1
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Prakash P, Khodke P, Balasubramaniam M, Davids BO, Hollis T, Davis J, Kumbhar B, Dash C. Three prime repair exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural, and conformational properties. J Biol Chem 2024; 300:107438. [PMID: 38838778 PMCID: PMC11259700 DOI: 10.1016/j.jbc.2024.107438] [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: 12/11/2023] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024] Open
Abstract
HIV-1 integration into the human genome is dependent on 3'-processing of the viral DNA. Recently, we reported that the cellular Three Prime Repair Exonuclease 1 (TREX1) enhances HIV-1 integration by degrading the unprocessed viral DNA, while the integration-competent 3'-processed DNA remained resistant. Here, we describe the mechanism by which the 3'-processed HIV-1 DNA resists TREX1-mediated degradation. Our kinetic studies revealed that the rate of cleavage (kcat) of the 3'-processed DNA was significantly lower (approximately 2-2.5-fold) than the unprocessed HIV-1 DNA by TREX1. The kcat values of human TREX1 for the processed U5 and U3 DNA substrates were 3.8 s-1 and 4.5 s-1, respectively. In contrast, the unprocessed U5 and U3 substrates were cleaved at 10.2 s-1 and 9.8 s-1, respectively. The efficiency of degradation (kcat/Km) of the 3'-processed DNA (U5-70.2 and U3-28.05 pM-1s-1) was also significantly lower than the unprocessed DNA (U5-103.1 and U3-65.3 pM-1s-1). Furthermore, the binding affinity (Kd) of TREX1 was markedly lower (∼2-fold) for the 3'-processed DNA than the unprocessed DNA. Molecular docking and dynamics studies revealed distinct conformational binding modes of TREX1 with the 3'-processed and unprocessed HIV-1 DNA. Particularly, the unprocessed DNA was favorably positioned in the active site with polar interactions with the catalytic residues of TREX1. Additionally, a stable complex was formed between TREX1 and the unprocessed DNA compared the 3'-processed DNA. These results pinpoint the mechanism by which TREX1 preferentially degrades the integration-incompetent HIV-1 DNA and reveal the unique structural and conformational properties of the integration-competent 3'-processed HIV-1 DNA.
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Affiliation(s)
- Prem Prakash
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Purva Khodke
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be-) University, Mumbai, Maharashtra, India
| | - Muthukumar Balasubramaniam
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Benem-Orom Davids
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, New York, USA
| | - Thomas Hollis
- Department of Biochemistry and Center for Structural Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Jamaine Davis
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Bajarang Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be-) University, Mumbai, Maharashtra, India
| | - Chandravanu Dash
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA; Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA; Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA.
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2
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Toufektchan E, Dananberg A, Striepen J, Hickling JH, Shim A, Chen Y, Nichols A, Duran Paez MA, Mohr L, Bakhoum SF, Maciejowski J. Intratumoral TREX1 Induction Promotes Immune Evasion by Limiting Type I IFN. Cancer Immunol Res 2024; 12:673-686. [PMID: 38408184 PMCID: PMC11148545 DOI: 10.1158/2326-6066.cir-23-1093] [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: 12/22/2023] [Revised: 02/06/2024] [Accepted: 02/23/2024] [Indexed: 02/28/2024]
Abstract
Chromosomal instability is a hallmark of human cancer that is associated with aggressive disease characteristics. Chromosome mis-segregations help fuel natural selection, but they risk provoking a cGAS-STING immune response through the accumulation of cytosolic DNA. The mechanisms of how tumors benefit from chromosomal instability while mitigating associated risks, such as enhanced immune surveillance, are poorly understood. Here, we identify cGAS-STING-dependent upregulation of the nuclease TREX1 as an adaptive, negative feedback mechanism that promotes immune evasion through digestion of cytosolic DNA. TREX1 loss diminishes tumor growth, prolongs survival of host animals, increases tumor immune infiltration, and potentiates response to immune checkpoint blockade selectively in tumors capable of mounting a type I IFN response downstream of STING. Together, these data demonstrate that TREX1 induction shields chromosomally unstable tumors from immune surveillance by dampening type I IFN production and suggest that TREX1 inhibitors might be used to selectively target tumors that have retained the inherent ability to mount an IFN response downstream of STING. See related article by Lim et al., p. 663.
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Affiliation(s)
- Eléonore Toufektchan
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Josefine Striepen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James H. Hickling
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Abraham Shim
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yanyang Chen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ashley Nichols
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mercedes A. Duran Paez
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lisa Mohr
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel F. Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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3
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Gu X, Chen Y, Cao K, Tu M, Liu W, Ju J. Therapeutic landscape in systemic lupus erythematosus: mtDNA activation of the cGAS-STING pathway. Int Immunopharmacol 2024; 133:112114. [PMID: 38652968 DOI: 10.1016/j.intimp.2024.112114] [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: 01/02/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Mitochondrial DNA (mtDNA) serves as a pivotal immune stimulus in the immune response. During stress, mitochondria release mtDNA into the cytoplasm, where it is recognized by the cytoplasmic DNA receptor cGAS. This activation initiates the cGAS-STING-IRF3 pathway, culminating in an inflammatory response. The cGAS-STING pathway has emerged as a critical mediator of inflammatory responses in microbial infections, stress, autoimmune diseases, chronic illnesses, and tissue injuries. Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by connective tissue involvement across various bodily systems. Its hallmark is the production of numerous autoantibodies, which prompt the immune system to target and damage the body's own tissues, resulting in organ and tissue damage. Increasing evidence implicates the cGAS-STING pathway as a significant contributor to SLE pathogenesis. This article aims to explore the role of the mtDNA-triggered cGAS-STING pathway and its mechanisms in SLE, with the goal of providing novel insights for clinical interventions.
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Affiliation(s)
- Xiaotian Gu
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China
| | - Yong Chen
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China
| | - Kunyu Cao
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China
| | - Miao Tu
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China
| | - Wan Liu
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China.
| | - Jiyu Ju
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang 261053, China.
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4
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Shim A, Luan X, Zhou W, Crow YJ, Maciejowski J. Mutations in the non-catalytic polyproline motif destabilize TREX1 and amplify cGAS-STING signaling. Hum Mol Genet 2024:ddae089. [PMID: 38796715 DOI: 10.1093/hmg/ddae089] [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: 02/16/2024] [Revised: 04/25/2024] [Indexed: 05/28/2024] Open
Abstract
The cGAS-STING pathway detects cytosolic DNA and activates a signaling cascade that results in a type I interferon (IFN) response. The endoplasmic reticulum (ER)-associated exonuclease TREX1 suppresses cGAS-STING by eliminating DNA from the cytosol. Mutations that compromise TREX1 function are linked to autoinflammatory disorders, including systemic lupus erythematosus (SLE) and Aicardi-Goutières syndrome (AGS). Despite key roles in regulating cGAS-STING and suppressing excessive inflammation, the impact of many disease-associated TREX1 mutations-particularly those outside of the core catalytic domains-remains poorly understood. Here, we characterize a recessive AGS-linked TREX1 P61Q mutation occurring within the poorly characterized polyproline helix (PPII) motif. In keeping with its position outside of the catalytic core or ER targeting motifs, neither the P61Q mutation, nor aggregate proline-to-alanine PPII mutation, disrupts TREX1 exonuclease activity, subcellular localization, or cGAS-STING regulation in overexpression systems. Introducing targeted mutations into the endogenous TREX1 locus revealed that PPII mutations destabilize the protein, resulting in impaired exonuclease activity and unrestrained cGAS-STING activation. Overall, these results demonstrate that TREX1 PPII mutations, including P61Q, impair proper immune regulation and lead to autoimmune disease through TREX1 destabilization.
