also caused a remarkable accumulation of nuclear poly(A)+ RNA adjacent to the nuclear speckles, which was abolished by extracellular uridine supply, indicating that the depletion of intracellular pyrimidine affects poly(A)+ RNA metabolism. Further analysis revealed that ataxia telangiectasia mutated (ATM), a serine and threonine kinase and a master regulator of DNA double-strand break (DSB) and nucleolar stress, is required for this poly(A)+ RNA nuclear accumulation phenomenon. This study reports new insights into novel aspects of nuclear poly(A)+ RNA metabolism, especially the relationship between mitochondrial respiratory-chain functions, pyrimidine metabolism, and nuclear RNA metabolism.
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Affiliation(s)
- Shuntaro Miyake
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Seiji Masuda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Japan,Department of Food Science and Nutrition, Faculty of Agriculture, Kindai University, Nara, Japan,Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Japan,Antiaging Center, Kindai University, Higashiosaka, Japan,CONTACT Seiji Masuda Department of Food Science and Nutrition, Faculty of Agriculture, Kindai University, Nara631-8505, Japan
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27
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Common computational tools for analyzing CRISPR screens. Emerg Top Life Sci 2021; 5:779-788. [PMID: 34881774 PMCID: PMC8786280 DOI: 10.1042/etls20210222] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022]
Abstract
CRISPR–Cas technology offers a versatile toolbox for genome editing, with applications in various cancer-related fields such as functional genomics, immunotherapy, synthetic lethality and drug resistance, metastasis, genome regulation, chromatic accessibility and RNA-targeting. The variety of screening platforms and questions in which they are used have caused the development of a wide array of analytical methods for CRISPR analysis. In this review, we focus on the algorithms and frameworks used in the computational analysis of pooled CRISPR knockout (KO) screens and highlight some of the most significant target discoveries made using these methods. Lastly, we offer perspectives on the design and analysis of state-of-art multiplex screening for genetic interactions.
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28
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Modell AE, Lim D, Nguyen TM, Sreekanth V, Choudhary A. CRISPR-based therapeutics: current challenges and future applications. Trends Pharmacol Sci 2021; 43:151-161. [PMID: 34952739 DOI: 10.1016/j.tips.2021.10.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/13/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
The discovery, only a decade ago, of the genome editing power of clustered regularly interspaced short palindromic repeats (CRISPR)-associated nucleases is already reinventing the therapeutic process, from how new drugs are discovered to novel ways to treat diseases. CRISPR-based screens can aid therapeutic development by quickly identifying a drug's mechanism of action and escape mutants. Additionally, CRISPR-Cas has advanced emerging ex vivo therapeutics, such as cell replacement therapies. However, Cas9 is limited as an in vivo therapeutic due to ineffective delivery, unwanted immune responses, off-target effects, unpredictable repair outcomes, and cellular stress. To address these limitations, controls that inhibit or degrade Cas9, biomolecule-Cas9 conjugates, and base editors have been developed. Herein, we discuss CRISPR-Cas systems that advance both conventional and emerging therapeutics.
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Affiliation(s)
- Ashley E Modell
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Donghyun Lim
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Tuan M Nguyen
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Vedagopuram Sreekanth
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA; Islet Cell and Regenerative Biology, Joslin Diabetes Center, Boston, MA, USA.
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29
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Tsujino T, Komura K, Inamoto T, Azuma H. CRISPR Screen Contributes to Novel Target Discovery in Prostate Cancer. Int J Mol Sci 2021; 22:ijms222312777. [PMID: 34884583 PMCID: PMC8658029 DOI: 10.3390/ijms222312777] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PCa) is one of the common malignancies in male adults. Recent advances in omics technology, especially in next-generation sequencing, have increased the opportunity to identify genes that correlate with cancer diseases, including PCa. In addition, a genetic screen based on CRISPR/Cas9 technology has elucidated the mechanisms of cancer progression and drug resistance, which in turn has enabled the discovery of new targets as potential genes for new therapeutic targets. In the era of precision medicine, such knowledge is crucial for clinicians in their decision-making regarding patient treatment. In this review, we focus on how CRISPR screen for PCa performed to date has contributed to the identification of biologically critical and clinically relevant target genes.
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Affiliation(s)
- Takuya Tsujino
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka 569-8686, Japan; (T.I.); (H.A.)
- Division of Urology, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Correspondence: (T.T.); (K.K.); Tel.: +81-72-683-1221 (T.T. & K.K.)
| | - Kazumasa Komura
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka 569-8686, Japan; (T.I.); (H.A.)
- Translational Research Program, Osaka Medical and Pharmaceutical University, Osaka 569-8686, Japan
- Correspondence: (T.T.); (K.K.); Tel.: +81-72-683-1221 (T.T. & K.K.)
| | - Teruo Inamoto
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka 569-8686, Japan; (T.I.); (H.A.)
| | - Haruhito Azuma
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka 569-8686, Japan; (T.I.); (H.A.)
