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Oh TJ, Krishnamurthy V, Han JW, Zhu J, Beg Z, Mehfooz A, Gworek B, Shapiro DJ, Zhang K. Spatiotemporal Control of Inflammatory Lytic Cell Death Through Optogenetic Induction of RIPK3 Oligomerization. J Mol Biol 2024; 436:168628. [PMID: 38797430 PMCID: PMC11234905 DOI: 10.1016/j.jmb.2024.168628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/21/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
Necroptosis is a programmed lytic cell death involving active cytokine production and plasma membrane rupture through distinct signaling cascades. However, it remains challenging to delineate this inflammatory cell death pathway at specific signaling nodes with spatiotemporal accuracy. To address this challenge, we developed an optogenetic system, termed Light-activatable Receptor-Interacting Protein Kinase 3 or La-RIPK3, to enable ligand-free, optical induction of RIPK3 oligomerization. La-RIPK3 activation dissects RIPK3-centric lytic cell death through the induction of RIPK3-containing necrosome, which mediates cytokine production and plasma membrane rupture. Bulk RNA-Seq analysis reveals that RIPK3 oligomerization results in partially overlapped gene expression compared to pharmacological induction of necroptosis. Additionally, La-RIPK3 activates separated groups of genes regulated by RIPK3 kinase-dependent and -independent processes. Using patterned light stimulation delivered by a spatial light modulator, we demonstrate precise spatiotemporal control of necroptosis in La-RIPK3-transduced HT-29 cells. Optogenetic control of proinflammatory lytic cell death could lead to the development of innovative experimental strategies to finetune the immune landscape for disease intervention.
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Affiliation(s)
- Teak-Jung Oh
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Vishnu Krishnamurthy
- High-throughput Screening Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jeong Won Han
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Junyao Zhu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zayn Beg
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Amna Mehfooz
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bryan Gworek
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - David J Shapiro
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; NSF Science and Technology Center for Quantitative Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Oh TJ, Gworek B, Mehfooz A, Zhang K. Gene Delivery and Analysis of Optogenetic Induction of Lytic Cell Death. Curr Protoc 2024; 4:e1023. [PMID: 38606936 PMCID: PMC11163966 DOI: 10.1002/cpz1.1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Necroptosis is a form of inflammatory lytic cell death involving active cytokine production and plasma membrane rupture. Progression of necroptosis is tightly regulated in time and space, and its signaling outcomes can shape the local inflammatory environment of cells and tissues. Pharmacological induction of necroptosis is well established, but the diffusive nature of chemical death inducers makes it challenging to study cell-cell communication precisely during necroptosis. Receptor-interacting protein kinase 3, or RIPK3, is a crucial signaling component of necroptosis, acting as a crucial signaling node for both canonical and non-canonical necroptosis. RIPK3 oligomerization is crucial to the formation of the necrosome, which regulates plasma membrane rupture and cytokine production. Commonly used necroptosis inducers can activate multiple downstream signaling pathways, confounding the signaling outcomes of RIPK3-mediated necroptosis. Opsin-free optogenetic techniques may provide an alternative strategy to address this issue. Optogenetics uses light-sensitive protein-protein interaction to modulate cell signaling. Compared to chemical-based approaches, optogenetic strategies allow for spatiotemporal modulation of signal transduction in live cells and animals. We developed an optogenetic system that allows for ligand-free optical control of RIPK3 oligomerization and necroptosis. This article describes the sample preparation, experimental setup, and optimization required to achieve robust optogenetic induction of RIPK3-mediated necroptosis in colorectal HT-29 cells. We expect that this optogenetic system could provide valuable insights into the dynamic nature of lytic cell death. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Production of lentivirus encoding the optogenetic RIPK3 system Support Protocol: Quantification of the titer of lentivirus Basic Protocol 2: Culturing, chemical transfection, and lentivirus transduction of HT-29 cells Basic Protocol 3: Optimization of optogenetic stimulation conditions Basic Protocol 4: Time-stamped live-cell imaging of HT-29 lytic cell death Basic Protocol 5: Quantification of HT-29 lytic cell death.
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Affiliation(s)
- Teak-Jung Oh
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Bryan Gworek
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Amna Mehfooz
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
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Liu R, Fang M, Chen X, Yang Y. The status and challenges of optogenetic tools for precise spatiotemporal control of RNA metabolism and function. Clin Transl Med 2022; 12:e1078. [PMID: 36245329 PMCID: PMC9574486 DOI: 10.1002/ctm2.1078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 01/28/2023] Open
Affiliation(s)
- Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research CenterState Key Laboratory of Bioreactor EngineeringShanghai Frontiers Science Center of Optogenetic Techniques for Cell MetabolismEast China University of Science and TechnologyShanghaiChina
| | - Mengyue Fang
- Optogenetics & Synthetic Biology Interdisciplinary Research CenterState Key Laboratory of Bioreactor EngineeringShanghai Frontiers Science Center of Optogenetic Techniques for Cell MetabolismEast China University of Science and TechnologyShanghaiChina,School of PharmacyEast China University of Science and TechnologyShanghaiChina
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research CenterState Key Laboratory of Bioreactor EngineeringShanghai Frontiers Science Center of Optogenetic Techniques for Cell MetabolismEast China University of Science and TechnologyShanghaiChina,School of PharmacyEast China University of Science and TechnologyShanghaiChina
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research CenterState Key Laboratory of Bioreactor EngineeringShanghai Frontiers Science Center of Optogenetic Techniques for Cell MetabolismEast China University of Science and TechnologyShanghaiChina,School of PharmacyEast China University of Science and TechnologyShanghaiChina
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