1
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Sinigaglia K, Cherian A, Du Q, Lacovich V, Vukić D, Melicherová J, Linhartova P, Zerad L, Stejskal S, Malik R, Prochazka J, Bondurand N, Sedláček R, O'Connell MA, Keegan LP. An ADAR1 dsRBD3-PKR kinase domain interaction on dsRNA inhibits PKR activation. Cell Rep 2024; 43:114618. [PMID: 39146181 DOI: 10.1016/j.celrep.2024.114618] [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: 12/04/2023] [Revised: 05/30/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024] Open
Abstract
Adar null mutant mouse embryos die with aberrant double-stranded RNA (dsRNA)-driven interferon induction, and Adar Mavs double mutants, in which interferon induction is prevented, die soon after birth. Protein kinase R (Pkr) is aberrantly activated in Adar Mavs mouse pup intestines before death, intestinal crypt cells die, and intestinal villi are lost. Adar Mavs Eifak2 (Pkr) triple mutant mice rescue all defects and have long-term survival. Adenosine deaminase acting on RNA 1 (ADAR1) and PKR co-immunoprecipitate from cells, suggesting PKR inhibition by direct interaction. AlphaFold studies on an inhibitory PKR dsRNA binding domain (dsRBD)-kinase domain interaction before dsRNA binding and on an inhibitory ADAR1 dsRBD3-PKR kinase domain interaction on dsRNA provide a testable model of the inhibition. Wild-type or editing-inactive human ADAR1 expressed in A549 cells inhibits activation of endogenous PKR. ADAR1 dsRNA binding is required for, but is not sufficient for, PKR inhibition. Mutating the ADAR1 dsRBD3-PKR contact prevents co-immunoprecipitation, ADAR1 inhibition of PKR activity, and co-localization of ADAR1 and PKR in cells.
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Affiliation(s)
- Ketty Sinigaglia
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Anna Cherian
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Qiupei Du
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Valentina Lacovich
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Dragana Vukić
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Janka Melicherová
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czechia
| | - Pavla Linhartova
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Lisa Zerad
- Laboratory of Embryology and Genetics of Human Malformation, Imagine Institute, INSERM UMR 1163, Université de Paris Cité, 75015 Paris, France
| | - Stanislav Stejskal
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia
| | - Radek Malik
- Laboratory of Epigenetic Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czechia
| | - Jan Prochazka
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czechia
| | - Nadège Bondurand
- Laboratory of Embryology and Genetics of Human Malformation, Imagine Institute, INSERM UMR 1163, Université de Paris Cité, 75015 Paris, France
| | - Radislav Sedláček
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czechia
| | - Mary A O'Connell
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia.
| | - Liam P Keegan
- Central European Institute for Technology at Masaryk University (CEITEC MU), Building E35, Kamenice 735/5, 625 00 Brno, Czechia.
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2
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Herbert A. Osteogenesis imperfecta type 10 and the cellular scaffolds underlying common immunological diseases. Genes Immun 2024; 25:265-276. [PMID: 38811682 DOI: 10.1038/s41435-024-00277-4] [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: 12/11/2023] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024]
Abstract
Osteogenesis imperfecta type 10 (OI10) is caused by loss of function codon variants in the gene SERPINH1 that encodes heat shock protein 47 (HSP47), rather than in a gene specifying bone formation. The HSP47 variants disrupt the folding of both collagen and the endonuclease IRE1α (inositol-requiring enzyme 1α) that splices X-Box Binding Protein 1 (XBP1) mRNA. Besides impairing bone development, variants likely affect osteoclast differentiation. Three distinct biochemical scaffold play key roles in the differentiation and regulated cell death of osteoclasts. These scaffolds consist of non-templated protein modifications, ordered lipid arrays, and protein filaments. The scaffold components are specified genetically, but assemble in response to extracellular perturbagens, pathogens, and left-handed Z-RNA helices encoded genomically by flipons. The outcomes depend on interactions between RIPK1, RIPK3, TRIF, and ZBP1 through short interaction motifs called RHIMs. The causal HSP47 nonsynonymous substitutions occur in a novel variant leucine repeat region (vLRR) that are distantly related to RHIMs. Other vLRR protein variants are causal for a variety of different mendelian diseases. The same scaffolds that drive mendelian pathology are associated with many other complex disease outcomes. Their assembly is triggered dynamically by flipons and other context-specific switches rather than by causal, mendelian, codon variants.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA, USA.
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3
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Yang H, Xu S, Hong X, Liu Y, Qian S, Lou Y, Wang W. ADAR1 prevents ZBP1-dependent PANoptosis via A-to-I RNA editing in developmental sevoflurane neurotoxicity. Cell Biol Toxicol 2024; 40:57. [PMID: 39060787 PMCID: PMC11281990 DOI: 10.1007/s10565-024-09905-1] [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: 03/18/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024]
Abstract
It is well established that sevoflurane exposure leads to widespread neuronal cell death in the developing brain. Adenosine deaminase acting on RNA-1 (ADAR1) dependent adenosine-to-inosine (A-to-I) RNA editing is dynamically regulated throughout brain development. The current investigation is designed to interrogate the contributed role of ADAR1 in developmental sevoflurane neurotoxicity. Herein, we provide evidence to show that developmental sevoflurane priming triggers neuronal pyroptosis, apoptosis and necroptosis (PANoptosis), and elicits the release of inflammatory factors including IL-1β, IL-18, TNF-α and IFN-γ. Additionally, ADAR1-P150, but not ADAR1-P110, depresses cellular PANoptosis and inflammatory response by competing with Z-DNA/RNA binding protein 1 (ZBP1) for binding to Z-RNA in the presence of sevoflurane. Further investigation demonstrates that ADAR1-dependent A-to-I RNA editing mitigates developmental sevoflurane-induced neuronal PANoptosis. To restore RNA editing, we utilize adeno-associated virus (AAV) to deliver engineered circular ADAR-recruiting guide RNAs (cadRNAs) into cells, which is capable of recruiting endogenous adenosine deaminases to promote cellular A-to-I RNA editing. As anticipated, AAV-cadRNAs diminishes sevoflurane-induced cellular Z-RNA production and PANoptosis, which could be abolished by ADAR1-P150 shRNA transfection. Moreover, AAV-cadRNAs delivery ameliorates developmental sevoflurane-induced spatial and emotional cognitive deficits without influence on locomotor activity. Taken together, these results illustrate that ADAR1-P150 exhibits a prominent role in preventing ZBP1-dependent PANoptosis through A-to-I RNA editing in developmental sevoflurane neurotoxicity. Application of engineered cadRNAs to rectify the compromised ADAR1-dependent A-to-I RNA editing provides an inspiring direction for possible clinical preventions and therapeutics.
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Affiliation(s)
- Huiling Yang
- Department of Anesthesiology, Affiliated Hangzhou Xixi Hospital, Zhejiang Chinese Medical University, Hangzhou, 310023, Zhejiang, China
| | - Sen Xu
- Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Xinya Hong
- Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Yusi Liu
- Center for Rehabilitation Medicine, Department of Anesthesiology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Shaojie Qian
- Center for Rehabilitation Medicine, Department of Anesthesiology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Yifei Lou
- Department of Anesthesiology, Affiliated Hangzhou Xixi Hospital, Zhejiang Chinese Medical University, Hangzhou, 310023, Zhejiang, China
| | - Wenyuan Wang
- Center for Rehabilitation Medicine, Department of Anesthesiology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China.
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4
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Gan WL, Ren X, Ng VHE, Ng L, Song Y, Tano V, Han J, An O, Xie J, Ng BYL, Tay DJT, Tang SJ, Shen H, Khare S, Chong KHC, Young DY, Wu B, DasGupta R, Chen L. Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver. Cell Rep 2024; 43:114400. [PMID: 38935501 DOI: 10.1016/j.celrep.2024.114400] [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: 10/05/2023] [Revised: 04/23/2024] [Accepted: 06/11/2024] [Indexed: 06/29/2024] Open
Abstract
ADAR1-mediated RNA editing establishes immune tolerance to endogenous double-stranded RNA (dsRNA) by preventing its sensing, primarily by MDA5. Although deleting Ifih1 (encoding MDA5) rescues embryonic lethality in ADAR1-deficient mice, they still experience early postnatal death, and removing other MDA5 signaling proteins does not yield the same rescue. Here, we show that ablation of MDA5 in a liver-specific Adar knockout (KO) murine model fails to rescue hepatic abnormalities caused by ADAR1 loss. Ifih1;Adar double KO (dKO) hepatocytes accumulate endogenous dsRNAs, leading to aberrant transition to a highly inflammatory state and recruitment of macrophages into dKO livers. Mechanistically, progranulin (PGRN) appears to mediate ADAR1 deficiency-induced liver pathology, promoting interferon signaling and attracting epidermal growth factor receptor (EGFR)+ macrophages into dKO liver, exacerbating hepatic inflammation. Notably, the PGRN-EGFR crosstalk communication and consequent immune responses are significantly repressed in ADAR1high tumors, revealing that pre-neoplastic or neoplastic cells can exploit ADAR1-dependent immune tolerance to facilitate immune evasion.
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Affiliation(s)
- Wei Liang Gan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xi Ren
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Larry Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Vincent Tano
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jian Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jinghe Xie
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, P.R. China
| | - Bryan Y L Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Haoqing Shen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shruti Khare
- Genome Institute of Singapore, Agency for Science Technology and Research, 60 Biopolis Street, Genome, #02-01, Singapore, Singapore
| | - Kelvin Han Chung Chong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Dan Yock Young
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Division of Gastroenterology and Hepatology, National University Health System, Singapore, Singapore
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Ramanuj DasGupta
- Genome Institute of Singapore, Agency for Science Technology and Research, 60 Biopolis Street, Genome, #02-01, Singapore, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University Singapore, Singapore, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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5
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Rehwinkel J, Mehdipour P. ADAR1: from basic mechanisms to inhibitors. Trends Cell Biol 2024:S0962-8924(24)00120-X. [PMID: 39030076 DOI: 10.1016/j.tcb.2024.06.006] [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: 02/13/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/21/2024]
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) converts adenosine to inosine in double-stranded RNA (dsRNA) molecules, a process known as A-to-I editing. ADAR1 deficiency in humans and mice results in profound inflammatory diseases characterised by the spontaneous induction of innate immunity. In cells lacking ADAR1, unedited RNAs activate RNA sensors. These include melanoma differentiation-associated gene 5 (MDA5) that induces the expression of cytokines, particularly type I interferons (IFNs), protein kinase R (PKR), oligoadenylate synthase (OAS), and Z-DNA/RNA binding protein 1 (ZBP1). Immunogenic RNAs 'defused' by ADAR1 may include transcripts from repetitive elements and other long duplex RNAs. Here, we review these recent fundamental discoveries and discuss implications for human diseases. Some tumours depend on ADAR1 to escape immune surveillance, opening the possibility of unleashing anticancer therapies with ADAR1 inhibitors.
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Affiliation(s)
- Jan Rehwinkel
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Parinaz Mehdipour
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, UK.