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Matsumoto K, Yoshida M. Mammalian Chemical Genomics towards Identifying Targets and Elucidating Modes-of-Action of Bioactive Compounds. Chembiochem 2021; 23:e202100561. [PMID: 34813140 DOI: 10.1002/cbic.202100561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/22/2021] [Indexed: 11/08/2022]
Abstract
The step of identifying target molecules and elucidating the mode of action of bioactive compounds is a major bottleneck for drug discovery from phenotypic screening. Genetic screening for genes that affect drug sensitivity or phenotypes of mammalian cultured cells is a powerful tool to obtain clues to their modes of action. Chemical genomic screening systems for comprehensively identifying such genes or genetic pathways have been established using shRNA libraries for RNA interference-mediated mRNA knockdown or sgRNA libraries for CRISPR/Cas9-mediated gene knockout. The combination of chemical genomic screening in mammalian cells with other approaches such as biochemical searches for target molecules, phenotypic profiling, and yeast genetics provides a systematic way to elucidate the mode of action by converging various pieces of information regarding target molecules, target pathways, and synthetic lethal pathways.
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Affiliation(s)
- Ken Matsumoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Saitama, 351-0198, Japan.,Seed Compounds Exploratory Unit for Drug Discovery Platform, Drug Discovery Platforms Cooperation Division, RIKEN Center for Sustainable Resource Science, Saitama, 351-0198, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Saitama, 351-0198, Japan.,Seed Compounds Exploratory Unit for Drug Discovery Platform, Drug Discovery Platforms Cooperation Division, RIKEN Center for Sustainable Resource Science, Saitama, 351-0198, Japan.,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Tokyo, 113-8657, Japan
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31
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Orthogonal genome-wide screens of bat cells identify MTHFD1 as a target of broad antiviral therapy. Proc Natl Acad Sci U S A 2021; 118:2104759118. [PMID: 34544865 DOI: 10.1073/pnas.2104759118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 11/18/2022] Open
Abstract
Bats are responsible for the zoonotic transmission of several major viral diseases, including those leading to the 2003 SARS outbreak and likely the ongoing COVID-19 pandemic. While comparative genomics studies have revealed characteristic adaptations of the bat innate immune system, functional genomic studies are urgently needed to provide a foundation for the molecular dissection of the viral tolerance in bats. Here we report the establishment of genome-wide RNA interference (RNAi) and CRISPR libraries for the screening of the model megabat, Pteropus alecto. We used the complementary RNAi and CRISPR libraries to interrogate P. alecto cells for infection with two different viruses: mumps virus and influenza A virus, respectively. Independent screening results converged on the endocytosis pathway and the protein secretory pathway as required for both viral infections. Additionally, we revealed a general dependence of the C1-tetrahydrofolate synthase gene, MTHFD1, for viral replication in bat cells and human cells. The MTHFD1 inhibitor, carolacton, potently blocked replication of several RNA viruses, including SARS-CoV-2. We also discovered that bats have lower expression levels of MTHFD1 than humans. Our studies provide a resource for systematic inquiry into the genetic underpinnings of bat biology and a potential target for developing broad-spectrum antiviral therapy.
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Pyrimidine Biosynthetic Enzyme CAD: Its Function, Regulation, and Diagnostic Potential. Int J Mol Sci 2021; 22:ijms221910253. [PMID: 34638594 PMCID: PMC8508918 DOI: 10.3390/ijms221910253] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/18/2021] [Accepted: 09/19/2021] [Indexed: 01/10/2023] Open
Abstract
CAD (Carbamoyl-phosphate synthetase 2, Aspartate transcarbamoylase, and Dihydroorotase) is a multifunctional protein that participates in the initial three speed-limiting steps of pyrimidine nucleotide synthesis. Over the past two decades, extensive investigations have been conducted to unmask CAD as a central player for the synthesis of nucleic acids, active intermediates, and cell membranes. Meanwhile, the important role of CAD in various physiopathological processes has also been emphasized. Deregulation of CAD-related pathways or CAD mutations cause cancer, neurological disorders, and inherited metabolic diseases. Here, we review the structure, function, and regulation of CAD in mammalian physiology as well as human diseases, and provide insights into the potential to target CAD in future clinical applications.
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33
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Mahajan S, Choudhary S, Kumar P, Tomar S. Antiviral strategies targeting host factors and mechanisms obliging +ssRNA viral pathogens. Bioorg Med Chem 2021; 46:116356. [PMID: 34416512 PMCID: PMC8349405 DOI: 10.1016/j.bmc.2021.116356] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 12/21/2022]
Abstract
The ongoing COVID-19 pandemic, periodic recurrence of viral infections, and the emergence of challenging variants has created an urgent need of alternative therapeutic approaches to combat the spread of viral infections, failing to which may pose a greater risk to mankind in future. Resilience against antiviral drugs or fast evolutionary rate of viruses is stressing the scientific community to identify new therapeutic approaches for timely control of disease. Host metabolic pathways are exquisite reservoir of energy to viruses and contribute a diverse array of functions for successful replication and pathogenesis of virus. Targeting the host factors rather than viral enzymes to cease viral infection, has emerged as an alternative antiviral strategy. This approach offers advantage in terms of increased threshold to viral resistance and can provide broad-spectrum antiviral action against different viruses. The article here provides substantial review of literature illuminating the host factors and molecular mechanisms involved in innate/adaptive responses to viral infection, hijacking of signalling pathways by viruses and the intracellular metabolic pathways required for viral replication. Host-targeted drugs acting on the pathways usurped by viruses are also addressed in this study. Host-directed antiviral therapeutics might prove to be a rewarding approach in controlling the unprecedented spread of viral infection, however the probability of cellular side effects or cytotoxicity on host cell should not be ignored at the time of clinical investigations.