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Affiliation(s)
- Abraham Shim
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 430 East 67th Street, New York, NY 10065, United States
| | - Xiaohan Luan
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, GD 518055, China
| | - Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, GD 518055, China
| | - Yanick J Crow
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road South, Edinburgh, United Kingdom
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, INSERM UMR1163, University Paris Cité, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 430 East 67th Street, New York, NY 10065, United States
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5
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Yao H, Wu Y, Zhong Y, Huang C, Guo Z, Jin Y, Wang X. Role of c-Fos in DNA damage repair. J Cell Physiol 2024; 239:e31216. [PMID: 38327128 DOI: 10.1002/jcp.31216] [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: 10/08/2023] [Revised: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 02/09/2024]
Abstract
c-Fos, a member of the immediate early gene, serves as a widely used marker of neuronal activation induced by various types of brain damage. In addition, c-Fos is believed to play a regulatory role in DNA damage repair. This paper reviews the literature on c-Fos' involvement in the regulation of DNA damage repair and indicates that genes of the Fos family can be induced by various forms of DNA damage. In addition, cells lacking c-Fos have difficulties in DNA repair. c-Fos is involved in tumorigenesis and progression as a proto-oncogene that maintains cancer cell survival, which may also be related to DNA repair. c-Fos may impact the repair of DNA damage by regulating the expression of downstream proteins, including ATR, ERCC1, XPF, and others. Nonetheless, the underlying mechanisms necessitate further exploration.
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Affiliation(s)
- Haiyang Yao
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yilun Wu
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiming Zhong
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenxuan Huang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zimo Guo
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yinpeng Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xianli Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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6
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Capdeville N, Schindele P, Puchta H. Increasing deletion sizes and the efficiency of CRISPR/Cas9-mediated mutagenesis by SunTag-mediated TREX1 recruitment. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:277-287. [PMID: 38113345 DOI: 10.1111/tpj.16586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
Previously, it has been shown that mutagenesis frequencies can be improved by directly fusing the human exonuclease TREX2 to Cas9, resulting in a strong increase in the frequency of smaller deletions at the cut site. Here, we demonstrate that, by using the SunTag system for recruitment of TREX2, the mutagenesis efficiency can be doubled in comparison to the direct fusion in Arabidopsis thaliana. Therefore, we also tested the efficiency of the system for targeted deletion formation by recruiting two other 3'-5' exonucleases, namely the human TREX1 and E. coli ExoI. It turns out that SunTag-mediated recruitment of TREX1 not only improved the general mutation induction efficiency slightly in comparison to TREX2, but that, more importantly, the mean size of the induced deletions was also enhanced, mainly via an increase of deletions of 25 bp or more. EcExoI also yielded a higher amount of larger deletions. However, only in the case of TREX1 and TREX2, the effect was predominately SunTag-dependent, indicating efficient target-specific recruitment. Using SunTag-mediated TREX1 recruitment at other genomic sites, we were able to obtain similar deletion patterns. Thus, we were able to develop an attractive novel editing tool that is especially useful for obtaining deletions in the range from 20 to 40 bp around the cut site. Such sizes are often required for the manipulation of cis-regulatory elements. This feature is closing an existing gap as previous approaches, based on single nucleases or paired nickases or nucleases, resulted in either shorter or longer deletions, respectively.
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Affiliation(s)
- Niklas Capdeville
- Department of Molecular Biology, Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Patrick Schindele
- Department of Molecular Biology, Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Holger Puchta
- Department of Molecular Biology, Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institute for Plant Sciences, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
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7
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Prakash P, Khodke P, Balasubramaniam M, Davids BO, Hollis T, Davis J, Pandhare J, Kumbhar B, Dash C. Three Prime Repair Exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural and conformational properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585766. [PMID: 38562877 PMCID: PMC10983988 DOI: 10.1101/2024.03.19.585766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
HIV-1 integration into the human genome is dependent on 3'-processing of the reverse transcribed viral DNA. Recently, we reported that the cellular Three Prime Repair Exonuclease 1 (TREX1) enhances HIV-1 integration by degrading the unprocessed viral DNA, while the integration-competent 3'-processed DNA remained resistant. Here, we describe the mechanism by which the 3'-processed HIV-1 DNA resists TREX1-mediated degradation. Our kinetic studies revealed that the rate of cleavage (kcat) of the 3'-processed DNA was significantly lower than the unprocessed HIV-1 DNA by TREX1. The efficiency of degradation (kcat/KM) of the 3'-processed DNA was also significantly lower than the unprocessed DNA. Furthermore, the binding affinity (Kd) of TREX1 was markedly lower to the 3'-processed DNA compared to the unprocessed DNA. Molecular docking and dynamics studies revealed distinct conformational binding modes of TREX1 with the 3'-processed and unprocessed HIV-1 DNA. Particularly, the unprocessed DNA was favorably positioned in the active site with polar interactions with the catalytic residues of TREX1. Additionally, a stable complex was formed between TREX1 and the unprocessed DNA compared the 3'-processed DNA. These results pinpoint the biochemical mechanism by which TREX1 preferentially degrades the integration-incompetent HIV-1 DNA and reveal the unique structural and conformational properties of the integration-competent 3'-processed HIV-1 DNA.
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Affiliation(s)
- Prem Prakash
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, 37208, USA
| | - Purva Khodke
- Sunandan Divatia School of Science, NMIMS University, Mumbai, 400056, India
| | - Muthukumar Balasubramaniam
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, 37208, USA
| | - Benem-Orom Davids
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, New York, 10032, USA
| | - Thomas Hollis
- Department of Biochemistry and Center for Structural Biology, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Jamaine Davis
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, 37208, USA
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, 37208, USA
| | - Bajarang Kumbhar
- Sunandan Divatia School of Science, NMIMS University, Mumbai, 400056, India
| | - Chandravanu Dash
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, 37208, USA
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, 37208, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, 37208, USA
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8
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Marple T, Son MY, Cheng X, Ko JH, Sung P, Hasty P. TREX2 deficiency suppresses spontaneous and genotoxin-associated mutagenesis. Cell Rep 2024; 43:113637. [PMID: 38175749 PMCID: PMC10883656 DOI: 10.1016/j.celrep.2023.113637] [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: 07/25/2023] [Revised: 09/15/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
TREX2, a 3'-5' exonuclease, is a part of the DNA damage tolerance (DDT) pathway that stabilizes replication forks (RFs) by ubiquitinating PCNA along with the ubiquitin E3 ligase RAD18 and other DDT factors. Mismatch repair (MMR) corrects DNA polymerase errors, including base mismatches and slippage. Here we demonstrate that TREX2 deletion reduces mutations in cells upon exposure to genotoxins, including those that cause base lesions and DNA polymerase slippage. Importantly, we show that TREX2 generates most of the spontaneous mutations in MMR-mutant cells derived from mice and people. TREX2-induced mutagenesis is dependent on the nuclease and DNA-binding attributes of TREX2. RAD18 deletion also reduces spontaneous mutations in MMR-mutant cells, albeit to a lesser degree. Inactivation of both MMR and TREX2 additively increases RF stalls, while it decreases DNA breaks, consistent with a synthetic phenotype.