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6
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Mannion J, Gifford V, Bellenie B, Fernando W, Ramos Garcia L, Wilson R, John SW, Udainiya S, Patin EC, Tiu C, Smith A, Goicoechea M, Craxton A, Moraes de Vasconcelos N, Guppy N, Cheung KMJ, Cundy NJ, Pierrat O, Brennan A, Roumeliotis TI, Benstead-Hume G, Alexander J, Muirhead G, Layzell S, Lyu W, Roulstone V, Allen M, Baldock H, Legrand A, Gabel F, Serrano-Aparicio N, Starling C, Guo H, Upton J, Gyrd-Hansen M, MacFarlane M, Seddon B, Raynaud F, Roxanis I, Harrington K, Haider S, Choudhary JS, Hoelder S, Tenev T, Meier P. A RIPK1-specific PROTAC degrader achieves potent antitumor activity by enhancing immunogenic cell death. Immunity 2024; 57:1514-1532.e15. [PMID: 38788712 PMCID: PMC11236506 DOI: 10.1016/j.immuni.2024.04.025] [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: 07/10/2023] [Revised: 02/14/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) functions as a critical stress sentinel that coordinates cell survival, inflammation, and immunogenic cell death (ICD). Although the catalytic function of RIPK1 is required to trigger cell death, its non-catalytic scaffold function mediates strong pro-survival signaling. Accordingly, cancer cells can hijack RIPK1 to block necroptosis and evade immune detection. We generated a small-molecule proteolysis-targeting chimera (PROTAC) that selectively degraded human and murine RIPK1. PROTAC-mediated depletion of RIPK1 deregulated TNFR1 and TLR3/4 signaling hubs, accentuating the output of NF-κB, MAPK, and IFN signaling. Additionally, RIPK1 degradation simultaneously promoted RIPK3 activation and necroptosis induction. We further demonstrated that RIPK1 degradation enhanced the immunostimulatory effects of radio- and immunotherapy by sensitizing cancer cells to treatment-induced TNF and interferons. This promoted ICD, antitumor immunity, and durable treatment responses. Consequently, targeting RIPK1 by PROTACs emerges as a promising approach to overcome radio- or immunotherapy resistance and enhance anticancer therapies.
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Affiliation(s)
- Jonathan Mannion
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Valentina Gifford
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Benjamin Bellenie
- Centre for Cancer Drug Discovery at the Institute of Cancer Research, London SM2 5NG, UK
| | - Winnie Fernando
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Laura Ramos Garcia
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Rebecca Wilson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Sidonie Wicky John
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Savita Udainiya
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Emmanuel C Patin
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London SW3 6JB, UK
| | - Crescens Tiu
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Angel Smith
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Maria Goicoechea
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Andrew Craxton
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Cambridge CB2 1QR, UK
| | | | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Kwai-Ming J Cheung
- Centre for Cancer Drug Discovery at the Institute of Cancer Research, London SM2 5NG, UK
| | - Nicholas J Cundy
- Centre for Cancer Drug Discovery at the Institute of Cancer Research, London SM2 5NG, UK
| | - Olivier Pierrat
- Centre for Cancer Drug Discovery at the Institute of Cancer Research, London SM2 5NG, UK
| | - Alfie Brennan
- Centre for Cancer Drug Discovery at the Institute of Cancer Research, London SM2 5NG, UK
| | | | - Graeme Benstead-Hume
- Functional Proteomics Group, The Institute of Cancer Research, London SW3 6JB, UK
| | - John Alexander
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Gareth Muirhead
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Scott Layzell
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, UK
| | - Wenxin Lyu
- Department of Immunology and Microbiology, LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Victoria Roulstone
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London SW3 6JB, UK
| | - Mark Allen
- Biological Services Unit, The Institute of Cancer Research, London SW3 6JB, UK
| | - Holly Baldock
- Biological Services Unit, The Institute of Cancer Research, London SW3 6JB, UK
| | - Arnaud Legrand
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Florian Gabel
- Centre for Cancer Drug Discovery at the Institute of Cancer Research, London SM2 5NG, UK
| | | | - Chris Starling
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Hongyan Guo
- Department of Microbiology and Immunology, LSU Health Shreveport, Shreveport, LA, USA
| | - Jason Upton
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Mads Gyrd-Hansen
- Department of Immunology and Microbiology, LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Marion MacFarlane
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Cambridge CB2 1QR, UK
| | - Benedict Seddon
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, UK
| | - Florence Raynaud
- Centre for Cancer Drug Discovery at the Institute of Cancer Research, London SM2 5NG, UK
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Kevin Harrington
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London SW3 6JB, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Jyoti S Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, London SW3 6JB, UK
| | - Swen Hoelder
- Centre for Cancer Drug Discovery at the Institute of Cancer Research, London SM2 5NG, UK
| | - Tencho Tenev
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK.
| | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK.
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7
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Koerner L, Wachsmuth L, Kumari S, Schwarzer R, Wagner T, Jiao H, Pasparakis M. ZBP1 causes inflammation by inducing RIPK3-mediated necroptosis and RIPK1 kinase activity-independent apoptosis. Cell Death Differ 2024; 31:938-953. [PMID: 38849574 PMCID: PMC11239871 DOI: 10.1038/s41418-024-01321-6] [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] [Received: 03/04/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Z-DNA binding protein 1 (ZBP1) has important functions in anti-viral immunity and in the regulation of inflammatory responses. ZBP1 induces necroptosis by directly engaging and activating RIPK3, however, the mechanisms by which ZBP1 induces inflammation and in particular the role of RIPK1 and the contribution of cell death-independent signaling remain elusive. Here we show that ZBP1 causes skin inflammation by inducing RIPK3-mediated necroptosis and RIPK1-caspase-8-mediated apoptosis in keratinocytes. ZBP1 induced TNFR1-independent skin inflammation in mice with epidermis-specific ablation of FADD by triggering keratinocyte necroptosis. Moreover, transgenic expression of C-terminally truncated constitutively active ZBP1 (ZBP1ca) in mouse epidermis caused skin inflammation that was only partially inhibited by abrogation of RIPK3-MLKL-dependent necroptosis and fully prevented by combined deficiency in MLKL and caspase-8. Importantly, ZBP1ca induced caspase-8-mediated skin inflammation by RHIM-dependent but kinase activity-independent RIPK1 signaling. Furthermore, ZBP1ca-induced inflammatory cytokine production in the skin was completely prevented by combined inhibition of apoptosis and necroptosis arguing against a cell death-independent pro-inflammatory function of ZBP1. Collectively, these results showed that ZBP1 induces inflammation by activating necroptosis and RIPK1 kinase activity-independent apoptosis.
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Affiliation(s)
- Lioba Koerner
- Institute for Genetics, University of Cologne, 50674, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Laurens Wachsmuth
- Institute for Genetics, University of Cologne, 50674, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Snehlata Kumari
- Institute for Genetics, University of Cologne, 50674, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- Frazer Institute, The University of Queensland, Faculty of Medicine, Brisbane, QLD, Australia
| | - Robin Schwarzer
- Institute for Genetics, University of Cologne, 50674, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- Genentech Inc, South San Francisco, CA, USA
| | - Theresa Wagner
- Institute for Genetics, University of Cologne, 50674, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Huipeng Jiao
- Institute for Genetics, University of Cologne, 50674, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Manolis Pasparakis
- Institute for Genetics, University of Cologne, 50674, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany.
- Center for Molecular Medicine (CMMC), Medical Faculty and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
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8
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Bae H, Jang Y, Karki R, Han JH. Implications of inflammatory cell death-PANoptosis in health and disease. Arch Pharm Res 2024; 47:617-631. [PMID: 38987410 DOI: 10.1007/s12272-024-01506-0] [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: 10/30/2023] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
Abstract
Regulated cell death (RCD) pathways, such as pyroptosis, apoptosis, and necroptosis, are essential for maintaining the body's balance, defending against pathogens, and eliminating abnormal cells that could lead to diseases like cancer. Although these pathways operate through distinct mechanisms, recent genetic and pharmacological studies have shown that they can interact and influence each other. The concept of "PANoptosis" has emerged, highlighting the interplay between pyroptosis, apoptosis, and necroptosis, especially during cellular responses to infections. This article provides a concise overview of PANoptosis and its molecular mechanisms, exploring its implications in various diseases. The review focuses on the extensive interactions among different RCD pathways, emphasizing the role of PANoptosis in infections, cytokine storms, inflammatory diseases, and cancer. Understanding PANoptosis is crucial for developing novel treatments for conditions involving infections, sterile inflammations, and cancer.
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Affiliation(s)
- Hyun Bae
- Department of Biological Sciences, College of Natural Science, Seoul National University, Seoul, 08826, South Korea
| | - Yeonseo Jang
- Department of Biological Sciences, College of Natural Science, Seoul National University, Seoul, 08826, South Korea
| | - Rajendra Karki
- Department of Biological Sciences, College of Natural Science, Seoul National University, Seoul, 08826, South Korea.
- Nexus Institute of Research and Innovation (NIRI), Kathmandu, Nepal.
| | - Joo-Hui Han
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Woosuk University, Wanju, 55338, Republic of Korea.
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9
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Li S, Deng X, Pathak D, Basavaraj R, Sun L, Cheng Y, Li JR, Burke M, Britz GW, Cheng C, Gao Y, Weng YL. Deficiency of m 6 A RNA methylation promotes ZBP1-mediated cell death. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.29.601251. [PMID: 38979320 PMCID: PMC11230363 DOI: 10.1101/2024.06.29.601251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
m 6 A RNA methylation suppresses the immunostimulatory potential of endogenous RNA. Deficiency of m 6 A provokes inflammatory responses and cell death, but the underlying mechanisms remain elusive. Here we showed that the noncoding RNA 7SK gains immunostimulatory potential upon m 6 A depletion and subsequently activates the RIG-I/MAVS axis to spark interferon (IFN) signaling cascades. Concomitant excess of IFN and m 6 A deficiency synergistically facilitate the formation of RNA G-quadruplexes (rG4) to promote ZBP1-mediated necroptotic cell death. Collectively, our findings delineate a hitherto uncharacterized mechanism that links m 6 A dysregulation with ZBP1 activity in triggering inflammatory cell death.
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10
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Chattopadhyay P, Mehta P, Kanika, Mishra P, Chen Liu CS, Tarai B, Budhiraja S, Pandey R. RNA editing in host lncRNAs as potential modulator in SARS-CoV-2 variants-host immune response dynamics. iScience 2024; 27:109846. [PMID: 38770134 PMCID: PMC11103575 DOI: 10.1016/j.isci.2024.109846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/18/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Both host and viral RNA editing plays a crucial role in host's response to infection, yet our understanding of host RNA editing remains limited. In this study of in-house generated RNA sequencing (RNA-seq) data of 211 hospitalized COVID-19 patients with PreVOC, Delta, and Omicron variants, we observed a significant differential editing frequency and patterns in long non-coding RNAs (lncRNAs), with Delta group displaying lower RNA editing compared to PreVOC/Omicron patients. Notably, multiple transcripts of UGDH-AS1 and NEAT1 exhibited high editing frequencies. Expression of ADAR1/APOBEC3A/APOBEC3G and differential abundance of repeats were possible modulators of differential editing across patient groups. We observed a shift in crucial infection-related pathways wherein the pathways were downregulated in Delta compared to PreVOC and Omicron. Our genomics-based evidence suggests that lncRNA editing influences stability, miRNA binding, and expression of both lncRNA and target genes. Overall, the study highlights the role of lncRNAs and how editing within host lncRNAs modulates the disease severity.