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Affiliation(s)
- Supreeti Mahajan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India.
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34
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Yu Y, Ding J, Zhu S, Alptekin A, Dong Z, Yan C, Zha Y, Ding HF. Therapeutic targeting of both dihydroorotate dehydrogenase and nucleoside transport in MYCN-amplified neuroblastoma. Cell Death Dis 2021; 12:821. [PMID: 34462431 PMCID: PMC8405683 DOI: 10.1038/s41419-021-04120-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023]
Abstract
Metabolic reprogramming is an integral part of the growth-promoting program driven by the MYC family of oncogenes. However, this reprogramming also imposes metabolic dependencies that could be exploited therapeutically. Here we report that the pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) is an attractive therapeutic target for MYCN-amplified neuroblastoma, a childhood cancer with poor prognosis. Gene expression profiling and metabolomic analysis reveal that MYCN promotes pyrimidine nucleotide production by transcriptional upregulation of DHODH and other enzymes of the pyrimidine-synthesis pathway. Genetic and pharmacological inhibition of DHODH suppresses the proliferation and tumorigenicity of MYCN-amplified neuroblastoma cell lines. Furthermore, we obtain evidence suggesting that serum uridine is a key factor in determining the efficacy of therapeutic agents that target DHODH. In the presence of physiological concentrations of uridine, neuroblastoma cell lines are highly resistant to DHODH inhibition. This uridine-dependent resistance to DHODH inhibitors can be abrogated by dipyridamole, an FDA-approved drug that blocks nucleoside transport. Importantly, dipyridamole synergizes with DHODH inhibition to suppress neuroblastoma growth in animal models. These findings suggest that a combination of targeting DHODH and nucleoside transport is a promising strategy to overcome intrinsic resistance to DHODH-based cancer therapeutics.
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Affiliation(s)
- Yajie Yu
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang, 443000, China
| | - Jane Ding
- Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Shunqin Zhu
- School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Ahmet Alptekin
- Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Zheng Dong
- Department of Cell Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
- Charlie Norwood VA Medical Center, Augusta, GA, 30904, USA
| | - Chunhong Yan
- Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Yunhong Zha
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang, 443000, China.
| | - Han-Fei Ding
- Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA.
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA.
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA.
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Calistri A, Luganini A, Mognetti B, Elder E, Sibille G, Conciatori V, Del Vecchio C, Sainas S, Boschi D, Montserrat N, Mirazimi A, Lolli ML, Gribaudo G, Parolin C. The New Generation hDHODH Inhibitor MEDS433 Hinders the In Vitro Replication of SARS-CoV-2 and Other Human Coronaviruses. Microorganisms 2021; 9:microorganisms9081731. [PMID: 34442810 PMCID: PMC8398173 DOI: 10.3390/microorganisms9081731] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/03/2021] [Accepted: 08/13/2021] [Indexed: 12/22/2022] Open
Abstract
Although coronaviruses (CoVs) have long been predicted to cause zoonotic diseases and pandemics with high probability, the lack of effective anti-pan-CoVs drugs rapidly usable against the emerging SARS-CoV-2 actually prevented a promptly therapeutic intervention for COVID-19. Development of host-targeting antivirals could be an alternative strategy for the control of emerging CoVs infections, as they could be quickly repositioned from one pandemic event to another. To contribute to these pandemic preparedness efforts, here we report on the broad-spectrum CoVs antiviral activity of MEDS433, a new inhibitor of the human dihydroorotate dehydrogenase (hDHODH), a key cellular enzyme of the de novo pyrimidine biosynthesis pathway. MEDS433 inhibited the in vitro replication of hCoV-OC43 and hCoV-229E, as well as of SARS-CoV-2, at low nanomolar range. Notably, the anti-SARS-CoV-2 activity of MEDS433 against SARS-CoV-2 was also observed in kidney organoids generated from human embryonic stem cells. Then, the antiviral activity of MEDS433 was reversed by the addition of exogenous uridine or the product of hDHODH, the orotate, thus confirming hDHODH as the specific target of MEDS433 in hCoVs-infected cells. Taken together, these findings suggest MEDS433 as a potential candidate to develop novel drugs for COVID-19, as well as broad-spectrum antiviral agents exploitable for future CoVs threats.