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Affiliation(s)
- Teresa Marple
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Mi Young Son
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Xiaodong Cheng
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Jun Ho Ko
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; The Mays Cancer Center, University of Texas Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Paul Hasty
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; The Mays Cancer Center, University of Texas Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229, USA; Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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9
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Shim A, Luan X, Zhou W, Crow Y, Maciejowski J. Mutations in the non-catalytic polyproline motif destabilize TREX1 and amplify cGAS-STING signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574136. [PMID: 38260344 PMCID: PMC10802300 DOI: 10.1101/2024.01.04.574136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The cGAS-STING pathway detects cytosolic DNA and activates a signaling cascade that results in a type I interferon (IFN) response. The endoplasmic reticulum (ER)-associated exonuclease TREX1 suppresses cGAS-STING by eliminating DNA from the cytosol. Mutations that compromise TREX1 function are linked to autoinflammatory disorders, including systemic lupus erythematosus (SLE) and Aicardi-Goutières syndrome (AGS). Despite key roles in regulating cGAS-STING and suppressing excessive inflammation, the impact of many disease-associated TREX1 mutations - particularly those outside of the core catalytic domains - remains poorly understood. Here, we characterize a recessive AGS-linked TREX1 P61Q mutation occurring within the poorly characterized polyproline helix (PPII) motif. In keeping with its position outside of the catalytic core or ER targeting motifs, neither the P61Q mutation, nor aggregate proline-to-alanine PPII mutation, disrupt TREX1 exonuclease activity, subcellular localization, or cGAS-STING regulation in overexpression systems. Introducing targeted mutations into the endogenous TREX1 locus revealed that PPII mutations destabilize the protein, resulting in impaired exonuclease activity and unrestrained cGAS-STING activation. Overall, these results demonstrate that TREX1 PPII mutations, including P61Q, impair proper immune regulation and lead to autoimmune disease through TREX1 destabilization.
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Affiliation(s)
- Abraham Shim
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaohan Luan
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yanick Crow
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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10
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Huang KW, Wu CY, Toh SI, Liu TC, Tu CI, Lin YH, Cheng AJ, Kao YT, Chu JW, Hsiao YY. Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids. Nucleic Acids Res 2023; 51:11927-11940. [PMID: 37870446 PMCID: PMC10681709 DOI: 10.1093/nar/gkad910] [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: 05/19/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
In various autoimmune diseases, dysfunctional TREX1 (Three prime Repair Exonuclease 1) leads to accumulation of endogenous single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and DNA/RNA hybrids in the cytoplasm and triggers immune activation through the cGAS-STING pathway. Although inhibition of TREX1 could be a useful strategy for cancer immunotherapy, profiling cellular functions in terms of its potential substrates is a key step. Particularly important is the functionality of processing DNA/RNA hybrids and RNA substrates. The exonuclease activity measurements conducted here establish that TREX1 can digest both ssRNA and DNA/RNA hybrids but not dsRNA. The newly solved structures of TREX1-RNA product and TREX1-nucleotide complexes show that 2'-OH does not impose steric hindrance or specific interactions for the recognition of RNA. Through all-atom molecular dynamics simulations, we illustrate that the 2'-OH-mediated intra-chain hydrogen bonding in RNA would affect the binding with TREX1 and thereby reduce the exonuclease activity. This notion of higher conformational rigidity in RNA leading TREX1 to exhibit weaker catalytic cleavage is further validated by the binding affinity measurements with various synthetic DNA-RNA junctions. The results of this work thus provide new insights into the mechanism by which TREX1 processes RNA and DNA/RNA hybrids and contribute to the molecular-level understanding of the complex cellular functions of TREX1 as an exonuclease.
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Affiliation(s)
- Kuan-Wei Huang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chia-Yun Wu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Shu-Ing Toh
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Tung-Chang Liu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chun-I Tu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yin-Hsin Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - An-Ju Cheng
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Ya-Ting Kao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jhih-Wei Chu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yu-Yuan Hsiao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Drug Development and Value Creation Research Center, Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
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11
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Potential health risks of mRNA-based vaccine therapy: A hypothesis. Med Hypotheses 2023; 171:111015. [PMID: 36718314 PMCID: PMC9876036 DOI: 10.1016/j.mehy.2023.111015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/08/2022] [Accepted: 01/24/2023] [Indexed: 01/26/2023]
Abstract
Therapeutic applications of synthetic mRNA were proposed more than 30 years ago, and are currently the basis of one of the vaccine platforms used at a massive scale as part of the public health strategy to get COVID-19 under control. To date, there are no published studies on the biodistribution, cellular uptake, endosomal escape, translation rates, functional half-life and inactivation kinetics of synthetic mRNA, rates and duration of vaccine-induced antigen expression in different cell types. Furthermore, despite the assumption that there is no possibility of genomic integration of therapeutic synthetic mRNA, only one recent study has examined interactions between vaccine mRNA and the genome of transfected cells, and reported that an endogenous retrotransposon, LINE-1 is unsilenced following mRNA entry to the cell, leading to reverse transcription of full length vaccine mRNA sequences, and nuclear entry. This finding should be a major safety concern, given the possibility of synthetic mRNA-driven epigenetic and genomic modifications arising. We propose that in susceptible individuals, cytosolic clearance of nucleotide modified synthetic (nms-mRNAs) is impeded. Sustained presence of nms-mRNA in the cytoplasm deregulates and activates endogenous transposable elements (TEs), causing some of the mRNA copies to be reverse transcribed. The cytosolic accumulation of the nms-mRNA and the reverse transcribed cDNA molecules activates RNA and DNA sensory pathways. Their concurrent activation initiates a synchronized innate response against non-self nucleic acids, prompting type-I interferon and pro-inflammatory cytokine production which, if unregulated, leads to autoinflammatory and autoimmune conditions, while activated TEs increase the risk of insertional mutagenesis of the reverse transcribed molecules, which can disrupt coding regions, enhance the risk of mutations in tumour suppressor genes, and lead to sustained DNA damage. Susceptible individuals would then expectedly have an increased risk of DNA damage, chronic autoinflammation, autoimmunity and cancer. In light of the current mass administration of nms-mRNA vaccines, it is essential and urgent to fully understand the intracellular cascades initiated by cellular uptake of synthetic mRNA and the consequences of these molecular events.
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12
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Anindya R. Cytoplasmic DNA in cancer cells: Several pathways that potentially limit DNase2 and TREX1 activities. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119278. [PMID: 35489653 DOI: 10.1016/j.bbamcr.2022.119278] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
The presence of DNA in the cytoplasm of tumor cells induces the dendritic cell to produce type-I IFNs. Classically, the presence of foreign DNA in host cells' cytoplasm during viral infection elicits cGAS-STING mediated type-I IFN signaling and cytokine production. It is likely that cytosolic DNA leads to senescence and immune surveillance in transformed cells during the early stages of carcinogenesis. However, multiple factors, such as loss of cell-cycle checkpoint, mitochondrial damage and chromosomal instability, can lead to persistent accumulation of DNA in the cytoplasm of metastatic tumor cells. That is why aberrant activation of the type I IFN pathway is frequently associated with highly aggressive tumors. Intriguingly, two powerful intracellular deoxyribonucleases, DNase2 and TREX1, can target the cytoplasmic DNA for degradation. Yet the tumor cells consistently accumulate cytoplasmic DNA. This review highlights recent work connecting the lack of DNase2 and TREX1 function to innate immune signaling. It also summarizes the possible mechanisms that limit the activity of DNase2 and TREX1 in tumor cells and contributes to chronic inflammation.