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Affiliation(s)
- Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kanika
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Pallavi Mishra
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Chinky Shiu Chen Liu
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 110017, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi 110017, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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11
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Herbert A. The ancient Z-DNA and Z-RNA specific Zα fold has evolved modern roles in immunity and transcription through the natural selection of flipons. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240080. [PMID: 39092141 PMCID: PMC11293857 DOI: 10.1098/rsos.240080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 08/04/2024]
Abstract
The Zα fold specifically binds to both Z-DNA and Z-RNA, left-handed nucleic acid structures that form under physiological conditions and are encoded by flipons. I trace the Zα fold back to unicellular organisms representing all three domains of life and to the realm of giant nucleocytoplasmic DNA viruses (NCVs). The canonical Zα fold is present in the earliest known holozoan unicellular symbiont Capsaspora owczarzaki and persists in vertebrates and some invertebrates, but not in plants or fungi. In metazoans, starting with porifera, Zα is incorporated into the double-stranded RNA editing enzyme ADAR and reflects an early symbiont relationship with NCV. In vertebrates, Zα is also present in ZBP1 and PKZ proteins that recognize host-derived Z-RNAs to defend against modern-day viruses. A related Zα fold, also likely to bind Z-DNA, is present in proteins thought to modulate gene expression, including a subset of prokaryote arsR proteins and the p15 (PC4) family present in algae. Other Zα variants that probably play a more general role in the reinitiation of transcription include the archaeal and human transcription factor E and the human RNA polymerase 3 subunit C proteins. The roles in immunity and transcription underlie the natural selection of flipons.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, 42 8th Street, Charlestown, MA02129, USA
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12
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Hu SB, Li JB. RNA editing and immune control: from mechanism to therapy. Curr Opin Genet Dev 2024; 86:102195. [PMID: 38643591 PMCID: PMC11162905 DOI: 10.1016/j.gde.2024.102195] [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: 01/18/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
Adenosine-to-inosine RNA editing, catalyzed by the enzymes ADAR1 and ADAR2, stands as a pervasive RNA modification. A primary function of ADAR1-mediated RNA editing lies in labeling endogenous double-stranded RNAs (dsRNAs) as 'self', thereby averting their potential to activate innate immune responses. Recent findings have highlighted additional roles of ADAR1, independent of RNA editing, that are crucial for immune control. Here, we focus on recent progress in understanding ADAR1's RNA editing-dependent and -independent roles in immune control. We describe how ADAR1 regulates various dsRNA innate immune receptors through distinct mechanisms. Furthermore, we discuss the implications of ADAR1 and RNA editing in diseases, including autoimmune diseases and cancers.
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Affiliation(s)
- Shi-Bin Hu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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13
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Cai ZY, Wu P, Liang H, Xie YZ, Zhang BX, He CL, Yang CR, Li H, Mo W, Yang ZH. A ZBP1 isoform blocks ZBP1-mediated cell death. Cell Rep 2024; 43:114221. [PMID: 38748877 DOI: 10.1016/j.celrep.2024.114221] [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: 01/08/2024] [Revised: 02/10/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
ZBP1 is an interferon (IFN)-induced nucleic acid (NA) sensor that senses unusual Z-form NA (Z-NA) to promote cell death and inflammation. However, the mechanisms that dampen ZBP1 activation to fine-tune inflammatory responses are unclear. Here, we characterize a short isoform of ZBP1 (referred to as ZBP1-S) as an intrinsic suppressor of the inflammatory signaling mediated by full-length ZBP1. Mechanistically, ZBP1-S depresses ZBP1-mediated cell death by competitive binding with Z-NA for Zα domains of ZBP1. Cells from mice (Ripk1D325A/D325A) with cleavage-resistant RIPK1-induced autoinflammatory (CRIA) syndrome are alive but sensitive to IFN-induced and ZBP1-dependent cell death. Intriguingly, Ripk1D325A/D325A cells die spontaneously when ZBP1-S is deleted, indicating that cell death driven by ZBP1 is under the control of ZBP1-S. Thus, our findings reveal that alternative splicing of Zbp1 represents autogenic inhibition for regulating ZBP1 signaling and indicate that uncoupling of Z-NA with ZBP1 could be an effective strategy against autoinflammations.
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Affiliation(s)
- Zhi-Yu Cai
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 310012, China
| | - Puqi Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hao Liang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yu-Ze Xie
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Bo-Xin Zhang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 310012, China
| | - Cai-Ling He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Cong-Rong Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hongda Li
- Institute for Brain Science and Disease, Key Laboratory of Major Brain Disease and Aging Research (Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Wei Mo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 310012, China; Department of Immunology, School of Basic Medical Science, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310012, China; Institute for Brain Science and Disease, Key Laboratory of Major Brain Disease and Aging Research (Ministry of Education), Chongqing Medical University, Chongqing 400016, China.
| | - Zhang-Hua Yang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 310012, China.
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14
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Huang E, Frydman C, Xiao X. Navigating the landscape of epitranscriptomics and host immunity. Genome Res 2024; 34:515-529. [PMID: 38702197 PMCID: PMC11146601 DOI: 10.1101/gr.278412.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Abstract
RNA modifications, also termed epitranscriptomic marks, encompass chemical alterations to individual nucleotides, including processes such as methylation and editing. These marks contribute to a wide range of biological processes, many of which are related to host immune system defense. The functions of immune-related RNA modifications can be categorized into three main groups: regulation of immunogenic RNAs, control of genes involved in innate immune response, and facilitation of adaptive immunity. Here, we provide an overview of recent research findings that elucidate the contributions of RNA modifications to each of these processes. We also discuss relevant methods for genome-wide identification of RNA modifications and their immunogenic substrates. Finally, we highlight recent advances in cancer immunotherapies that aim to reduce cancer cell viability by targeting the enzymes responsible for RNA modifications. Our presentation of these dynamic research avenues sets the stage for future investigations in this field.
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Affiliation(s)
- Elaine Huang
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Clara Frydman
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA;
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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15
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Lai K, Wang J, Lin S, Chen Z, Lin G, Ye K, Yuan Y, Lin Y, Zhong CQ, Wu J, Ma H, Xu Y. Sensing of mitochondrial DNA by ZBP1 promotes RIPK3-mediated necroptosis and ferroptosis in response to diquat poisoning. Cell Death Differ 2024; 31:635-650. [PMID: 38493248 PMCID: PMC11094118 DOI: 10.1038/s41418-024-01279-5] [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: 12/12/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Diquat (DQ) poisoning is a severe medical condition associated with life-threatening implications and multiorgan dysfunction. Despite its clinical significance, the precise underlying mechanism remains inadequately understood. This study elucidates that DQ induces instability in the mitochondrial genome of endothelial cells, resulting in the accumulation of Z-form DNA. This process activates Z-DNA binding protein 1 (ZBP1), which then interacts with receptor-interacting protein kinase 3 (RIPK3), ultimately leading to RIPK3-dependent necroptotic and ferroptotic signaling cascades. Specific deletion of either Zbp1 or Ripk3 in endothelial cells simultaneously inhibits both necroptosis and ferroptosis. This dual inhibition significantly reduces organ damage and lowers mortality rate. Notably, our investigation reveals that RIPK3 has a dual role. It not only phosphorylates MLKL to induce necroptosis but also phosphorylates FSP1 to inhibit its enzymatic activity, promoting ferroptosis. The study further shows that deletion of mixed lineage kinase domain-like (Mlkl) and the augmentation of ferroptosis suppressor protein 1 (FSP1)-dependent non-canonical vitamin K cycling can provide partial protection against DQ-induced organ damage. Combining Mlkl deletion with vitamin K treatment demonstrates a heightened efficacy in ameliorating multiorgan damage and lethality induced by DQ. Taken together, this study identifies ZBP1 as a crucial sensor for DQ-induced mitochondrial Z-form DNA, initiating RIPK3-dependent necroptosis and ferroptosis. These findings suggest that targeting the ZBP1/RIPK3-dependent necroptotic and ferroptotic pathways could be a promising approach for drug interventions aimed at mitigating the adverse consequences of DQ poisoning.
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Affiliation(s)
- Kunmei Lai
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
- Central Laboratory, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Junjie Wang
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Siyi Lin
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Zhimin Chen
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Guo Lin
- Department of Intensive Care Unit, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Keng Ye
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Ying Yuan
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Yujiao Lin
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Chuan-Qi Zhong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jianfeng Wu
- Laboratory Animal Research Center, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Huabin Ma
- Central Laboratory, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
| | - Yanfang Xu
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Central Laboratory, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
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16
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Meier P, Legrand AJ, Adam D, Silke J. Immunogenic cell death in cancer: targeting necroptosis to induce antitumour immunity. Nat Rev Cancer 2024; 24:299-315. [PMID: 38454135 DOI: 10.1038/s41568-024-00674-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/26/2024] [Indexed: 03/09/2024]
Abstract
Most metastatic cancers remain incurable due to the emergence of apoptosis-resistant clones, fuelled by intratumour heterogeneity and tumour evolution. To improve treatment, therapies should not only kill cancer cells but also activate the immune system against the tumour to eliminate any residual cancer cells that survive treatment. While current cancer therapies rely heavily on apoptosis - a largely immunologically silent form of cell death - there is growing interest in harnessing immunogenic forms of cell death such as necroptosis. Unlike apoptosis, necroptosis generates second messengers that act on immune cells in the tumour microenvironment, alerting them of danger. This lytic form of cell death optimizes the provision of antigens and adjuvanticity for immune cells, potentially boosting anticancer treatment approaches by combining cellular suicide and immune response approaches. In this Review, we discuss the mechanisms of necroptosis and how it activates antigen-presenting cells, drives cross-priming of CD8+ T cells and induces antitumour immune responses. We also examine the opportunities and potential drawbacks of such strategies for exposing cancer cells to immunological attacks.
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Affiliation(s)
- Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, UK.
| | - Arnaud J Legrand
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, UK
| | - Dieter Adam
- Institut für Immunologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - John Silke
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
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17
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Wang S, Song A, Xie J, Wang YY, Wang WD, Zhang MJ, Wu ZZ, Yang QC, Li H, Zhang J, Sun ZJ. Fn-OMV potentiates ZBP1-mediated PANoptosis triggered by oncolytic HSV-1 to fuel antitumor immunity. Nat Commun 2024; 15:3669. [PMID: 38693119 PMCID: PMC11063137 DOI: 10.1038/s41467-024-48032-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/17/2024] [Indexed: 05/03/2024] Open
Abstract
Oncolytic viruses (OVs) show promise as a cancer treatment by selectively replicating in tumor cells and promoting antitumor immunity. However, the current immunogenicity induced by OVs for tumor treatment is relatively weak, necessitating a thorough investigation of the mechanisms underlying its induction of antitumor immunity. Here, we show that HSV-1-based OVs (oHSVs) trigger ZBP1-mediated PANoptosis (a unique innate immune inflammatory cell death modality), resulting in augmented antitumor immune effects. Mechanistically, oHSV enhances the expression of interferon-stimulated genes, leading to the accumulation of endogenous Z-RNA and subsequent activation of ZBP1. To further enhance the antitumor potential of oHSV, we conduct a screening and identify Fusobacterium nucleatum outer membrane vesicle (Fn-OMV) that can increase the expression of PANoptosis execution proteins. The combination of Fn-OMV and oHSV demonstrates potent antitumor immunogenicity. Taken together, our study provides a deeper understanding of oHSV-induced antitumor immunity, and demonstrates a promising strategy that combines oHSV with Fn-OMV.