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Affiliation(s)
- Arianna Calistri
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (A.C.); (V.C.); (C.D.V.); (C.P.)
| | - Anna Luganini
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy; (A.L.); (B.M.); (G.S.)
| | - Barbara Mognetti
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy; (A.L.); (B.M.); (G.S.)
| | - Elizabeth Elder
- Public Health Agency of Sweden, 17182 Solna, Sweden; (E.E.); (A.M.)
| | - Giulia Sibille
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy; (A.L.); (B.M.); (G.S.)
| | - Valeria Conciatori
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (A.C.); (V.C.); (C.D.V.); (C.P.)
| | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (A.C.); (V.C.); (C.D.V.); (C.P.)
| | - Stefano Sainas
- Department of Sciences and Drug Technology, University of Turin, 10125 Turin, Italy; (S.S.); (D.B.); (M.L.L.)
| | - Donatella Boschi
- Department of Sciences and Drug Technology, University of Turin, 10125 Turin, Italy; (S.S.); (D.B.); (M.L.L.)
| | - Nuria Montserrat
- Pluripotency for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain;
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina, 28029 Madrid, Spain
| | - Ali Mirazimi
- Public Health Agency of Sweden, 17182 Solna, Sweden; (E.E.); (A.M.)
- Karolinska Institute and Karolinska University Hospital, Department of Laboratory Medicine, Unit of Clinical Microbiology, 17177 Stockholm, Sweden
- National Veterinary Institute, 75189 Uppsala, Sweden
| | - Marco Lucio Lolli
- Department of Sciences and Drug Technology, University of Turin, 10125 Turin, Italy; (S.S.); (D.B.); (M.L.L.)
| | - Giorgio Gribaudo
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy; (A.L.); (B.M.); (G.S.)
- Correspondence: ; Tel.: +39-011-6704648
| | - Cristina Parolin
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy; (A.C.); (V.C.); (C.D.V.); (C.P.)
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Jones CE, Tan WS, Grey F, Hughes DJ. Discovering antiviral restriction factors and pathways using genetic screens. J Gen Virol 2021; 102. [PMID: 34020727 PMCID: PMC8295917 DOI: 10.1099/jgv.0.001603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Viral infections activate the powerful interferon (IFN) response that induces the expression of several hundred IFN stimulated genes (ISGs). The principal role of this extensive response is to create an unfavourable environment for virus replication and to limit spread; however, untangling the biological consequences of this large response is complicated. In addition to a seemingly high degree of redundancy, several ISGs are usually required in combination to limit infection as individual ISGs often have low to moderate antiviral activity. Furthermore, what ISG or combination of ISGs are antiviral for a given virus is usually not known. For these reasons, and since the function(s) of many ISGs remains unexplored, genome-wide approaches are well placed to investigate what aspects of this response result in an appropriate, virus-specific phenotype. This review discusses the advances screening approaches have provided for the study of host defence mechanisms, including clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9), ISG expression libraries and RNA interference (RNAi) technologies.
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Affiliation(s)
- Chloe E Jones
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Wenfang S Tan
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Finn Grey
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - David J Hughes
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
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Zhang J, Terán G, Popa M, Madapura H, Ladds MJGW, Lianoudaki D, Grünler J, Arsenian-Henriksson M, McCormack E, Rottenberg ME, Catrina SB, Laín S, Darekar S. DHODH inhibition modulates glucose metabolism and circulating GDF15, and improves metabolic balance. iScience 2021; 24:102494. [PMID: 34113829 PMCID: PMC8169992 DOI: 10.1016/j.isci.2021.102494] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/25/2021] [Accepted: 04/27/2021] [Indexed: 12/18/2022] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is essential for the de novo synthesis of pyrimidine ribonucleotides, and as such, its inhibitors have been long used to treat autoimmune diseases and are in clinical trials for cancer and viral infections. Interestingly, DHODH is located in the inner mitochondrial membrane and contributes to provide ubiquinol to the respiratory chain. Thus, DHODH provides the link between nucleotide metabolism and mitochondrial function. Here we show that pharmacological inhibition of DHODH reduces mitochondrial respiration, promotes glycolysis, and enhances GLUT4 translocation to the cytoplasmic membrane and that by activating tumor suppressor p53, increases the expression of GDF15, a cytokine that reduces appetite and prolongs lifespan. In addition, similar to the antidiabetic drug metformin, we observed that in db/db mice, DHODH inhibitors elevate levels of circulating GDF15 and reduce food intake. Further analysis using this model for obesity-induced diabetes revealed that DHODH inhibitors delay pancreatic β cell death and improve metabolic balance.