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Affiliation(s)
- Roy Anindya
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy 502284, India.
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13
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Zhou W, Richmond-Buccola D, Wang Q, Kranzusch PJ. Structural basis of human TREX1 DNA degradation and autoimmune disease. Nat Commun 2022; 13:4277. [PMID: 35879334 PMCID: PMC9314330 DOI: 10.1038/s41467-022-32055-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/11/2022] [Indexed: 01/13/2023] Open
Abstract
TREX1 is a cytosolic DNA nuclease essential for regulation of cGAS-STING immune signaling. Existing structures of mouse TREX1 establish a mechanism of DNA degradation and provide a key model to explain autoimmune disease, but these structures incompletely explain human disease-associated mutations and have limited ability to guide development of small-molecule therapeutics. Here we determine crystal structures of human TREX1 in apo and DNA-bound conformations that provide high-resolution detail of all human-specific features. A 1.25 Å structure of human TREX1 establishes a complete model of solvation of the exonuclease active site and a 2.2 Å structure of the human TREX1-DNA complex enables identification of specific substitutions involved in DNA recognition. We map each TREX1 mutation associated with autoimmune disease and establish distinct categories of substitutions predicted to impact enzymatic function, protein stability, and interaction with cGAS-DNA liquid droplets. Our results explain how human-specific substitutions regulate TREX1 function and provide a foundation for structure-guided design of TREX1 therapeutics.
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Affiliation(s)
- Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
| | - Desmond Richmond-Buccola
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Qiannan Wang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
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14
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Amico G, Hemphill WO, Severino M, Moratti C, Pascarella R, Bertamino M, Napoli F, Volpi S, Rosamilia F, Signa S, Perrino F, Zedde M, Ceccherini I. Genotype-Phenotype Correlation and Functional Insights for Two Monoallelic TREX1 Missense Variants Affecting the Catalytic Core. Genes (Basel) 2022; 13:genes13071179. [PMID: 35885962 PMCID: PMC9323106 DOI: 10.3390/genes13071179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 02/01/2023] Open
Abstract
The TREX1 exonuclease degrades DNA to prevent aberrant nucleic-acid sensing through the cGAS-STING pathway, and dominant Aicardi–Goutières Syndrome type 1 (AGS1) represents one of numerous TREX1-related autoimmune diseases. Monoallelic TREX1 mutations were identified in patients showing early-onset cerebrovascular disease, ascribable to small vessel disease, and CADASIL-like neuroimaging. We report the clinical-neuroradiological features of two patients with AGS-like (Patient A) and CADASIL-like (Patient B) phenotypes carrying the heterozygous p.A136V and p.R174G TREX1 variants, respectively. Genetic findings, obtained by a customized panel including 183 genes associated with monogenic stroke, were combined with interferon signature testing and biochemical assays to determine the mutations’ effects in vitro. Our results for the p.A136V variant are inconsistent with prior biochemistry-pathology correlates for dominant AGS-causing TREX1 mutants. The p.R174G variant modestly altered exonuclease activity in a manner consistent with perturbation of substrate interaction rather than catalysis, which represents the first robust enzymological data for a TREX1 variant identified in a CADASIL-like patient. In conclusion, functional analysis allowed us to interpret the impact of TREX1 variants on patients’ phenotypes. While the p.A136V variant is unlikely to be causative for AGS in Patient A, Patient B’s phenotype is potentially related to the p.R174G variant. Therefore, further functional investigations of TREX1 variants found in CADASIL-like patients are warranted to determine any causal link and interrogate the molecular disease mechanism(s).
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Affiliation(s)
- Giulia Amico
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy;
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Wayne O. Hemphill
- Center for Structural Biology, Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Correspondence: (W.O.H.); (F.P.)
| | | | - Claudio Moratti
- Neuroradiology Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (C.M.); (R.P.)
| | - Rosario Pascarella
- Neuroradiology Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (C.M.); (R.P.)
| | - Marta Bertamino
- Physical Medicine and Rehabilitation Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Flavia Napoli
- Departments of Pediatrics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
| | - Stefano Volpi
- Autoinflammatory Diseases and Immunodeficiencies Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.V.); (S.S.)
| | - Francesca Rosamilia
- Biostatistic Unit, Health Science Department (DISSAL), University of Genoa, 16132 Genoa, Italy;
| | - Sara Signa
- Autoinflammatory Diseases and Immunodeficiencies Center, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.V.); (S.S.)
| | - Fred Perrino
- Center for Structural Biology, Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Correspondence: (W.O.H.); (F.P.)
| | - Marialuisa Zedde
- Neurology Unit, Stroke Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy;
| | - Isabella Ceccherini
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy;
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15
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Venkatadri R, Sabapathy V, Dogan M, Mohammad S, Harvey S, Simpson SR, Grayson J, Yan N, Perrino FW, Sharma R. Targeting Bcl6 in the TREX1 D18N murine model ameliorates autoimmunity by modulating T follicular helper cells and Germinal center B cells. Eur J Immunol 2022; 52:825-834. [PMID: 35112355 PMCID: PMC9089306 DOI: 10.1002/eji.202149324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 01/04/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022]
Abstract
The Three Prime Repair EXonuclease I (TREX1) is critical for degrading post‐apoptosis DNA. Mice expressing catalytically inactive TREX1 (TREX1 D18N) develop lupus‐like autoimmunity due to chronic sensing of undegraded TREX1 DNA substrates, production of the inflammatory cytokines, and the inappropriate activation of innate and adaptive immunity. This study aimed to investigate Thelper (Th) dysregulation in the TREX1 D18N model system as a potential mechanism for lupus‐like autoimmunity. Comparison of immune cells in secondary lymphoid organs, spleen and peripheral lymph nodes (LNs) between TREX1 D18N mice and the TREX1 null mice revealed that the TREX1 D18N mice exhibit a Th1 bias. Additionally, the T‐follicular helper cells (Tfh) and the germinal celter (GC) B cells were also elevated in the TREX1 D18N mice. Targeting Bcl6, a lineage‐defining transcription factor for Tfh and GC B cells, with a commercially available Bcl6 inhibitor, FX1, attenuated Tfh, GC, and Th1 responses, and rescued TREX1 D18N mice from autoimmunity. The study presents Tfh and GC B‐cell responses as potential targets in autoimmunity and that Bcl6 inhibitors may offer therapeutic approach in TREX1‐associated or other lupus‐like diseases.