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Affiliation(s)
- Shuo Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
| | - An Song
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
| | - Jun Xie
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Province Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yuan-Yuan Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
| | - Wen-Da Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
| | - Meng-Jie Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
| | - Zhi-Zhong Wu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
| | - Qi-Chao Yang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
| | - Hao Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
| | - Junjie Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China.
- Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Province Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Zhi-Jun Sun
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China.
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18
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Huang Y, Jiang W, Zhou R. DAMP sensing and sterile inflammation: intracellular, intercellular and inter-organ pathways. Nat Rev Immunol 2024:10.1038/s41577-024-01027-3. [PMID: 38684933 DOI: 10.1038/s41577-024-01027-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2024] [Indexed: 05/02/2024]
Abstract
Damage-associated molecular patterns (DAMPs) are endogenous molecules that are released from host cells as a result of cell death or damage. The release of DAMPs in tissues is associated with loss of tissue homeostasis. Sensing of DAMPs by innate immune receptors triggers inflammation, which can be beneficial in initiating the processes that restore tissue homeostasis but can also drive inflammatory diseases. In recent years, the sensing of intracellular DAMPs has received extensive attention in the field of sterile inflammation. However, emerging studies have shown that DAMPs that originate from neighbouring cells, and even from distal tissues or organs, also mediate sterile inflammatory responses. This multi-level sensing of DAMPs is crucial for intercellular, trans-tissue and trans-organ communication. Here, we summarize how DAMP-sensing receptors detect DAMPs from intracellular, intercellular or distal tissue and organ sources to mediate sterile inflammation. We also discuss the possibility of targeting DAMPs or their corresponding receptors to treat inflammatory diseases.
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Affiliation(s)
- Yi Huang
- Key Laboratory of Immune Response and Immunotherapy, Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
| | - Wei Jiang
- Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Rongbin Zhou
- Key Laboratory of Immune Response and Immunotherapy, Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China.
- Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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19
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Jarmoskaite I, Li JB. Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity. RNA (NEW YORK, N.Y.) 2024; 30:500-511. [PMID: 38531645 PMCID: PMC11019752 DOI: 10.1261/rna.079953.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Innate immunity must be tightly regulated to enable sensitive pathogen detection while averting autoimmunity triggered by pathogen-like host molecules. A hallmark of viral infection, double-stranded RNAs (dsRNAs) are also abundantly encoded in mammalian genomes, necessitating surveillance mechanisms to distinguish "self" from "nonself." ADAR1, an RNA editing enzyme, has emerged as an essential safeguard against dsRNA-induced autoimmunity. By converting adenosines to inosines (A-to-I) in long dsRNAs, ADAR1 covalently marks endogenous dsRNAs, thereby blocking the activation of the cytoplasmic dsRNA sensor MDA5. Moreover, beyond its editing function, ADAR1 binding to dsRNA impedes the activation of innate immune sensors PKR and ZBP1. Recent landmark studies underscore the utility of silencing ADAR1 for cancer immunotherapy, by exploiting the ADAR1-dependence developed by certain tumors to unleash an antitumor immune response. In this perspective, we summarize the genetic and mechanistic evidence for ADAR1's multipronged role in suppressing dsRNA-mediated autoimmunity and explore the evolving roles of ADAR1 as an immuno-oncology target.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- AIRNA Corporation, Cambridge, Massachusetts 02142, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, California 94305, USA
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20
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Ma M, Jiang W, Zhou R. DAMPs and DAMP-sensing receptors in inflammation and diseases. Immunity 2024; 57:752-771. [PMID: 38599169 DOI: 10.1016/j.immuni.2024.03.002] [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: 12/18/2023] [Revised: 02/17/2024] [Accepted: 03/01/2024] [Indexed: 04/12/2024]
Abstract
Damage-associated molecular patterns (DAMPs) are endogenous danger molecules produced in cellular damage or stress, and they can activate the innate immune system. DAMPs contain multiple types of molecules, including nucleic acids, proteins, ions, glycans, and metabolites. Although these endogenous molecules do not trigger immune response under steady-state condition, they may undergo changes in distribution, physical or chemical property, or concentration upon cellular damage or stress, and then they become DAMPs that can be sensed by innate immune receptors to induce inflammatory response. Thus, DAMPs play an important role in inflammation and inflammatory diseases. In this review, we summarize the conversion of homeostatic molecules into DAMPs; the diverse nature and classification, cellular origin, and sensing of DAMPs; and their role in inflammation and related diseases. Furthermore, we discuss the clinical strategies to treat DAMP-associated diseases via targeting DAMP-sensing receptors.
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Affiliation(s)
- Ming Ma
- Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Wei Jiang
- Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China
| | - Rongbin Zhou
- Key Laboratory of Immune Response and Immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, Anhui, China; Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China.
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21
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Song Q, Qi Z, Wang K, Wang N. Z-nucleic acid sensor ZBP1 in sterile inflammation. Clin Immunol 2024; 261:109938. [PMID: 38346464 DOI: 10.1016/j.clim.2024.109938] [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: 10/06/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
Z-DNA binding protein 1 (ZBP1), a cytosolic nucleic acid sensor for Z-form nucleic acids (Z-NA), can detect both exogenous and endogenous nucleic acids. Upon sensing of self Z-NA or exposure to diverse noxious stimuli, ZBP1 regulates inflammation by activating nuclear factor kappa B and interferon regulating factor 3 signaling pathways. In addition, ZBP1 promotes the assembly of ZBP1 PANoptosome, which initiates caspase 3-mediated apoptosis, mixed lineage kinase domain like pseudokinase (MLKL)-mediated necroptosis, and gasdermin D (GSDMD)-mediated pyroptosis (PANoptosis), leading to the release of various damage-associated molecular patterns. Thereby, ZBP1 is implicated in the development and progression of diverse sterile inflammatory diseases. This review outlines the expression, structure, and function of ZBP1, along with its dual roles in controlling inflammation and cell death to orchestrate innate immunity in sterile inflammation, especially autoimmune diseases, and cancers. ZBP1 has emerged as an attractive therapeutic target for various sterile inflammatory diseases.
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Affiliation(s)
- Qixiang Song
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan, China; Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, Hunan, China
| | - Zehong Qi
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan, China; Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, Hunan, China
| | - Kangkai Wang
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan, China; Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, Hunan, China.
| | - Nian Wang
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan, China; Sepsis Translational Medicine Key Lab of Hunan Province, Changsha, Hunan, China.
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22
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de Reuver R, Maelfait J. Novel insights into double-stranded RNA-mediated immunopathology. Nat Rev Immunol 2024; 24:235-249. [PMID: 37752355 DOI: 10.1038/s41577-023-00940-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2023] [Indexed: 09/28/2023]
Abstract
Recent progress in human and mouse genetics has transformed our understanding of the molecular mechanisms by which recognition of self double-stranded RNA (self-dsRNA) causes immunopathology. Novel mouse models recapitulate loss-of-function mutations in the RNA editing enzyme ADAR1 that are found in patients with Aicardi-Goutières syndrome (AGS) - a monogenic inflammatory disease associated with increased levels of type I interferon. Extensive analyses of the genotype-phenotype relationships in these mice have now firmly established a causal relationship between increased intracellular concentrations of endogenous immunostimulatory dsRNA and type I interferon-driven immunopathology. Activation of the dsRNA-specific immune sensor MDA5 perpetuates the overproduction of type I interferons, and chronic engagement of the interferon-inducible innate immune receptors PKR and ZBP1 by dsRNA drives immunopathology by activating an integrated stress response or by inducing excessive cell death. Biochemical and genetic data support a role for the p150 isoform of ADAR1 in the cytosol in suppressing the spontaneous, pathological response to self-dsRNA.
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Affiliation(s)
- Richard de Reuver
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jonathan Maelfait
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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23
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Yang K, Jeltema D, Yan N. Innate immune sensing of macromolecule homeostasis. Adv Immunol 2024; 161:17-51. [PMID: 38763701 DOI: 10.1016/bs.ai.2024.03.004] [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: 05/21/2024]
Abstract
The innate immune system uses a distinct set of germline-encoded pattern recognition receptors to recognize molecular patterns initially thought to be unique to microbial invaders, named pathogen-associated molecular patterns. The concept was later further developed to include similar molecular patterns originating from host cells during tissue damage, known as damage-associated molecular patterns. However, recent advances in the mechanism of monogenic inflammatory diseases have highlighted a much more expansive repertoire of cellular functions that are monitored by innate immunity. Here, we summarize several examples in which an innate immune response is triggered when homeostasis of macromolecule in the cell is disrupted in non-infectious or sterile settings. These ever-growing sensing mechanisms expand the repertoire of innate immune recognition, positioning it not only as a key player in host defense but also as a gatekeeper of cellular homeostasis. Therapeutics inspired by these advances to restore cellular homeostasis and correct the immune system could have far-reaching implications.
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Affiliation(s)
- Kun Yang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Devon Jeltema
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Nan Yan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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24
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Wang Z, Zhang D, Qiu X, Inuzuka H, Xiong Y, Liu J, Chen L, Chen H, Xie L, Kaniskan HÜ, Chen X, Jin J, Wei W. Structurally Specific Z-DNA Proteolysis Targeting Chimera Enables Targeted Degradation of Adenosine Deaminase Acting on RNA 1. J Am Chem Soc 2024; 146:7584-7593. [PMID: 38469801 PMCID: PMC10988290 DOI: 10.1021/jacs.3c13646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Given the prevalent advancements in DNA- and RNA-based PROTACs, there remains a significant need for the exploration and expansion of more specific DNA-based tools, thus broadening the scope and repertoire of DNA-based PROTACs. Unlike conventional A- or B-form DNA, Z-form DNA is a configuration that exclusively manifests itself under specific stress conditions and with specific target sequences, which can be recognized by specific reader proteins, such as ADAR1 or ZBP1, to exert downstream biological functions. The core of our innovation lies in the strategic engagement of Z-form DNA with ADAR1 and its degradation is achieved by leveraging a VHL ligand conjugated to Z-form DNA to recruit the E3 ligase. This ingenious construct engendered a series of Z-PROTACs, which we utilized to selectively degrade the Z-DNA-binding protein ADAR1, a molecule that is frequently overexpressed in cancer cells. This meticulously orchestrated approach triggers a cascade of PANoptotic events, notably encompassing apoptosis and necroptosis, by mitigating the blocking effect of ADAR1 on ZBP1, particularly in cancer cells compared with normal cells. Moreover, the Z-PROTAC design exhibits a pronounced predilection for ADAR1, as opposed to other Z-DNA readers, such as ZBP1. As such, Z-PROTAC likely elicits a positive immunological response, subsequently leading to a synergistic augmentation of cancer cell death. In summary, the Z-DNA-based PROTAC (Z-PROTAC) approach introduces a modality generated by the conformational change from B- to Z-form DNA, which harnesses the structural specificity intrinsic to potentiate a selective degradation strategy. This methodology is an inspiring conduit for the advancement of PROTAC-based therapeutic modalities, underscoring its potential for selectivity within the therapeutic landscape of PROTACs to target undruggable proteins.