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Affiliation(s)
- Juan Zhang
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Graciela Terán
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Mihaela Popa
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021 Bergen, Norway
| | - Harsha Madapura
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21 Stockholm, Sweden
| | | | - Danai Lianoudaki
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21 Stockholm, Sweden
| | - Jacob Grünler
- Department of Endocrinology and Diabetes, Karolinska University Hospital, 17176 Stockholm, Sweden
- Center for Diabetes, Academic Specialist Centrum, 11365 Stockholm, Sweden
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Emmet McCormack
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021 Bergen, Norway
- Department of Medicine, Haematology Section, Haukeland University Hospital, Bergen, Norway
| | - Martin Enrique Rottenberg
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Sergiu-Bogdan Catrina
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden
- Department of Endocrinology and Diabetes, Karolinska University Hospital, 17176 Stockholm, Sweden
- Center for Diabetes, Academic Specialist Centrum, 11365 Stockholm, Sweden
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21 Stockholm, Sweden
| | - Suhas Darekar
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21 Stockholm, Sweden
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Zhou Y, Tao L, Zhou X, Zuo Z, Gong J, Liu X, Zhou Y, Liu C, Sang N, Liu H, Zou J, Gou K, Yang X, Zhao Y. DHODH and cancer: promising prospects to be explored. Cancer Metab 2021; 9:22. [PMID: 33971967 PMCID: PMC8107416 DOI: 10.1186/s40170-021-00250-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/10/2021] [Indexed: 02/08/2023] Open
Abstract
Human dihydroorotate dehydrogenase (DHODH) is a flavin-dependent mitochondrial enzyme catalyzing the fourth step in the de novo pyrimidine synthesis pathway. It is originally a target for the treatment of the non-neoplastic diseases involving in rheumatoid arthritis and multiple sclerosis, and is re-emerging as a validated therapeutic target for cancer therapy. In this review, we mainly unravel the biological function of DHODH in tumor progression, including its crucial role in de novo pyrimidine synthesis and mitochondrial respiratory chain in cancer cells. Moreover, various DHODH inhibitors developing in the past decades are also been displayed, and the specific mechanism between DHODH and its additional effects are illustrated. Collectively, we detailly discuss the association between DHODH and tumors in recent years here, and believe it will provide significant evidences and potential strategies for utilizing DHODH as a potential target in preclinical and clinical cancer therapies.
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Affiliation(s)
- Yue Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Lei Tao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Xia Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Zeping Zuo
- The Laboratory of Anesthesiology and Critical Care Medicine, Translational Neuroscience Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jin Gong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Xiaocong Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Yang Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Chunqi Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Na Sang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Huan Liu
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Jiao Zou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Kun Gou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Xiaowei Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Yinglan Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China. .,West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
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39
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Joly JH, Chew BTL, Graham NA. The landscape of metabolic pathway dependencies in cancer cell lines. PLoS Comput Biol 2021; 17:e1008942. [PMID: 33872312 PMCID: PMC8084347 DOI: 10.1371/journal.pcbi.1008942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 04/29/2021] [Accepted: 04/06/2021] [Indexed: 01/22/2023] Open
Abstract
The metabolic reprogramming of cancer cells creates metabolic vulnerabilities that can be therapeutically targeted. However, our understanding of metabolic dependencies and the pathway crosstalk that creates these vulnerabilities in cancer cells remains incomplete. Here, by integrating gene expression data with genetic loss-of-function and pharmacological screening data from hundreds of cancer cell lines, we identified metabolic vulnerabilities at the level of pathways rather than individual genes. This approach revealed that metabolic pathway dependencies are highly context-specific such that cancer cells are vulnerable to inhibition of one metabolic pathway only when activity of another metabolic pathway is altered. Notably, we also found that the no single metabolic pathway was universally essential, suggesting that cancer cells are not invariably dependent on any metabolic pathway. In addition, we confirmed that cell culture medium is a major confounding factor for the analysis of metabolic pathway vulnerabilities. Nevertheless, we found robust associations between metabolic pathway activity and sensitivity to clinically approved drugs that were independent of cell culture medium. Lastly, we used parallel integration of pharmacological and genetic dependency data to confidently identify metabolic pathway vulnerabilities. Taken together, this study serves as a comprehensive characterization of the landscape of metabolic pathway vulnerabilities in cancer cell lines.
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Affiliation(s)
- James H Joly
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, United States of America
| | - Brandon T L Chew
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, United States of America
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, United States of America.,Norris Comprehensive Cancer Center, University of Southern California, University of Southern California, Los Angeles, California, United States of America.,Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
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40
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Dubreuil MM, Morgens DW, Okumoto K, Honsho M, Contrepois K, Lee-McMullen B, Traber GM, Sood RS, Dixon SJ, Snyder MP, Fujiki Y, Bassik MC. Systematic Identification of Regulators of Oxidative Stress Reveals Non-canonical Roles for Peroxisomal Import and the Pentose Phosphate Pathway. Cell Rep 2021; 30:1417-1433.e7. [PMID: 32023459 DOI: 10.1016/j.celrep.2020.01.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/07/2019] [Accepted: 01/02/2020] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) play critical roles in metabolism and disease, yet a comprehensive analysis of the cellular response to oxidative stress is lacking. To systematically identify regulators of oxidative stress, we conducted genome-wide Cas9/CRISPR and shRNA screens. This revealed a detailed picture of diverse pathways that control oxidative stress response, ranging from the TCA cycle and DNA repair machineries to iron transport, trafficking, and metabolism. Paradoxically, disrupting the pentose phosphate pathway (PPP) at the level of phosphogluconate dehydrogenase (PGD) protects cells against ROS. This dramatically alters metabolites in the PPP, consistent with rewiring of upper glycolysis to promote antioxidant production. In addition, disruption of peroxisomal import unexpectedly increases resistance to oxidative stress by altering the localization of catalase. Together, these studies provide insights into the roles of peroxisomal matrix import and the PPP in redox biology and represent a rich resource for understanding the cellular response to oxidative stress.