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Affiliation(s)
- Rajkumar Venkatadri
- Center for Immunity, Inflammation and Regenerative Medicine (CIIR), Division of Nephrology, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Vikram Sabapathy
- Center for Immunity, Inflammation and Regenerative Medicine (CIIR), Division of Nephrology, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Murat Dogan
- Center for Immunity, Inflammation and Regenerative Medicine (CIIR), Division of Nephrology, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Saleh Mohammad
- Center for Immunity, Inflammation and Regenerative Medicine (CIIR), Division of Nephrology, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Scott Harvey
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Sean R Simpson
- Department of Biochemistry, Wake Forest Baptist Medical Center, Winston-Salem, NC, United States
| | - Jason Grayson
- Department of Biochemistry, Wake Forest Baptist Medical Center, Winston-Salem, NC, United States
| | - Nan Yan
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Fred W Perrino
- Department of Biochemistry, Wake Forest Baptist Medical Center, Winston-Salem, NC, United States
| | - Rahul Sharma
- Center for Immunity, Inflammation and Regenerative Medicine (CIIR), Division of Nephrology, Department of Medicine, University of Virginia, Charlottesville, VA, United States
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16
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Nader GPDF, Agüera-Gonzalez S, Routet F, Gratia M, Maurin M, Cancila V, Cadart C, Palamidessi A, Ramos RN, San Roman M, Gentili M, Yamada A, Williart A, Lodillinsky C, Lagoutte E, Villard C, Viovy JL, Tripodo C, Galon J, Scita G, Manel N, Chavrier P, Piel M. Compromised nuclear envelope integrity drives TREX1-dependent DNA damage and tumor cell invasion. Cell 2021; 184:5230-5246.e22. [PMID: 34551315 DOI: 10.1016/j.cell.2021.08.035] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/07/2021] [Accepted: 08/29/2021] [Indexed: 11/18/2022]
Abstract
Although mutations leading to a compromised nuclear envelope cause diseases such as muscular dystrophies or accelerated aging, the consequences of mechanically induced nuclear envelope ruptures are less known. Here, we show that nuclear envelope ruptures induce DNA damage that promotes senescence in non-transformed cells and induces an invasive phenotype in human breast cancer cells. We find that the endoplasmic reticulum (ER)-associated exonuclease TREX1 translocates into the nucleus after nuclear envelope rupture and is required to induce DNA damage. Inside the mammary duct, cellular crowding leads to nuclear envelope ruptures that generate TREX1-dependent DNA damage, thereby driving the progression of in situ carcinoma to the invasive stage. DNA damage and nuclear envelope rupture markers were also enriched at the invasive edge of human tumors. We propose that DNA damage in mechanically challenged nuclei could affect the pathophysiology of crowded tissues by modulating proliferation and extracellular matrix degradation of normal and transformed cells.
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Affiliation(s)
| | | | - Fiona Routet
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
| | - Matthieu Gratia
- Institut Curie, PSL Research University, INSERM, U932, Paris, France
| | - Mathieu Maurin
- Institut Curie, PSL Research University, INSERM, U932, Paris, France
| | - Valeria Cancila
- Tumor Immunology Unit, University of Palermo, Corso Tukory 211, 90234 Palermo, Italy
| | - Clotilde Cadart
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR 144, Paris, France
| | - Andrea Palamidessi
- FIRC Institute of Molecular Oncology, IFOM, Via Adamello 16, 20139 Milano, Italy; Department of Oncology and Hemato-Oncology, University of Milan, IFOM, Via Adamello 16, 20139 Milano, Italy
| | - Rodrigo Nalio Ramos
- INSERM, Sorbonne Université, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Laboratory of Integrative Cancer Immunology, Paris, France
| | - Mabel San Roman
- Institut Curie, PSL Research University, INSERM, U932, Paris, France
| | - Matteo Gentili
- Institut Curie, PSL Research University, INSERM, U932, Paris, France
| | - Ayako Yamada
- Institut Curie, Université PSL, CNRS, UMR 168, Paris, France
| | - Alice Williart
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR 144, Paris, France
| | - Catalina Lodillinsky
- Research Area, Instituto de Oncología Ángel H. Roffo, Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Emilie Lagoutte
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
| | | | | | - Claudio Tripodo
- Tumor Immunology Unit, University of Palermo, Corso Tukory 211, 90234 Palermo, Italy
| | - Jérôme Galon
- INSERM, Sorbonne Université, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Centre de Recherche des Cordeliers, Laboratory of Integrative Cancer Immunology, Paris, France
| | - Giorgio Scita
- Research Area, Instituto de Oncología Ángel H. Roffo, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nicolas Manel
- Institut Curie, PSL Research University, INSERM, U932, Paris, France.
| | - Philippe Chavrier
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France.
| | - Matthieu Piel
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR 144, Paris, France.
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17
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Zhang Y, Qin Z, Sun W, Chu F, Zhou F. Function of Protein S-Palmitoylation in Immunity and Immune-Related Diseases. Front Immunol 2021; 12:661202. [PMID: 34557182 PMCID: PMC8453015 DOI: 10.3389/fimmu.2021.661202] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 08/23/2021] [Indexed: 02/04/2023] Open
Abstract
Protein S-palmitoylation is a covalent and reversible lipid modification that specifically targets cysteine residues within many eukaryotic proteins. In mammalian cells, the ubiquitous palmitoyltransferases (PATs) and serine hydrolases, including acyl protein thioesterases (APTs), catalyze the addition and removal of palmitate, respectively. The attachment of palmitoyl groups alters the membrane affinity of the substrate protein changing its subcellular localization, stability, and protein-protein interactions. Forty years of research has led to the understanding of the role of protein palmitoylation in significantly regulating protein function in a variety of biological processes. Recent global profiling of immune cells has identified a large body of S-palmitoylated immunity-associated proteins. Localization of many immune molecules to the cellular membrane is required for the proper activation of innate and adaptive immune signaling. Emerging evidence has unveiled the crucial roles that palmitoylation plays to immune function, especially in partitioning immune signaling proteins to the membrane as well as to lipid rafts. More importantly, aberrant PAT activity and fluctuations in palmitoylation levels are strongly correlated with human immunologic diseases, such as sensory incompetence or over-response to pathogens. Therefore, targeting palmitoylation is a novel therapeutic approach for treating human immunologic diseases. In this review, we discuss the role that palmitoylation plays in both immunity and immunologic diseases as well as the significant potential of targeting palmitoylation in disease treatment.
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18
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Berndt N, Wolf C, Fischer K, Cura Costa E, Knuschke P, Zimmermann N, Schmidt F, Merkel M, Chara O, Lee-Kirsch MA, Günther C. Photosensitivity and cGAS-dependent type I IFN activation in lupus patients with TREX1 deficiency. J Invest Dermatol 2021; 142:633-640.e6. [PMID: 34400195 DOI: 10.1016/j.jid.2021.04.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 03/22/2021] [Accepted: 04/22/2021] [Indexed: 01/07/2023]
Abstract
The exonuclease three prime repair exonuclease 1 (TREX1) safeguards the cell against DNA accumulation in the cytosol and thereby prevents innate immune activation and autoimmunity. TREX1 mutations lead to chronic DNA damage and cell-intrinsic type I interferon (IFN) response. Associated disease phenotypes include Aicardi-Goutières syndrome, familial chilblain lupus and systemic lupus erythematosus. Given the role of ultraviolet (UV) light in lupus pathogenesis, we assessed sensitivity to UV light in lupus patients with TREX1 mutation by phototesting which revealed an enhanced photosensitivity. TREX1-deficient fibroblasts and keratinocytes generated increased levels of reactive oxygen species in response to UV irradiation as well as increased levels of 8-oxo-guanine lesions after oxidative stress. Likewise, the primary UV-induced DNA lesions cyclobutane pyrimidine dimers (CPD) were induced more strongly in TREX1-deficient cells. Further analysis revealed that single-stranded DNA regions, frequently formed during DNA replication and repair, promote CPD formation. Together, this resulted in a strong UV-induced DNA damage response that was associated with a cyclic GMP-AMP synthase (cGAS)-dependent type I IFN activation. In conclusion, these findings link chronic DNA damage to photosensitivity and type I IFN production in TREX1 deficiency and explain the induction of disease flares upon UV exposure in lupus patients with TREX1 mutation.