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Affiliation(s)
- Zhen Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Dingpeng Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Xing Qiu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Li Chen
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - He Chen
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Ling Xie
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 United States
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xian Chen
- Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
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25
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Bhatt U, Cucchiarini A, Luo Y, Evans CW, Mergny JL, Iyer KS, Smith NM. Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA. Genome Res 2024; 34:217-230. [PMID: 38355305 PMCID: PMC10984386 DOI: 10.1101/gr.278236.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Secondary structure is a principal determinant of lncRNA function, predominantly regarding scaffold formation and interfaces with target molecules. Noncanonical secondary structures that form in nucleic acids have known roles in regulating gene expression and include G-quadruplexes (G4s), intercalated motifs (iMs), and R-loops (RLs). In this paper, we used the computational tools G4-iM Grinder and QmRLFS-finder to predict the formation of each of these structures throughout the lncRNA transcriptome in comparison to protein-coding transcripts. The importance of the predicted structures in lncRNAs in biological contexts was assessed by combining our results with publicly available lncRNA tissue expression data followed by pathway analysis. The formation of predicted G4 (pG4) and iM (piM) structures in select lncRNA sequences was confirmed in vitro using biophysical experiments under near-physiological conditions. We find that the majority of the tested pG4s form highly stable G4 structures, and identify many previously unreported G4s in biologically important lncRNAs. In contrast, none of the piM sequences are able to form iM structures, consistent with the idea that RNA is unable to form stable iMs. Unexpectedly, these C-rich sequences instead form Z-RNA structures, which have not been previously observed in regions containing cytosine repeats and represent an interesting and underexplored target for protein-RNA interactions. Our results highlight the prevalence and potential structure-associated functions of noncanonical secondary structures in lncRNAs, and show G4 and Z-RNA structure formation in many lncRNA sequences for the first time, furthering the understanding of the structure-function relationship in lncRNAs.
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Affiliation(s)
- Uditi Bhatt
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Yu Luo
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - K Swaminathan Iyer
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia;
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26
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Zhang D, Zhu L, Gao Y, Wang Y, Li P. RNA editing enzymes: structure, biological functions and applications. Cell Biosci 2024; 14:34. [PMID: 38493171 PMCID: PMC10944622 DOI: 10.1186/s13578-024-01216-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
With the advancement of sequencing technologies and bioinformatics, over than 170 different RNA modifications have been identified. However, only a few of these modifications can lead to base pair changes, which are called RNA editing. RNA editing is a ubiquitous modification in mammalian transcriptomes and is an important co/posttranscriptional modification that plays a crucial role in various cellular processes. There are two main types of RNA editing events: adenosine to inosine (A-to-I) editing, catalyzed by ADARs on double-stranded RNA or ADATs on tRNA, and cytosine to uridine (C-to-U) editing catalyzed by APOBECs. This article provides an overview of the structure, function, and applications of RNA editing enzymes. We discuss the structural characteristics of three RNA editing enzyme families and their catalytic mechanisms in RNA editing. We also explain the biological role of RNA editing, particularly in innate immunity, cancer biogenesis, and antiviral activity. Additionally, this article describes RNA editing tools for manipulating RNA to correct disease-causing mutations, as well as the potential applications of RNA editing enzymes in the field of biotechnology and therapy.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
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27
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Liu H, Liu YX, Fan W, Fan B. Metformin switches cell death modes to soothe the apical periodontitis via ZBP1. FASEB J 2024; 38:e23549. [PMID: 38446465 DOI: 10.1096/fj.202302073r] [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: 10/11/2023] [Revised: 01/08/2024] [Accepted: 02/26/2024] [Indexed: 03/07/2024]
Abstract
Apical periodontitis (AP) is a disease caused by pathogenic microorganisms and featured with the degradation of periapical hard tissue. Our recent research showed the crucial role of Z-DNA binding protein 1 (ZBP1)-mediated necroptosis and apoptosis in the pathogenesis of AP. However, the specific regulatory mechanisms of ZBP1 in AP are not fully elucidated. It was found that metformin has a regulatory role in cell necroptosis and apoptosis. But whether and how metformin regulates necroptosis and apoptosis through the ZBP1 in the context of AP remains unknown. This study provided evidence that lipopolysaccharide (LPS) promotes the synthesis of left-handed Z-nucleic acids (Z-NA), which in turn activates ZBP1. Knockout of Zbp1 by CRISPR/Cas9 technology significantly reduced LPS-induced necroptosis and apoptosis in vitro. By using Zbp1-knockout mice, periapical bone destruction was alleviated. Moreover, type I interferon induced the expression of interferon-stimulated genes (ISGs), which serve as a major source of Z-NA. In addition, the RNA-editing enzyme Adenosine Deaminase RNA specific 1 (ADAR1) prevented the accumulation of endogenous Z-NA. Meanwhile, metformin suppressed the ZBP1-mediated necroptosis by inhibiting the expression of ZBP1 and the accumulation of ISGs. Metformin also promoted mitochondrial apoptosis, which is critical for the elimination of intracellular bacterial infection. The enhanced apoptosis further promoted the healing of infected apical bone tissues. In summary, these results demonstrated that the recognition of Z-NA by ZBP1 plays an important role in AP pathogenesis. Metformin suppressed ZBP1-mediated necroptosis and promoted apoptosis, thereby contributing to the soothing of inflammation and bone healing in AP.
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Affiliation(s)
- Hui Liu
- The State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yu-Xuan Liu
- The State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Wei Fan
- The State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Bing Fan
- The State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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28
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Yoshinaga M, Takeuchi O. Regulation of inflammatory diseases via the control of mRNA decay. Inflamm Regen 2024; 44:14. [PMID: 38491500 PMCID: PMC10941436 DOI: 10.1186/s41232-024-00326-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/02/2024] [Indexed: 03/18/2024] Open
Abstract
Inflammation orchestrates a finely balanced process crucial for microorganism elimination and tissue injury protection. A multitude of immune and non-immune cells, alongside various proinflammatory cytokines and chemokines, collectively regulate this response. Central to this regulation is post-transcriptional control, governing gene expression at the mRNA level. RNA-binding proteins such as tristetraprolin, Roquin, and the Regnase family, along with RNA modifications, intricately dictate the mRNA decay of pivotal mediators and regulators in the inflammatory response. Dysregulated activity of these factors has been implicated in numerous human inflammatory diseases, underscoring the significance of post-transcriptional regulation. The increasing focus on targeting these mechanisms presents a promising therapeutic strategy for inflammatory and autoimmune diseases. This review offers an extensive overview of post-transcriptional regulation mechanisms during inflammatory responses, delving into recent advancements, their implications in human diseases, and the strides made in therapeutic exploitation.
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Affiliation(s)
- Masanori Yoshinaga
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
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29
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Luca D, Lee S, Hirota K, Okabe Y, Uehori J, Izawa K, Lanz AL, Schütte V, Sivri B, Tsukamoto Y, Hauck F, Behrendt R, Roers A, Fujita T, Nishikomori R, Lee-Kirsch MA, Kato H. Aberrant RNA sensing in regulatory T cells causes systemic autoimmunity. SCIENCE ADVANCES 2024; 10:eadk0820. [PMID: 38427731 PMCID: PMC10906915 DOI: 10.1126/sciadv.adk0820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024]
Abstract
Chronic and aberrant nucleic acid sensing causes type I IFN-driven autoimmune diseases, designated type I interferonopathies. We found a significant reduction of regulatory T cells (Tregs) in patients with type I interferonopathies caused by mutations in ADAR1 or IFIH1 (encoding MDA5). We analyzed the underlying mechanisms using murine models and found that Treg-specific deletion of Adar1 caused peripheral Treg loss and scurfy-like lethal autoimmune disorders. Similarly, knock-in mice with Treg-specific expression of an MDA5 gain-of-function mutant caused apoptosis of peripheral Tregs and severe autoimmunity. Moreover, the impact of ADAR1 deficiency on Tregs is multifaceted, involving both MDA5 and PKR sensing. Together, our results highlight the dysregulation of Treg homeostasis by intrinsic aberrant RNA sensing as a potential determinant for type I interferonopathies.
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Affiliation(s)
- Domnica Luca
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Sumin Lee
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Laboratory of Regulatory Information, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Keiji Hirota
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
- Laboratory of Integrative Biological Science, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasutaka Okabe
- Laboratory of Immune Homeostasis, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan
| | - Junji Uehori
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kazushi Izawa
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Anna-Lisa Lanz
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Munich Centre for Rare Diseases (M-ZSE), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Verena Schütte
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Burcu Sivri
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Yuta Tsukamoto
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Fabian Hauck
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Munich Centre for Rare Diseases (M-ZSE), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Rayk Behrendt
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Axel Roers
- Institute of Immunology, University of Heidelberg, Heidelberg, Germany
| | - Takashi Fujita
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Laboratory of Regulatory Information, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Ryuta Nishikomori
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, University Hospital Carl Gustav Carus and Medical Faculty, Technische Universität Dresden, Dresden, Germany
- University Center for Rare Diseases, University Hospital Carl Gustav Carus and Medical Faculty, Technische Universität Dresden, Dresden, Germany
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
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30
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Zhan J, Wang J, Liang Y, Wang L, Huang L, Liu S, Zeng X, Zeng E, Wang H. Apoptosis dysfunction: unravelling the interplay between ZBP1 activation and viral invasion in innate immune responses. Cell Commun Signal 2024; 22:149. [PMID: 38402193 PMCID: PMC10893743 DOI: 10.1186/s12964-024-01531-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/13/2024] [Indexed: 02/26/2024] Open
Abstract
Apoptosis plays a pivotal role in pathogen elimination and maintaining homeostasis. However, viruses have evolved strategies to evade apoptosis, enabling their persistence within the host. Z-DNA binding protein 1 (ZBP1) is a potent innate immune sensor that detects cytoplasmic nucleic acids and activates the innate immune response to clear pathogens. When apoptosis is inhibited by viral invasion, ZBP1 can be activated to compensate for the effect of apoptosis by triggering an innate immune response. This review examined the mechanisms of apoptosis inhibition and ZBP1 activation during viral invasion. The authors outlined the mechanisms of ZBP1-induced type I interferon, pyroptosis and necroptosis, as well as the crosstalk between ZBP1 and the cGAS-STING signalling pathway. Furthermore, ZBP1 can reverse the suppression of apoptotic signals induced by viruses. Intriguingly, a positive feedback loop exists in the ZBP1 signalling pathway, which intensifies the innate immune response while triggering a cytokine storm, leading to tissue and organ damage. The prudent use of ZBP1, which is a double-edged sword, has significant clinical implications for treating infections and inflammation.
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Affiliation(s)
- Jianhao Zhan
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
- HuanKui Academy, Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Jisheng Wang
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Yuqing Liang
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Lisha Wang
- HuanKui Academy, Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Le Huang
- HuanKui Academy, Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Shanshan Liu
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330006, China
| | - Xiaoping Zeng
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330006, China
- Medical College, Jinhua Polytechnic, Jinhua, Zhejiang Province, 321017, China
| | - Erming Zeng
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China.
| | - Hongmei Wang
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330006, China.