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Affiliation(s)
- Michael M Dubreuil
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - David W Morgens
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Kanji Okumoto
- Department of Biology, Faculty of Sciences, Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masanori Honsho
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | | | | | - Ria S Sood
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Scott J Dixon
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305-5120, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Michael C Bassik
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305-5120, USA.
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41
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Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program. Mol Cell 2021; 80:452-469.e9. [PMID: 33157015 PMCID: PMC7654708 DOI: 10.1016/j.molcel.2020.10.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 08/19/2020] [Accepted: 10/14/2020] [Indexed: 12/22/2022]
Abstract
Although TP53 is the most commonly mutated gene in human cancers, the p53-dependent transcriptional programs mediating tumor suppression remain incompletely understood. Here, to uncover critical components downstream of p53 in tumor suppression, we perform unbiased RNAi and CRISPR-Cas9-based genetic screens in vivo. These screens converge upon the p53-inducible gene Zmat3, encoding an RNA-binding protein, and we demonstrate that ZMAT3 is an important tumor suppressor downstream of p53 in mouse KrasG12D-driven lung and liver cancers and human carcinomas. Integrative analysis of the ZMAT3 RNA-binding landscape and transcriptomic profiling reveals that ZMAT3 directly modulates exon inclusion in transcripts encoding proteins of diverse functions, including the p53 inhibitors MDM4 and MDM2, splicing regulators, and components of varied cellular processes. Interestingly, these exons are enriched in NMD signals, and, accordingly, ZMAT3 broadly affects target transcript stability. Collectively, these studies reveal ZMAT3 as a novel RNA-splicing and homeostasis regulator and a key component of p53-mediated tumor suppression.
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42
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Oughtred R, Rust J, Chang C, Breitkreutz B, Stark C, Willems A, Boucher L, Leung G, Kolas N, Zhang F, Dolma S, Coulombe‐Huntington J, Chatr‐aryamontri A, Dolinski K, Tyers M. The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci 2021; 30:187-200. [PMID: 33070389 PMCID: PMC7737760 DOI: 10.1002/pro.3978] [Citation(s) in RCA: 719] [Impact Index Per Article: 239.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023]
Abstract
The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.org) is an open-access database resource that houses manually curated protein and genetic interactions from multiple species including yeast, worm, fly, mouse, and human. The ~1.93 million curated interactions in BioGRID can be used to build complex networks to facilitate biomedical discoveries, particularly as related to human health and disease. All BioGRID content is curated from primary experimental evidence in the biomedical literature, and includes both focused low-throughput studies and large high-throughput datasets. BioGRID also captures protein post-translational modifications and protein or gene interactions with bioactive small molecules including many known drugs. A built-in network visualization tool combines all annotations and allows users to generate network graphs of protein, genetic and chemical interactions. In addition to general curation across species, BioGRID undertakes themed curation projects in specific aspects of cellular regulation, for example the ubiquitin-proteasome system, as well as specific disease areas, such as for the SARS-CoV-2 virus that causes COVID-19 severe acute respiratory syndrome. A recent extension of BioGRID, named the Open Repository of CRISPR Screens (ORCS, orcs.thebiogrid.org), captures single mutant phenotypes and genetic interactions from published high throughput genome-wide CRISPR/Cas9-based genetic screens. BioGRID-ORCS contains datasets for over 1,042 CRISPR screens carried out to date in human, mouse and fly cell lines. The biomedical research community can freely access all BioGRID data through the web interface, standardized file downloads, or via model organism databases and partner meta-databases.
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Affiliation(s)
- Rose Oughtred
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Jennifer Rust
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Christie Chang
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | | | - Chris Stark
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Andrew Willems
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Lorrie Boucher
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Genie Leung
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Nadine Kolas
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Frederick Zhang
- Arthur and Sonia Labatt Brain Tumor Research Center and Developmental and Stem Cell BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
| | - Sonam Dolma
- Arthur and Sonia Labatt Brain Tumor Research Center and Developmental and Stem Cell BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
| | | | | | - Kara Dolinski
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Mike Tyers
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
- Institute for Research in Immunology and CancerUniversité de MontréalQuebecCanada
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43
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Pasquer QTL, Tsakoumagkos IA, Hoogendoorn S. From Phenotypic Hit to Chemical Probe: Chemical Biology Approaches to Elucidate Small Molecule Action in Complex Biological Systems. Molecules 2020; 25:E5702. [PMID: 33287212 PMCID: PMC7730769 DOI: 10.3390/molecules25235702] [Citation(s) in RCA: 8] [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: 11/09/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 01/22/2023] Open
Abstract
Biologically active small molecules have a central role in drug development, and as chemical probes and tool compounds to perturb and elucidate biological processes. Small molecules can be rationally designed for a given target, or a library of molecules can be screened against a target or phenotype of interest. Especially in the case of phenotypic screening approaches, a major challenge is to translate the compound-induced phenotype into a well-defined cellular target and mode of action of the hit compound. There is no "one size fits all" approach, and recent years have seen an increase in available target deconvolution strategies, rooted in organic chemistry, proteomics, and genetics. This review provides an overview of advances in target identification and mechanism of action studies, describes the strengths and weaknesses of the different approaches, and illustrates the need for chemical biologists to integrate and expand the existing tools to increase the probability of evolving screen hits to robust chemical probes.