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Affiliation(s)
- Nicole Berndt
- Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Christine Wolf
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Kristina Fischer
- Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Emanuel Cura Costa
- Systems Biology Group (SysBio), Institute of Physics of Liquids and Biological Systems (IFLySIB), National Scientific and Technical Research Council (CONICET) and University of La Plata, La Plata, Argentina
| | - Peter Knuschke
- Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Nick Zimmermann
- Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Franziska Schmidt
- Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Martin Merkel
- Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Osvaldo Chara
- Systems Biology Group (SysBio), Institute of Physics of Liquids and Biological Systems (IFLySIB), National Scientific and Technical Research Council (CONICET) and University of La Plata, La Plata, Argentina; Center for Information Services and High-Performance Computing (ZIH), TU Dresden, Dresden, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Claudia Günther
- Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany.
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19
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Davids BO, Balasubramaniam M, Sapp N, Prakash P, Ingram S, Li M, Craigie R, Hollis T, Pandhare J, Dash C. Human Three Prime Repair Exonuclease 1 Promotes HIV-1 Integration by Preferentially Degrading Unprocessed Viral DNA. J Virol 2021; 95:e0055521. [PMID: 34105995 PMCID: PMC8354242 DOI: 10.1128/jvi.00555-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/25/2021] [Indexed: 11/20/2022] Open
Abstract
Three prime repair exonuclease 1 (TREX1) is the most abundant 3'→5' exonuclease in mammalian cells. It has been suggested that TREX1 degrades HIV-1 DNA to enable the virus to evade the innate immune system. However, the exact role of TREX1 during early steps of HIV-1 infection is not clearly understood. In this study, we report that HIV-1 infection is associated with upregulation, perinuclear accumulation, and nuclear localization of TREX1. However, TREX1 overexpression did not affect reverse transcription or nuclear entry of the virus. Surprisingly, HIV-1 DNA integration was increased in TREX1-overexpressing cells, suggesting a role of the exonuclease in the post-nuclear entry step of infection. Accordingly, preintegration complexes (PICs) extracted from TREX1-overexpressing cells retained higher levels of DNA integration activity. TREX1 depletion resulted in reduced levels of proviral integration, and PICs formed in TREX1-depleted cells retained lower DNA integration activity. Addition of purified TREX1 to PICs also enhanced DNA integration activity, suggesting that TREX1 promotes HIV-1 integration by stimulating PIC activity. To understand the mechanism, we measured TREX1 exonuclease activity on substrates containing viral DNA ends. These studies revealed that TREX1 preferentially degrades the unprocessed viral DNA, but the integration-competent 3'-processed viral DNA remains resistant to degradation. Finally, we observed that TREX1 addition stimulates the activity of HIV-1 intasomes assembled with the unprocessed viral DNA but not that of intasomes containing the 3'-processed viral DNA. These biochemical analyses provide a mechanism by which TREX1 directly promotes HIV-1 integration. Collectively, our study demonstrates that HIV-1 infection upregulates TREX1 to facilitate viral DNA integration. IMPORTANCE Productive HIV-1 infection is dependent on a number of cellular factors. Therefore, a clear understanding of how the virus exploits the cellular machinery will identify new targets for inhibiting HIV-1 infection. The three prime repair exonuclease 1 (TREX1) is the most active cellular exonuclease in mammalian cells. It has been reported that TREX1 prevents accumulation of HIV-1 DNA and enables the virus to evade the host innate immune response. Here, we show that HIV-1 infection results in the upregulation, perinuclear accumulation, and nuclear localization of TREX1. We also provide evidence that TREX1 promotes HIV-1 integration by preferentially degrading viral DNAs that are incompatible with chromosomal insertion. These observations identify a novel role of TREX1 in a post-nuclear entry step of HIV-1 infection.
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Affiliation(s)
- Benem-Orom Davids
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Muthukumar Balasubramaniam
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Nicklas Sapp
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Prem Prakash
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Shalonda Ingram
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas Hollis
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee, USA
| | - Chandravanu Dash
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
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20
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Aicardi-Goutières syndrome-associated mutation at ADAR1 gene locus activates innate immune response in mouse brain. J Neuroinflammation 2021; 18:169. [PMID: 34332594 PMCID: PMC8325854 DOI: 10.1186/s12974-021-02217-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background Aicardi-Goutières syndrome (AGS) is a severe infant or juvenile-onset autoimmune disease characterized by inflammatory encephalopathy with an elevated type 1 interferon-stimulated gene (ISG) expression signature in the brain. Mutations in seven different protein-coding genes, all linked to DNA/RNA metabolism or sensing, have been identified in AGS patients, but none of them has been demonstrated to activate the IFN pathway in the brain of an animal. The molecular mechanism of inflammatory encephalopathy in AGS has not been well defined. Adenosine Deaminase Acting on RNA 1 (ADAR1) is one of the AGS-associated genes. It carries out A-to-I RNA editing that converts adenosine to inosine at double-stranded RNA regions. Whether an AGS-associated mutation in ADAR1 activates the IFN pathway and causes autoimmune pathogenesis in the brain is yet to be determined. Methods Mutations in the ADAR1 gene found in AGS patients were introduced into the mouse genome via CRISPR/Cas9 technology. Molecular activities of the specific p.K999N mutation were investigated by measuring the RNA editing levels in brain mRNA substrates of ADAR1 through RNA sequencing analysis. IFN pathway activation in the brain was assessed by measuring ISG expression at the mRNA and protein level through real-time RT-PCR and Luminex assays, respectively. The locations in the brain and neural cell types that express ISGs were determined by RNA in situ hybridization (ISH). Potential AGS-related brain morphologic changes were assessed with immunohistological analysis. Von Kossa and Luxol Fast Blue staining was performed on brain tissue to assess calcification and myelin, respectively. Results Mice bearing the ADAR1 p.K999N were viable though smaller than wild type sibs. RNA sequencing analysis of neuron-specific RNA substrates revealed altered RNA editing activities of the mutant ADAR1 protein. Mutant mice exhibited dramatically elevated levels of multiple ISGs within the brain. RNA ISH of brain sections showed selective activation of ISG expression in neurons and microglia in a patchy pattern. ISG-15 mRNA was upregulated in ADAR1 mutant brain neurons whereas CXCL10 mRNA was elevated in adjacent astroglia. No calcification or gliosis was detected in the mutant brain. Conclusions We demonstrated that an AGS-associated mutation in ADAR1, specifically the p.K999N mutation, activates the IFN pathway in the mouse brain. The ADAR1 p.K999N mutant mouse replicates aspects of the brain interferonopathy of AGS. Neurons and microglia express different ISGs. Basal ganglia calcification and leukodystrophy seen in AGS patients were not observed in K999N mutant mice, indicating that development of the full clinical phenotype may need an additional stimulus besides AGS mutations. This mutant mouse presents a robust tool for the investigation of AGS and neuroinflammatory diseases including the modeling of potential “second hits” that enable severe phenotypes of clinically variable diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-021-02217-9.