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330006, China.
- Medical College, Jinhua Polytechnic, Jinhua, Zhejiang Province, 321017, China.
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31
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Klein B, Reynolds MB, Xu B, Gharaee-Kermani M, Gao Y, Berthier CC, Henning S, Loftus SN, McNeely KE, Victory AM, Dobry C, Hile GA, Ma F, Turnier JL, Gudjonsson JE, O’Riordan MX, Kahlenberg JM. Epidermal ZBP1 stabilizes mitochondrial Z-DNA to drive UV-induced IFN signaling in autoimmune photosensitivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576771. [PMID: 38328232 PMCID: PMC10849619 DOI: 10.1101/2024.01.23.576771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Photosensitivity is observed in numerous autoimmune diseases and drives poor quality of life and disease flares. Elevated epidermal type I interferon (IFN) production primes for photosensitivity and enhanced inflammation, but the substrates that sustain and amplify this cycle remain undefined. Here, we show that IFN-induced Z-DNA binding protein 1 (ZBP1) stabilizes ultraviolet (UV)B-induced cytosolic Z-DNA derived from oxidized mitochondrial DNA. ZBP1 is significantly upregulated in the epidermis of adult and pediatric patients with autoimmune photosensitivity. Strikingly, lupus keratinocytes accumulate extensive cytosolic Z-DNA after UVB, and transfection of keratinocytes with Z-DNA results in stronger IFN production through cGAS-STING activation compared to B-DNA. ZBP1 knockdown abrogates UV-induced IFN responses, whereas overexpression results in a lupus-like phenotype with spontaneous Z-DNA accumulation and IFN production. Our results highlight Z-DNA and ZBP1 as critical mediators for UVB-induced inflammation and uncover how type I IFNs prime for cutaneous inflammation in photosensitivity.
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Affiliation(s)
- Benjamin Klein
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Mack B. Reynolds
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor
| | - Bin Xu
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Mehrnaz Gharaee-Kermani
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan
| | - Yiqing Gao
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Celine C. Berthier
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Svenja Henning
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Shannon N. Loftus
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Kelsey E. McNeely
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Amanda M. Victory
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Craig Dobry
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan
| | - Grace A. Hile
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan
| | - Feiyang Ma
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan
| | - Jessica L. Turnier
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Michigan, Ann Arbor
| | | | - Mary X. O’Riordan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor
| | - J. Michelle Kahlenberg
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan
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32
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Newton K, Strasser A, Kayagaki N, Dixit VM. Cell death. Cell 2024; 187:235-256. [PMID: 38242081 DOI: 10.1016/j.cell.2023.11.044] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/18/2023] [Accepted: 11/30/2023] [Indexed: 01/21/2024]
Abstract
Cell death supports morphogenesis during development and homeostasis after birth by removing damaged or obsolete cells. It also curtails the spread of pathogens by eliminating infected cells. Cell death can be induced by the genetically programmed suicide mechanisms of apoptosis, necroptosis, and pyroptosis, or it can be a consequence of dysregulated metabolism, as in ferroptosis. Here, we review the signaling mechanisms underlying each cell-death pathway, discuss how impaired or excessive activation of the distinct cell-death processes can promote disease, and highlight existing and potential therapies for redressing imbalances in cell death in cancer and other diseases.
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Affiliation(s)
- Kim Newton
- Physiological Chemistry Department, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Andreas Strasser
- WEHI: Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Nobuhiko Kayagaki
- Physiological Chemistry Department, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Vishva M Dixit
- Physiological Chemistry Department, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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33
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Cottrell KA, Andrews RJ, Bass BL. The competitive landscape of the dsRNA world. Mol Cell 2024; 84:107-119. [PMID: 38118451 PMCID: PMC10843539 DOI: 10.1016/j.molcel.2023.11.033] [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: 10/16/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/22/2023]
Abstract
The ability to sense and respond to infection is essential for life. Viral infection produces double-stranded RNAs (dsRNAs) that are sensed by proteins that recognize the structure of dsRNA. This structure-based recognition of viral dsRNA allows dsRNA sensors to recognize infection by many viruses, but it comes at a cost-the dsRNA sensors cannot always distinguish between "self" and "nonself" dsRNAs. "Self" RNAs often contain dsRNA regions, and not surprisingly, mechanisms have evolved to prevent aberrant activation of dsRNA sensors by "self" RNA. Here, we review current knowledge about the life of endogenous dsRNAs in mammals-the biosynthesis and processing of dsRNAs, the proteins they encounter, and their ultimate degradation. We highlight mechanisms that evolved to prevent aberrant dsRNA sensor activation and the importance of competition in the regulation of dsRNA sensors and other dsRNA-binding proteins.
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Affiliation(s)
- Kyle A Cottrell
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA.
| | - Ryan J Andrews
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
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34
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Ai Y, Meng Y, Yan B, Zhou Q, Wang X. The biochemical pathways of apoptotic, necroptotic, pyroptotic, and ferroptotic cell death. Mol Cell 2024; 84:170-179. [PMID: 38181758 DOI: 10.1016/j.molcel.2023.11.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/16/2023] [Accepted: 11/30/2023] [Indexed: 01/07/2024]
Abstract
Apoptosis, the first regulated form of cell death discovered in mammalian cells, is executed by caspase-3/7, which are dormant in living cells but become activated by upstream caspase-8 or caspase-9 in responding to extracellular cytokines or intracellular stress signals, respectively. The same cell death-inducing cytokines also cause necroptosis when caspase-8 is inhibited, resulting in the activation of receptor-interacting protein kinase 3 (RIPK3), which phosphorylates pseudokinase MLKL to trigger its oligomerization and membrane-disrupting activity. Caspase-1/4/5/11, known as inflammatory caspases, instead induce pyroptosis by cleaving gasdermin D, whose caspase-cleaved N terminus forms pores on the plasma membrane. The membrane protein NINJ1 amplifies the extent of membrane rupture initiated by gasdermin D. Additionally, disturbance of peroxidation of polyunsaturated fatty acid tails of membrane phospholipids triggers ferroptosis, an iron-dependent and caspases-independent necrotic death. This review will discuss how these regulated cell death pathways act individually and interconnectively in particular cell types to carry out specific physiological and pathological functions.
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Affiliation(s)
- Youwei Ai
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yutong Meng
- National Institute of Biological Sciences, Beijing and Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, No. 7 Life Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Bo Yan
- Department of Neurology, Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qinyi Zhou
- National Institute of Biological Sciences, Beijing and Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, No. 7 Life Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Xiaodong Wang
- National Institute of Biological Sciences, Beijing and Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, No. 7 Life Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
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35
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Pandeya A, Kanneganti TD. Therapeutic potential of PANoptosis: innate sensors, inflammasomes, and RIPKs in PANoptosomes. Trends Mol Med 2024; 30:74-88. [PMID: 37977994 PMCID: PMC10842719 DOI: 10.1016/j.molmed.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/20/2023] [Accepted: 10/04/2023] [Indexed: 11/19/2023]
Abstract
The innate immune system initiates cell death pathways in response to pathogens and cellular stress. Cell death can be either non-lytic (apoptosis) or lytic (PANoptosis, pyroptosis, and necroptosis). PANoptosis has been identified as an inflammatory, lytic cell death pathway driven by caspases and RIPKs that is regulated by PANoptosome complexes, making it distinct from other cell death pathways. Several PANoptosome complexes (including ZBP1-, AIM2-, RIPK1-, and NLRP12-PANoptosomes) have been characterized to date. Furthermore, PANoptosis is implicated in infectious and inflammatory diseases, cancers, and homeostatic perturbations. Therefore, targeting its molecular components offers significant potential for therapeutic development. This review covers PANoptosomes and their assembly, PANoptosome-mediated cell death mechanisms, and ongoing progress in developing therapeutics that target PANoptosis.
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Affiliation(s)
- Ankit Pandeya
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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36
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Nakano H. Necroptosis and Its Involvement in Various Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:129-143. [PMID: 38467977 DOI: 10.1007/978-981-99-9781-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Necroptosis is a regulated form of cell death involved in the development of various pathological conditions. In contrast to apoptosis, plasma membrane rupture (PMR) occurs in cells in the relatively early stage of necroptosis; therefore, necroptosis induces a strong inflammatory response. Stimuli, including tumor necrosis factor (TNF), interferon (IFN)α/β, lipopolysaccharide, polyI:C, and viral infection, induce the formation of necrosomes that lead to membrane rupture and the release of intracellular contents, termed danger-associated molecular patterns (DAMPs). DAMPs are the collective term for molecules that normally reside in the cytoplasm or nucleus in living cells without inducing inflammation but induce strong inflammatory responses when released outside cells. Recent studies have provided a better understanding of the mechanisms underlying PMR and the release of DAMPs. Moreover, necroptosis is involved in various pathological conditions, and mutations in necroptosis-related genes can cause hereditary autoinflammatory syndromes. Thus, manipulating necroptosis signaling pathways may be useful for treating diseases involving necroptosis.
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Affiliation(s)
- Hiroyasu Nakano
- Department of Biochemistry, Faculty of Medicine, Toho University School of Medicine, Tokyo, Japan.
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37
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Nassour J, Przetocka S, Karlseder J. Telomeres as hotspots for innate immunity and inflammation. DNA Repair (Amst) 2024; 133:103591. [PMID: 37951043 PMCID: PMC10842095 DOI: 10.1016/j.dnarep.2023.103591] [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: 07/24/2023] [Revised: 10/05/2023] [Accepted: 10/24/2023] [Indexed: 11/13/2023]
Abstract
Aging is marked by the gradual accumulation of deleterious changes that disrupt organ function, creating an altered physiological state that is permissive for the onset of prevalent human diseases. While the exact mechanisms governing aging remain a subject of ongoing research, there are several cellular and molecular hallmarks that contribute to this biological process. This review focuses on two factors, namely telomere dysfunction and inflammation, which have emerged as crucial contributors to the aging process. We aim to discuss the mechanistic connections between these two distinct hallmarks and provide compelling evidence highlighting the loss of telomere protection as a driver of pro-inflammatory states associated with aging. By reevaluating the interplay between telomeres, innate immunity, and inflammation, we present novel perspectives on the etiology of aging and its associated diseases.
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Affiliation(s)
- Joe Nassour
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 E. 17th Ave, Aurora, CO 80045, USA; The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Sara Przetocka
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Jan Karlseder
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA.
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38
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Weng S, Yang X, Yu N, Wang PC, Xiong S, Ruan H. Harnessing ADAR-Mediated Site-Specific RNA Editing in Immune-Related Disease: Prediction and Therapeutic Implications. Int J Mol Sci 2023; 25:351. [PMID: 38203521 PMCID: PMC10779106 DOI: 10.3390/ijms25010351] [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: 10/31/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
ADAR (Adenosine Deaminases Acting on RNA) proteins are a group of enzymes that play a vital role in RNA editing by converting adenosine to inosine in RNAs. This process is a frequent post-transcriptional event observed in metazoan transcripts. Recent studies indicate widespread dysregulation of ADAR-mediated RNA editing across many immune-related diseases, such as human cancer. We comprehensively review ADARs' function as pattern recognizers and their capability to contribute to mediating immune-related pathways. We also highlight the potential role of site-specific RNA editing in maintaining homeostasis and its relationship to various diseases, such as human cancers. More importantly, we summarize the latest cutting-edge computational approaches and data resources for predicting and analyzing RNA editing sites. Lastly, we cover the recent advancement in site-directed ADAR editing tool development. This review presents an up-to-date overview of ADAR-mediated RNA editing, how site-specific RNA editing could potentially impact disease pathology, and how they could be harnessed for therapeutic applications.