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Affiliation(s)
| | | | - Sascha Hoogendoorn
- Department of Organic Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211 Genève, Switzerland; (Q.T.L.P.); (I.A.T.)
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44
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Coelho AR, Oliveira PJ. Dihydroorotate dehydrogenase inhibitors in SARS-CoV-2 infection. Eur J Clin Invest 2020; 50:e13366. [PMID: 32735689 PMCID: PMC7435507 DOI: 10.1111/eci.13366] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/23/2020] [Accepted: 07/23/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Ana R Coelho
- CNC-Center for Neuroscience and Cell Biology, UC-Biotech, University of Coimbra, Cantanhede, Portugal
| | - Paulo J Oliveira
- CNC-Center for Neuroscience and Cell Biology, UC-Biotech, University of Coimbra, Cantanhede, Portugal
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45
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Orr RG, Foley SJ, Sherman C, Abreu I, Galotto G, Liu B, González-Guerrero M, Vidali L. Robust Survival-Based RNA Interference of Gene Families Using in Tandem Silencing of Adenine Phosphoribosyltransferase. PLANT PHYSIOLOGY 2020; 184:607-619. [PMID: 32764132 PMCID: PMC7536682 DOI: 10.1104/pp.20.00865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 05/07/2023]
Abstract
RNA interference (RNAi) enables flexible and dynamic interrogation of entire gene families or essential genes without the need for exogenous proteins, unlike CRISPR-Cas technology. Unfortunately, isolation of plants undergoing potent gene silencing requires laborious design, visual screening, and physical separation for downstream characterization. Here, we developed an adenine phosphoribosyltransferase (APT)-based RNAi technology (APTi) in Physcomitrella patens that improves upon the multiple limitations of current RNAi techniques. APTi exploits the prosurvival output of transiently silencing APT in the presence of 2-fluoroadenine, thereby establishing survival itself as a reporter of RNAi. To maximize the silencing efficacy of gene targets, we created vectors that facilitate insertion of any gene target sequence in tandem with the APT silencing motif. We tested the efficacy of APTi with two gene families, the actin-dependent motor, myosin XI (a,b), and the putative chitin receptor Lyk5 (a,b,c). The APTi approach resulted in a homogenous population of transient P. patens mutants specific for our gene targets with zero surviving background plants within 8 d. The observed mutants directly corresponded to a maximal 93% reduction of myosin XI protein and complete loss of chitin-induced calcium spiking in the Lyk5-RNAi background. The positive selection nature of APTi represents a fundamental improvement in RNAi technology and will contribute to the growing demand for technologies amenable to high-throughput phenotyping.
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Affiliation(s)
- Robert G Orr
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Stephen J Foley
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Catherine Sherman
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, Massachusetts 01605
| | - Isidro Abreu
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Madrid 28223, Spain
| | - Giulia Galotto
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Boyuan Liu
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Madrid 28223, Spain
| | - Luis Vidali
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
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46
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Wilkinson IVL, Terstappen GC, Russell AJ. Combining experimental strategies for successful target deconvolution. Drug Discov Today 2020; 25:S1359-6446(20)30373-1. [PMID: 32971235 DOI: 10.1016/j.drudis.2020.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/10/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
Investment in phenotypic drug discovery has led to increased demand for rapid and robust target deconvolution to aid successful drug development. Although methods for target identification and mechanism of action (MoA) discovery are flourishing, they typically lead to lists of putative targets. Validating which target(s) are involved in the therapeutic mechanism of a compound poses a significant challenge, requiring direct binding, target engagement, and functional studies in relevant physiological contexts. A combination of orthogonal approaches can allow target identification beyond the proteome as well as aid prioritisation for resource-intensive target validation studies.
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Affiliation(s)
- Isabel V L Wilkinson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Georg C Terstappen
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK
| | - Angela J Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK.