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21
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Kron NS, Fieber LA. Co-expression analysis identifies neuro-inflammation as a driver of sensory neuron aging in Aplysia californica. PLoS One 2021; 16:e0252647. [PMID: 34116561 PMCID: PMC8195618 DOI: 10.1371/journal.pone.0252647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/20/2021] [Indexed: 01/08/2023] Open
Abstract
Aging of the nervous system is typified by depressed metabolism, compromised proteostasis, and increased inflammation that results in cognitive impairment. Differential expression analysis is a popular technique for exploring the molecular underpinnings of neural aging, but technical drawbacks of the methodology often obscure larger expression patterns. Co-expression analysis offers a robust alternative that allows for identification of networks of genes and their putative central regulators. In an effort to expand upon previous work exploring neural aging in the marine model Aplysia californica, we used weighted gene correlation network analysis to identify co-expression networks in a targeted set of aging sensory neurons in these animals. We identified twelve modules, six of which were strongly positively or negatively associated with aging. Kyoto Encyclopedia of Genes analysis and investigation of central module transcripts identified signatures of metabolic impairment, increased reactive oxygen species, compromised proteostasis, disrupted signaling, and increased inflammation. Although modules with immune character were identified, there was no correlation between genes in Aplysia that increased in expression with aging and the orthologous genes in oyster displaying long-term increases in expression after a virus-like challenge. This suggests anti-viral response is not a driver of Aplysia sensory neuron aging.
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Affiliation(s)
- N. S. Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
| | - L. A. Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
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22
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Gazquez-Gutierrez A, Witteveldt J, R Heras S, Macias S. Sensing of transposable elements by the antiviral innate immune system. RNA (NEW YORK, N.Y.) 2021; 27:rna.078721.121. [PMID: 33888553 PMCID: PMC8208052 DOI: 10.1261/rna.078721.121] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/17/2021] [Indexed: 05/15/2023]
Abstract
Around half of the genome in mammals is composed of transposable elements (TEs) such as DNA transposons and retrotransposons. Several mechanisms have evolved to prevent their activity and the detrimental impact of their insertional mutagenesis. Despite these potentially negative effects, TEs are essential drivers of evolution, and in certain settings, beneficial to their hosts. For instance, TEs have rewired the antiviral gene regulatory network and are required for early embryonic development. However, due to structural similarities between TE-derived and viral nucleic acids, cells can misidentify TEs as invading viruses and trigger the major antiviral innate immune pathway, the type I interferon (IFN) response. This review will focus on the different settings in which the role of TE-mediated IFN activation has been documented, including cancer and senescence. Importantly, TEs may also play a causative role in the development of complex autoimmune diseases characterised by constitutive type I IFN activation. All these observations suggest the presence of strong but opposing forces driving the coevolution of TEs and antiviral defence. A better biological understanding of the TE replicative cycle as well as of the antiviral nucleic acid sensing mechanisms will provide insights into how these two biological processes interact and will help to design better strategies to treat human diseases characterised by aberrant TE expression and/or type I IFN activation.
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Affiliation(s)
| | - Jeroen Witteveldt
- University of Edinburgh - Institute of Immunology and Infection Research
| | - Sara R Heras
- GENYO. Centre for Genomics and Oncological Research, Pfizer University of Granada
| | - Sara Macias
- Institute of Immunology and Infection Research
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23
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Hemphill WO, Simpson SR, Liu M, Salsbury FR, Hollis T, Grayson JM, Perrino FW. TREX1 as a Novel Immunotherapeutic Target. Front Immunol 2021; 12:660184. [PMID: 33868310 PMCID: PMC8047136 DOI: 10.3389/fimmu.2021.660184] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in the TREX1 3' → 5' exonuclease are associated with a spectrum of autoimmune disease phenotypes in humans and mice. Failure to degrade DNA activates the cGAS-STING DNA-sensing pathway signaling a type-I interferon (IFN) response that ultimately drives immune system activation. TREX1 and the cGAS-STING DNA-sensing pathway have also been implicated in the tumor microenvironment, where TREX1 is proposed to degrade tumor-derived DNA that would otherwise activate cGAS-STING. If tumor-derived DNA were not degraded, the cGAS-STING pathway would be activated to promote IFN-dependent antitumor immunity. Thus, we hypothesize TREX1 exonuclease inhibition as a novel immunotherapeutic strategy. We present data demonstrating antitumor immunity in the TREX1 D18N mouse model and discuss theory surrounding the best strategy for TREX1 inhibition. Potential complications of TREX1 inhibition as a therapeutic strategy are also discussed.
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Affiliation(s)
- Wayne O. Hemphill
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Sean R. Simpson
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Mingyong Liu
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Freddie R. Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, NC, United States
| | - Thomas Hollis
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Jason M. Grayson
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Fred W. Perrino
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
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24
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Santa P, Garreau A, Serpas L, Ferriere A, Blanco P, Soni C, Sisirak V. The Role of Nucleases and Nucleic Acid Editing Enzymes in the Regulation of Self-Nucleic Acid Sensing. Front Immunol 2021; 12:629922. [PMID: 33717156 PMCID: PMC7952454 DOI: 10.3389/fimmu.2021.629922] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of microbial nucleic acids by the innate immune system is mediated by numerous intracellular nucleic acids sensors. Upon the detection of nucleic acids these sensors induce the production of inflammatory cytokines, and thus play a crucial role in the activation of anti-microbial immunity. In addition to microbial genetic material, nucleic acid sensors can also recognize self-nucleic acids exposed extracellularly during turn-over of cells, inefficient efferocytosis, or intracellularly upon mislocalization. Safeguard mechanisms have evolved to dispose of such self-nucleic acids to impede the development of autoinflammatory and autoimmune responses. These safeguard mechanisms involve nucleases that are either specific to DNA (DNases) or RNA (RNases) as well as nucleic acid editing enzymes, whose biochemical properties, expression profiles, functions and mechanisms of action will be detailed in this review. Fully elucidating the role of these enzymes in degrading and/or processing of self-nucleic acids to thwart their immunostimulatory potential is of utmost importance to develop novel therapeutic strategies for patients affected by inflammatory and autoimmune diseases.
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Affiliation(s)
- Pauline Santa
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Anne Garreau
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Lee Serpas
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | | | - Patrick Blanco
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
- Immunology and Immunogenetic Department, Bordeaux University Hospital, Bordeaux, France
| | - Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | - Vanja Sisirak
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
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25
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Mohr L, Toufektchan E, von Morgen P, Chu K, Kapoor A, Maciejowski J. ER-directed TREX1 limits cGAS activation at micronuclei. Mol Cell 2021; 81:724-738.e9. [PMID: 33476576 PMCID: PMC7897315 DOI: 10.1016/j.molcel.2020.12.037] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 11/18/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
Micronuclei are aberrant nuclear compartments that can form as a result of chromosome mis-segregation. Frequent loss of micronuclear envelope integrity exposes DNA to the cytoplasm, leading to chromosome fragmentation and immune activation. Here, we use micronuclei purification to show that the endoplasmic reticulum (ER)-associated nuclease TREX1 inhibits cGAS activation at micronuclei by degrading micronuclear DNA upon micronuclear envelope rupture. We demonstrate that the ER accesses ruptured micronuclei and plays a critical role in enabling TREX1 nucleolytic attack. TREX1 mutations, previously implicated in immune disease, untether TREX1 from the ER, disrupt TREX1 localization to micronuclei, diminish micronuclear DNA damage, and enhance cGAS activation. These results establish ER-directed resection of micronuclear DNA by TREX1 as a critical regulator of cytosolic DNA sensing in chromosomally unstable cells and provide a mechanistic basis for the importance of TREX1 ER tethering in preventing autoimmunity.