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Affiliation(s)
- Shenghui Weng
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Xinyi Yang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Nannan Yu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Peng-Cheng Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Hang Ruan
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou 215123, China
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39
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Wang L, Zhu Y, Zhang L, Guo L, Wang X, Pan Z, Jiang X, Wu F, He G. Mechanisms of PANoptosis and relevant small-molecule compounds for fighting diseases. Cell Death Dis 2023; 14:851. [PMID: 38129399 PMCID: PMC10739961 DOI: 10.1038/s41419-023-06370-2] [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: 07/04/2023] [Revised: 11/10/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Pyroptosis, apoptosis, and necroptosis are mainly programmed cell death (PCD) pathways for host defense and homeostasis. PANoptosis is a newly distinct inflammatory PCD pathway that is uniquely regulated by multifaceted PANoptosome complexes and highlights significant crosstalk and coordination among pyroptosis (P), apoptosis (A), and/or necroptosis(N). Although some studies have focused on the possible role of PANpoptosis in diseases, the pathogenesis of PANoptosis is complex and underestimated. Furthermore, the progress of PANoptosis and related agonists or inhibitors in disorders has not yet been thoroughly discussed. In this perspective, we provide perspectives on PANoptosome and PANoptosis in the context of diverse pathological conditions and human diseases. The treatment targeting on PANoptosis is also summarized. In conclusion, PANoptosis is involved in plenty of disorders including but not limited to microbial infections, cancers, acute lung injury/acute respiratory distress syndrome (ALI/ARDS), ischemia-reperfusion, and organic failure. PANoptosis seems to be a double-edged sword in diverse conditions, as PANoptosis induces a negative impact on treatment and prognosis in disorders like COVID-19 and ALI/ARDS, while PANoptosis provides host protection from HSV1 or Francisella novicida infection, and kills cancer cells and suppresses tumor growth in colorectal cancer, adrenocortical carcinoma, and other cancers. Compounds and endogenous molecules focused on PANoptosis are promising therapeutic strategies, which can act on PANoptosomes-associated members to regulate PANoptosis. More researches on PANoptosis are needed to better understand the pathology of human conditions and develop better treatment.
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Affiliation(s)
- Lian Wang
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Yanghui Zhu
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Lu Zhang
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Linghong Guo
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Xiaoyun Wang
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Zhaoping Pan
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Xian Jiang
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China.
| | - Fengbo Wu
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China.
| | - Gu He
- Department of Dermatology & Venerology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China.
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
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40
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Zambrano-Mila MS, Witzenberger M, Rosenwasser Z, Uzonyi A, Nir R, Ben-Aroya S, Levanon EY, Schwartz S. Dissecting the basis for differential substrate specificity of ADAR1 and ADAR2. Nat Commun 2023; 14:8212. [PMID: 38081817 PMCID: PMC10713624 DOI: 10.1038/s41467-023-43633-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Millions of adenosines are deaminated throughout the transcriptome by ADAR1 and/or ADAR2 at varying levels, raising the question of what are the determinants guiding substrate specificity and how these differ between the two enzymes. We monitor how secondary structure modulates ADAR2 vs ADAR1 substrate selectivity, on the basis of systematic probing of thousands of synthetic sequences transfected into cell lines expressing exclusively ADAR1 or ADAR2. Both enzymes induce symmetric, strand-specific editing, yet with distinct offsets with respect to structural disruptions: -26 nt for ADAR2 and -35 nt for ADAR1. We unravel the basis for these differences in offsets through mutants, domain-swaps, and ADAR homologs, and find it to be encoded by the differential RNA binding domain (RBD) architecture. Finally, we demonstrate that this offset-enhanced editing can allow an improved design of ADAR2-recruiting therapeutics, with proof-of-concept experiments demonstrating increased on-target and potentially decreased off-target editing.
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Affiliation(s)
- Marlon S Zambrano-Mila
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Monika Witzenberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Zohar Rosenwasser
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Anna Uzonyi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Shay Ben-Aroya
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Erez Y Levanon
- Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel.
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41
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Cai H, Lv M, Wang T. PANoptosis in cancer, the triangle of cell death. Cancer Med 2023; 12:22206-22223. [PMID: 38069556 PMCID: PMC10757109 DOI: 10.1002/cam4.6803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 12/31/2023] Open
Abstract
BACKGROUND PANoptosis is a novel form of programmed cell death (PCD) found in 2019 that is regulated by the PANoptosome. PANoptosis combines essential features of pyroptosis, apoptosis, and necroptosis, forming a "death triangle" of cells. While apoptosis, pyroptosis, and necroptosis have been extensively studied for their roles in human inflammatory diseases and many other clinical conditions, historically they were considered as independent processes. However, emerging evidence indicates that these PCDs exhibit cross talk and interactions, resulting in the development of the concept of PANoptosis. METHODS In this review, we offer a concise summary of the fundamental mechanisms of apoptosis, pyroptosis, and necroptosis. We subsequently introduce the notion of PANoptosis and detail the assembly mechanism of the PANoptosome complex which is responsible for inducing cell death. We also describe some regulatory networks of PANoptosis. RESULTS PANoptosis now has been associated with various human diseases including cancer. Although the exact function of PANoptosis in each tumor is not fully understood, it represents a prospective avenue for cancer therapy, offering promise for advancements in cancer therapy. CONCLUSIONS In the future, in-depth study of PANoptosis will continue to help us in understanding the fundamental processes underlying cell death and provide scientific support for cancer research.
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Affiliation(s)
- Hantao Cai
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Division of Immunology, Medical School, Nanjing University, Nanjing, China
| | - Mingming Lv
- Department of Breast, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Tingting Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Division of Immunology, Medical School, Nanjing University, Nanjing, China
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Yang T, Wang G, Zhang M, Hu X, Li Q, Yun F, Xing Y, Song X, Zhang H, Hu G, Qian Y. Triggering endogenous Z-RNA sensing for anti-tumor therapy through ZBP1-dependent necroptosis. Cell Rep 2023; 42:113377. [PMID: 37922310 DOI: 10.1016/j.celrep.2023.113377] [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: 01/13/2022] [Revised: 08/15/2023] [Accepted: 10/19/2023] [Indexed: 11/05/2023] Open
Abstract
ZBP1 senses viral Z-RNAs to induce necroptotic cell death to restrain viral infection. ZBP1 is also thought to recognize host cell-derived Z-RNAs to regulate organ development and tissue inflammation in mice. However, it remains unknown how the host-derived Z-RNAs are formed and how these endogenous Z-RNAs are sensed by ZBP1. Here, we report that oxidative stress strongly induces host cell endogenous Z-RNAs, and the Z-RNAs then localize to stress granules for direct sensing by ZBP1 to trigger necroptosis. Oxidative stress triggers dramatically increase Z-RNA levels in tumor cells, and the Z-RNAs then directly trigger tumor cell necroptosis through ZBP1. Localization of the induced Z-RNAs to stress granules is essential for ZBP1 sensing. Oxidative stress-induced Z-RNAs significantly promote tumor chemotherapy via ZBP1-driven necroptosis. Thus, our study identifies oxidative stress as a critical trigger for Z-RNA formation and demonstrates how Z-RNAs are directly sensed by ZBP1 to trigger anti-tumor necroptotic cell death.
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Affiliation(s)
- Tao Yang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guodong Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mingxiang Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Xiaohu Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qi Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Fenglin Yun
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yingying Xing
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyang Song
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Haibing Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guohong Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Youcun Qian
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China.
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43
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Herbert A. The Intransitive Logic of Directed Cycles and Flipons Enhances the Evolution of Molecular Computers by Augmenting the Kolmogorov Complexity of Genomes. Int J Mol Sci 2023; 24:16482. [PMID: 38003672 PMCID: PMC10671625 DOI: 10.3390/ijms242216482] [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: 09/18/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Cell responses are usually viewed as transitive events with fixed inputs and outputs that are regulated by feedback loops. In contrast, directed cycles (DCs) have all nodes connected, and the flow is in a single direction. Consequently, DCs can regenerate themselves and implement intransitive logic. DCs are able to couple unrelated chemical reactions to each edge. The output depends upon which node is used as input. DCs can also undergo selection to minimize the loss of thermodynamic entropy while maximizing the gain of information entropy. The intransitive logic underlying DCs enhances their programmability and impacts their evolution. The natural selection of DCs favors the persistence, adaptability, and self-awareness of living organisms and does not depend solely on changes to coding sequences. Rather, the process can be RNA-directed. I use flipons, nucleic acid sequences that change conformation under physiological conditions, as a simple example and then describe more complex DCs. Flipons are often encoded by repeats and greatly increase the Kolmogorov complexity of genomes by adopting alternative structures. Other DCs allow cells to regenerate, recalibrate, reset, repair, and rewrite themselves, going far beyond the capabilities of current computational devices. Unlike Turing machines, cells are not designed to halt but rather to regenerate.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA
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44
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Hu SB, Heraud-Farlow J, Sun T, Liang Z, Goradia A, Taylor S, Walkley CR, Li JB. ADAR1p150 prevents MDA5 and PKR activation via distinct mechanisms to avert fatal autoinflammation. Mol Cell 2023; 83:3869-3884.e7. [PMID: 37797622 DOI: 10.1016/j.molcel.2023.09.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/14/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023]
Abstract
Effective immunity requires the innate immune system to distinguish foreign nucleic acids from cellular ones. Cellular double-stranded RNAs (dsRNAs) are edited by the RNA-editing enzyme ADAR1 to evade being recognized as viral dsRNA by cytoplasmic dsRNA sensors, including MDA5 and PKR. The loss of ADAR1-mediated RNA editing of cellular dsRNA activates MDA5. Additional RNA-editing-independent functions of ADAR1 have been proposed, but a specific mechanism has not been delineated. We now demonstrate that the loss of ADAR1-mediated RNA editing specifically activates MDA5, whereas loss of the cytoplasmic ADAR1p150 isoform or its dsRNA-binding activity enabled PKR activation. Deleting both MDA5 and PKR resulted in complete rescue of the embryonic lethality of Adar1p150-/- mice to adulthood, contrasting with the limited or no rescue by removing MDA5 or PKR alone. Our findings demonstrate that MDA5 and PKR are the primary in vivo effectors of fatal autoinflammation following the loss of ADAR1p150.
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Affiliation(s)
- Shi-Bin Hu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jacki Heraud-Farlow
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC 3065, Australia
| | - Tao Sun
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Zhen Liang
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC 3065, Australia
| | - Ankita Goradia
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Scott Taylor
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, VIC 3065, Australia.
