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Callow MG, Watanabe C, Wickliffe KE, Bainer R, Kummerfield S, Weng J, Cuellar T, Janakiraman V, Chen H, Chih B, Liang Y, Haley B, Newton K, Costa MR. CRISPR whole-genome screening identifies new necroptosis regulators and RIPK1 alternative splicing. Cell Death Dis 2018; 9:261. [PMID: 29449584 PMCID: PMC5833675 DOI: 10.1038/s41419-018-0301-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/04/2018] [Indexed: 12/04/2022]
Abstract
The necroptotic cell death pathway is a key component of human pathogen defense that can become aberrantly derepressed during tissue homeostasis to contribute to multiple types of tissue damage and disease. While formation of the necrosome kinase signaling complex containing RIPK1, RIPK3, and MLKL has been extensively characterized, additional mechanisms of its regulation and effector functions likely remain to be discovered. We screened 19,883 mouse protein-coding genes by CRISPR/Cas9-mediated gene knockout for resistance to cytokine-induced necroptosis and identified 112 regulators and mediators of necroptosis, including 59 new candidate pathway components with minimal or no effect on cell growth in the absence of necroptosis induction. Among these, we further characterized the function of PTBP1, an RNA binding protein whose activity is required to maintain RIPK1 protein abundance by regulating alternative splice-site selection.
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Affiliation(s)
- Marinella G Callow
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Colin Watanabe
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Katherine E Wickliffe
- Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Russell Bainer
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Sarah Kummerfield
- Department of Bioinformatics and Computational Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Julie Weng
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Trinna Cuellar
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, USA
| | | | - Honglin Chen
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ben Chih
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yuxin Liang
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Michael R Costa
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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Lill JR, Wertz IE. Toward understanding ubiquitin-modifying enzymes: from pharmacological targeting to proteomics. Trends Pharmacol Sci 2014; 35:187-207. [PMID: 24717260 DOI: 10.1016/j.tips.2014.01.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 01/24/2014] [Accepted: 01/24/2014] [Indexed: 11/20/2022]
Abstract
Ubiquitination is a highly conserved post-translational modification that regulates protein trafficking, function, and turnover. Ubiquitin ligases (E3s) conjugate ubiquitin polypeptides on substrates, whereas deubiquitnases (DUBs) reverse ubiquitination. Engineering of chemical antagonists and inhibitors of ubiquitin ligases and DUBs has considerably aided the study of enzymes that participate in ubiquitin modification of substrates. In addition, proteomic tools have been developed to characterize the enzymes, substrates, and modifications regulated by DUBs and E3s. Here we review inhibitors and antagonists that have been developed against DUBs and E3s, focusing on enzymes that participate in ubiquitin editing or in the reciprocal ubiquitin regulation of substrates. We outline the cellular biology that is regulated by these DUBs and E3s and highlight how the inhibitory compounds have improved our understanding of these pathways. Finally, we discuss the challenges and future directions for pharmacologically targeting ubiquitin-modifying enzymes, as well as the development of proteomic methods to evaluate ubiquitin modification of substrates.
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Affiliation(s)
- Jennie R Lill
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, M/S 413A, South San Francisco, CA 94080, USA.
| | - Ingrid E Wertz
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, M/S 40, South San Francisco, CA 94080, USA.
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