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47
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Affiliation(s)
- Cason R. King
- Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Andrew Mehle
- Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
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48
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Kim YJ, Cubitt B, Cai Y, Kuhn JH, Vitt D, Kohlhof H, de la Torre JC. Novel Dihydroorotate Dehydrogenase Inhibitors with Potent Interferon-Independent Antiviral Activity against Mammarenaviruses In Vitro. Viruses 2020; 12:v12080821. [PMID: 32751087 PMCID: PMC7472048 DOI: 10.3390/v12080821] [Citation(s) in RCA: 8] [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: 06/27/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/22/2022] Open
Abstract
Mammarenaviruses cause chronic infections in rodents, which are their predominant natural hosts. Human infection with some of these viruses causes high-consequence disease, posing significant issues in public health. Currently, no FDA-licensed mammarenavirus vaccines are available, and anti-mammarenavirus drugs are limited to an off-label use of ribavirin, which is only partially efficacious and associated with severe side effects. Dihydroorotate dehydrogenase (DHODH) inhibitors, which block de novo pyrimidine biosynthesis, have antiviral activity against viruses from different families, including Arenaviridae, the taxonomic home of mammarenaviruses. Here, we evaluate five novel DHODH inhibitors for their antiviral activity against mammarenaviruses. All tested DHODH inhibitors were potently active against lymphocytic choriomeningitis virus (LCMV) (half-maximal effective concentrations [EC50] in the low nanomolar range, selectivity index [SI] > 1000). The tested DHODH inhibitors did not affect virion cell entry or budding, but rather interfered with viral RNA synthesis. This interference resulted in a potent interferon-independent inhibition of mammarenavirus multiplication in vitro, including the highly virulent Lassa and Junín viruses.
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Affiliation(s)
- Yu-Jin Kim
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (Y.-J.K.); (B.C.)
| | - Beatrice Cubitt
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (Y.-J.K.); (B.C.)
| | - Yingyun Cai
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, MD 21702, USA; (Y.C.); (J.H.K.)
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, MD 21702, USA; (Y.C.); (J.H.K.)
| | - Daniel Vitt
- Immunic Therapeutics, New York City, NY 10036, USA; (D.V.); (H.K.)
| | - Hella Kohlhof
- Immunic Therapeutics, New York City, NY 10036, USA; (D.V.); (H.K.)
| | - Juan C. de la Torre
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (Y.-J.K.); (B.C.)
- Correspondence:
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49
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Haley B, Roudnicky F. Functional Genomics for Cancer Drug Target Discovery. Cancer Cell 2020; 38:31-43. [PMID: 32442401 DOI: 10.1016/j.ccell.2020.04.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/06/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022]
Abstract
Functional genomics describes a field of biology that uses a range of approaches for assessing gene function with high-throughput molecular, genetic, and cellular technologies. The near limitless potential for applying these concepts to study the activities of all genetic loci has completely upended how today's cancer biologists tackle drug target discovery. We provide an overview of contemporary functional genomics platforms, highlighting areas of distinction and complementarity across technologies, so as to aid in the development or interpretation of cancer-focused screening efforts.
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Affiliation(s)
- Benjamin Haley
- Molecular Biology Department, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Filip Roudnicky
- Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland.
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50
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Gonçalves E, Segura‐Cabrera A, Pacini C, Picco G, Behan FM, Jaaks P, Coker EA, van der Meer D, Barthorpe A, Lightfoot H, Mironenko T, Beck A, Richardson L, Yang W, Lleshi E, Hall J, Tolley C, Hall C, Mali I, Thomas F, Morris J, Leach AR, Lynch JT, Sidders B, Crafter C, Iorio F, Fawell S, Garnett MJ. Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens. Mol Syst Biol 2020; 16:e9405. [PMID: 32627965 PMCID: PMC7336273 DOI: 10.15252/msb.20199405] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/26/2022] Open
Abstract
Low success rates during drug development are due, in part, to the difficulty of defining drug mechanism-of-action and molecular markers of therapeutic activity. Here, we integrated 199,219 drug sensitivity measurements for 397 unique anti-cancer drugs with genome-wide CRISPR loss-of-function screens in 484 cell lines to systematically investigate cellular drug mechanism-of-action. We observed an enrichment for positive associations between the profile of drug sensitivity and knockout of a drug's nominal target, and by leveraging protein-protein networks, we identified pathways underpinning drug sensitivity. This revealed an unappreciated positive association between mitochondrial E3 ubiquitin-protein ligase MARCH5 dependency and sensitivity to MCL1 inhibitors in breast cancer cell lines. We also estimated drug on-target and off-target activity, informing on specificity, potency and toxicity. Linking drug and gene dependency together with genomic data sets uncovered contexts in which molecular networks when perturbed mediate cancer cell loss-of-fitness and thereby provide independent and orthogonal evidence of biomarkers for drug development. This study illustrates how integrating cell line drug sensitivity with CRISPR loss-of-function screens can elucidate mechanism-of-action to advance drug development.
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Affiliation(s)
| | - Aldo Segura‐Cabrera
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteHinxtonUK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Andrew R Leach
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteHinxtonUK
| | - James T Lynch
- Research and Early DevelopmentOncology R&DAstraZenecaCambridgeUK
| | - Ben Sidders
- Research and Early DevelopmentOncology R&DAstraZenecaCambridgeUK
| | - Claire Crafter
- Research and Early DevelopmentOncology R&DAstraZenecaCambridgeUK
| | - Francesco Iorio
- Wellcome Sanger InstituteHinxtonUK
- Human TechnopoleMilanoItaly
| | - Stephen Fawell
- Research and Early DevelopmentOncology R&DAstraZenecaWalthamMAUSA
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