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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45
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Chen W, Gullett JM, Tweedell RE, Kanneganti TD. Innate immune inflammatory cell death: PANoptosis and PANoptosomes in host defense and disease. Eur J Immunol 2023; 53:e2250235. [PMID: 36782083 PMCID: PMC10423303 DOI: 10.1002/eji.202250235] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023]
Abstract
Regulated cell death (RCD) triggered by innate immune activation is an important strategy for host survival during pathogen invasion and perturbations of cellular homeostasis. There are two main categories of RCD, including nonlytic and lytic pathways. Apoptosis is the most well-characterized nonlytic RCD, and the inflammatory pyroptosis and necroptosis pathways are among the best known lytic forms. While these were historically viewed as independent RCD pathways, extensive evidence of cross-talk among their molecular components created a knowledge gap in our mechanistic understanding of RCD and innate immune pathway components, which led to the identification of PANoptosis. PANoptosis is a unique innate immune inflammatory RCD pathway that is regulated by PANoptosome complexes upon sensing pathogens, pathogen-associated molecular patterns (PAMPs), damage-associated molecular patterns (DAMPs) or the cytokines produced downstream. Cytosolic innate immune sensors and regulators, such as ZBP1, AIM2 and RIPK1, promote the assembly of PANoptosomes to drive PANoptosis. In this review, we discuss the molecular components of the known PANoptosomes and highlight the mechanisms of PANoptosome assembly, activation and regulation identified to date. We also discuss how PANoptosomes and mutations in PANoptosome components are linked to diseases. Given the impact of RCD, and PANoptosis specifically, across the disease spectrum, improved understanding of PANoptosomes and their regulation will be critical for identifying new therapeutic targets and strategies.
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Affiliation(s)
- Wen Chen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jessica M. Gullett
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Rebecca E. Tweedell
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
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46
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Pang J, Vince JE. The role of caspase-8 in inflammatory signalling and pyroptotic cell death. Semin Immunol 2023; 70:101832. [PMID: 37625331 DOI: 10.1016/j.smim.2023.101832] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/20/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
The programmed cell death machinery exhibits surprising flexibility, capable of crosstalk and non-apoptotic roles. Much of this complexity arises from the diverse functions of caspase-8, a cysteine-aspartic acid protease typically associated with activating caspase-3 and - 7 to induce apoptosis. However, recent research has revealed that caspase-8 also plays a role in regulating the lytic gasdermin cell death machinery, contributing to pyroptosis and immune responses in contexts such as infection, autoinflammation, and T-cell signalling. In mice, loss of caspase-8 results in embryonic lethality from unrestrained necroptotic killing, while in humans caspase-8 deficiency can lead to an autoimmune lymphoproliferative syndrome, immunodeficiency, inflammatory bowel disease or, when it can't cleave its substrate RIPK1, early onset periodic fevers. This review focuses on non-canonical caspase-8 signalling that drives immune responses, including its regulation of inflammatory gene transcription, activation within inflammasome complexes, and roles in pyroptotic cell death. Ultimately, a deeper understanding of caspase-8 function will aid in determining whether, and when, targeting caspase-8 pathways could be therapeutically beneficial in human diseases.
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Affiliation(s)
- Jiyi Pang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - James E Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia.
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47
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Dorrity TJ, Shin H, Wiegand KA, Aruda J, Closser M, Jung E, Gertie JA, Leone A, Polfer R, Culbertson B, Yu L, Wu C, Ito T, Huang Y, Steckelberg AL, Wichterle H, Chung H. Long 3'UTRs predispose neurons to inflammation by promoting immunostimulatory double-stranded RNA formation. Sci Immunol 2023; 8:eadg2979. [PMID: 37862432 PMCID: PMC11056275 DOI: 10.1126/sciimmunol.adg2979] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 08/18/2023] [Indexed: 10/22/2023]
Abstract
Loss of RNA homeostasis underlies numerous neurodegenerative and neuroinflammatory diseases. However, the molecular mechanisms that trigger neuroinflammation are poorly understood. Viral double-stranded RNA (dsRNA) triggers innate immune responses when sensed by host pattern recognition receptors (PRRs) present in all cell types. Here, we report that human neurons intrinsically carry exceptionally high levels of immunostimulatory dsRNAs and identify long 3'UTRs as giving rise to neuronal dsRNA structures. We found that the neuron-enriched ELAVL family of genes (ELAVL2, ELAVL3, and ELAVL4) can increase (i) 3'UTR length, (ii) dsRNA load, and (iii) activation of dsRNA-sensing PRRs such as MDA5, PKR, and TLR3. In wild-type neurons, neuronal dsRNAs signaled through PRRs to induce tonic production of the antiviral type I interferon. Depleting ELAVL2 in WT neurons led to global shortening of 3'UTR length, reduced immunostimulatory dsRNA levels, and rendered WT neurons susceptible to herpes simplex virus and Zika virus infection. Neurons deficient in ADAR1, a dsRNA-editing enzyme mutated in the neuroinflammatory disorder Aicardi-Goutières syndrome, exhibited intolerably high levels of dsRNA that triggered PRR-mediated toxic inflammation and neuronal death. Depleting ELAVL2 in ADAR1 knockout neurons led to prolonged neuron survival by reducing immunostimulatory dsRNA levels. In summary, neurons are specialized cells where PRRs constantly sense "self" dsRNAs to preemptively induce protective antiviral immunity, but maintaining RNA homeostasis is paramount to prevent pathological neuroinflammation.
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Affiliation(s)
- Tyler J. Dorrity
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Heegwon Shin
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kenenni A. Wiegand
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Justin Aruda
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael Closser
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neuroscience and Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
| | - Emily Jung
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jake A. Gertie
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Medical Scientist Training Program, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Amanda Leone
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Rachel Polfer
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Bruce Culbertson
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Medical Scientist Training Program, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lisa Yu
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Christine Wu
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Takamasa Ito
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yuefeng Huang
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Anna-Lena Steckelberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Hynek Wichterle
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neuroscience and Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
| | - Hachung Chung
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
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48
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Shen S, Zhang LS. The regulation of antiviral innate immunity through non-m 6A RNA modifications. Front Immunol 2023; 14:1286820. [PMID: 37915585 PMCID: PMC10616867 DOI: 10.3389/fimmu.2023.1286820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
The post-transcriptional RNA modifications impact the dynamic regulation of gene expression in diverse biological and physiological processes. Host RNA modifications play an indispensable role in regulating innate immune responses against virus infection in mammals. Meanwhile, the viral RNAs can be deposited with RNA modifications to interfere with the host immune responses. The N6-methyladenosine (m6A) has boosted the recent emergence of RNA epigenetics, due to its high abundance and a transcriptome-wide widespread distribution in mammalian cells, proven to impact antiviral innate immunity. However, the other types of RNA modifications are also involved in regulating antiviral responses, and the functional roles of these non-m6A RNA modifications have not been comprehensively summarized. In this Review, we conclude the regulatory roles of 2'-O-methylation (Nm), 5-methylcytidine (m5C), adenosine-inosine editing (A-to-I editing), pseudouridine (Ψ), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N6,2'-O-dimethyladenosine (m6Am), and N4-acetylcytidine (ac4C) in antiviral innate immunity. We provide a systematic introduction to the biogenesis and functions of these non-m6A RNA modifications in viral RNA, host RNA, and during virus-host interactions, emphasizing the biological functions of RNA modification regulators in antiviral responses. Furthermore, we discussed the recent research progress in the development of antiviral drugs through non-m6A RNA modifications. Collectively, this Review conveys knowledge and inspiration to researchers in multiple disciplines, highlighting the challenges and future directions in RNA epitranscriptome, immunology, and virology.
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Affiliation(s)
- Shenghai Shen
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Li-Sheng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
- Department of Chemistry, The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
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49
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Liu A, Ying S. Aicardi-Goutières syndrome: A monogenic type I interferonopathy. Scand J Immunol 2023; 98:e13314. [PMID: 37515439 DOI: 10.1111/sji.13314] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/26/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023]
Abstract
Aicardi-Goutières syndrome (AGS) is a rare monogenic autoimmune disease that primarily affects the brains of children patients. Its main clinical features include encephalatrophy, basal ganglia calcification, leukoencephalopathy, lymphocytosis and increased interferon-α (IFN-α) levels in the patient's cerebrospinal fluid (CSF) and serum. AGS may be caused by mutations in any one of nine genes (TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR1, IFIH1, LSM11 and RNU7-1) that result in accumulation of self-nucleic acids in the cytoplasm or aberrant sensing of self-nucleic acids. This triggers overproduction of type I interferons (IFNs) and subsequently causes AGS, the prototype of type I interferonopathies. This review describes the discovery history of AGS with various genotypes and provides the latest knowledge of clinical manifestations and causative genes of AGS. The relationship between AGS and type I interferonopathy and potential therapeutic methods for AGS are also discussed in this review.
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Affiliation(s)
- Anran Liu
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Songcheng Ying
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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50
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Zhang W, Tanneti NS, Fausto A, Nouel J, Reyes H, Weiss SR, Li Y. The vaccinia virus E3L dsRNA binding protein detects distinct production patterns of exogenous and endogenous dsRNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.557600. [PMID: 37790463 PMCID: PMC10542517 DOI: 10.1101/2023.09.21.557600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Double-stranded RNA (dsRNA) is a pathogen associated molecular pattern recognized by multiple pattern recognition receptors and induces innate immune responses. Viral infections can generate dsRNA during virus replication. Genetic mutations can also lead to endogenous dsRNA accumulation. DsRNA is present in multiple conformations such as the A form (A-dsRNA) or Z form (Z-dsRNA). A-dsRNA has been detected from multiple viruses with positive-stranded RNA genomes (+ssRNA) but rarely from viruses with negative RNA genomes (-RNA); Z-dsRNA can be detected from influenza virus and poxvirus infections. Viruses have evolved mechanisms to antagonize cellular antiviral responses triggered by dsRNAs. For example, the vaccinia-virus E3L protein can bind and sequester dsRNA to evade host immune responses. The E3L protein encodes a Z-DNA and a dsRNA binding domains that bind to Z-form nucleic acids or dsRNA, respectively. Here we developed recombinant E3L proteins to detect dsRNA and Z-dsRNA generated from viral infections or endogenous cellular mutations. We demonstrate that the E3L recombinant protein specifically detects A-dsRNA generated from +ssRNA viruses but not-RNA viruses. We observe that among various virus infections assayed, only the influenza A virus generates Z-RNA that can be detected by anti-Z-NA antibody but not by the E3L recombinant protein containing the Z-DNA domain. The E3L recombinant protein can also detect endogenous dsRNA in PNPT1 or SUV3L1 knockout cells. Together we concluded that A-dsRNA can be produced and detected from viruses with +ssRNA genomes but not-RNA genomes, and Z-dsRNA can be produced and detected from influenza A virus. Importance The detection of dsRNAs, which exist in the A-dsRNA or Z-RNA conformation, is important for the induction of innate immune responses. dsRNA are generated during a virus infection due to virus replication, or can accumulate to genetic mutations. We engineered recombinant vaccinia virus E3L protein that can detect A-dsRNA generated during infection with a positive-sense RNA genome virus but not a negative-sense RNA genome virus. Infection with influenza A virus generates Z-RNA that can be detected with an anti-z-antibody but not the E3L recombinant protein. The E3L recombinant protein also detects endogenous dsRNA in PNPT1 or SUV3L knockout cells. These findings highlight important characteristics of dsRNA structure and detection.
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