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Affiliation(s)
- Lisa Mohr
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Eléonore Toufektchan
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Patrick von Morgen
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kevan Chu
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aakanksha Kapoor
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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26
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TREX2 Exonuclease Causes Spontaneous Mutations and Stress-Induced Replication Fork Defects in Cells Expressing RAD51 K133A. Cell Rep 2020; 33:108543. [PMID: 33357432 PMCID: PMC7896812 DOI: 10.1016/j.celrep.2020.108543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/23/2020] [Accepted: 12/01/2020] [Indexed: 01/01/2023] Open
Abstract
DNA damage tolerance (DDT) and homologous recombination (HR) stabilize replication forks (RFs). RAD18/UBC13/three prime repair exonuclease 2 (TREX2)-mediated proliferating cell nuclear antigen (PCNA) ubiquitination is central to DDT, an error-prone lesion bypass pathway. RAD51 is the recombinase for HR. The RAD51 K133A mutation increased spontaneous mutations and stress-induced RF stalls and nascent strand degradation. Here, we report in RAD51K133A cells that this phenotype is reduced by expressing a TREX2 H188A mutation that deletes its exonuclease activity. In RAD51K133A cells, knocking out RAD18 or overexpressing PCNA reduces spontaneous mutations, while expressing ubiquitination-incompetent PCNAK164R increases mutations, indicating DDT as causal. Deleting TREX2 in cells deficient for the RF maintenance proteins poly(ADP-ribose) polymerase 1 (PARP1) or FANCB increased nascent strand degradation that was rescued by TREX2H188A, implying that TREX2 prohibits degradation independent of catalytic activity. A possible explanation for this occurrence is that TREX2H188A associates with UBC13 and ubiquitinates PCNA, suggesting a dual role for TREX2 in RF maintenance.
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27
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Turnier JL, Kahlenberg JM. The Role of Cutaneous Type I IFNs in Autoimmune and Autoinflammatory Diseases. THE JOURNAL OF IMMUNOLOGY 2020; 205:2941-2950. [PMID: 33229366 DOI: 10.4049/jimmunol.2000596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/18/2020] [Indexed: 01/31/2023]
Abstract
IFNs are well known as mediators of the antimicrobial response but also serve as important immunomodulatory cytokines in autoimmune and autoinflammatory diseases. An increasingly critical role for IFNs in evolution of skin inflammation in these patients has been recognized. IFNs are produced not only by infiltrating immune but also resident skin cells, with increased baseline IFN production priming for inflammatory cell activation, immune response amplification, and development of skin lesions. The IFN response differs by cell type and host factors and may be modified by other inflammatory pathway activation specific to individual diseases, leading to differing clinical phenotypes. Understanding the contribution of IFNs to skin and systemic disease pathogenesis is key to development of new therapeutics and improved patient outcomes. In this review, we summarize the immunomodulatory role of IFNs in skin, with a focus on type I, and provide insight into IFN dysregulation in autoimmune and autoinflammatory diseases.
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Affiliation(s)
- Jessica L Turnier
- Department of Pediatrics, Division of Rheumatology, University of Michigan, Ann Arbor, MI 48109; and
| | - J Michelle Kahlenberg
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI 48109
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28
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Yamashita S, Kogasaka Y, Hiradate Y, Tanemura K, Sendai Y. Suppression of mosaic mutation by co-delivery of CRISPR associated protein 9 and three-prime repair exonuclease 2 into porcine zygotes via electroporation. J Reprod Dev 2020; 66:41-48. [PMID: 31761839 PMCID: PMC7040215 DOI: 10.1262/jrd.2019-088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/01/2019] [Indexed: 12/15/2022] Open
Abstract
Gene-modified animals, including pigs, can be generated efficiently by introducing CRISPR associated protein 9 (CRISPR/Cas9) into zygotes. However, in many cases, these zygotes tend to become mosaic mutants with various different mutant cell types, making it difficult to analyze the phenotype of gene-modified founder animals. To reduce the mosaic mutations, we introduced three-prime repair exonuclease 2 (Trex2), an exonuclease that improves gene editing efficiency, into porcine zygotes along with CRISPR/Cas9 via electroporation. Although the rate of porcine blastocyst formation decreased due to electroporation (25.9 ± 4.6% vs. 41.2 ± 2.0%), co-delivery of murine Trex2 (mTrex2) mRNA with CRISPR/Cas9 did not affect it any further (25.9 ± 4.6% vs. 31.0 ± 4.6%). In addition, there was no significant difference in the diameter of blastocysts carrying CRISPR/Cas9 (164.7 ± 10.2 μm), and those with CRISPR/Cas9 + mTrex2 (151.9 ± 5.1 μm) as compared to those from the control group (178.9 ± 9.0 μm). These results revealed that mTrex2 did not affect the development of pre-implantation embryo. We also found bi-allelic, as well as mono-allelic, non-mosaic homozygous mutations in the blastocysts. Most importantly, co-delivery of mTrex2 mRNA with CRISPR/Cas9 increased non-mosaic mutant blastocysts (29.3 ± 4.5%) and reduced mosaic mutant blastocysts (70.7 ± 4.5%) as compared to CRISPR/Cas9 alone (5.6 ± 6.4% and 92.6 ± 8.6%, respectively). These data suggest that the co-delivery of CRISPR/Cas9 and mTrex2 is a useful method to suppress mosaic mutation.
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Affiliation(s)
- Shiro Yamashita
- Biological Sciences Section, Central Research Institute for Feed and Livestock of Zen-noh, Ibaraki 300-4204, Japan
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, Miyagi 980-8572, Japan
| | - Yuhei Kogasaka
- Biological Sciences Section, Central Research Institute for Feed and Livestock of Zen-noh, Ibaraki 300-4204, Japan
| | - Yuuki Hiradate
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, Miyagi 980-8572, Japan
| | - Kentaro Tanemura
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, Miyagi 980-8572, Japan
| | - Yutaka Sendai
- Biological Sciences Section, Central Research Institute for Feed and Livestock of Zen-noh, Ibaraki 300-4204, Japan
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29
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Simpson SR, Rego SL, Harvey SE, Liu M, Hemphill WO, Venkatadri R, Sharma R, Grayson JM, Perrino FW. T Cells Produce IFN-α in the TREX1 D18N Model of Lupus-like Autoimmunity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:348-359. [PMID: 31826941 PMCID: PMC6946867 DOI: 10.4049/jimmunol.1900220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 11/07/2019] [Indexed: 01/09/2023]
Abstract
Autoimmunity can result when cells fail to properly dispose of DNA. Mutations in the three-prime repair exonuclease 1 (TREX1) cause a spectrum of human autoimmune diseases resembling systemic lupus erythematosus. The cytosolic dsDNA sensor, cyclic GMP-AMP synthase (cGAS), and the stimulator of IFN genes (STING) are required for pathogenesis, but specific cells in which DNA sensing and subsequent type I IFN (IFN-I) production occur remain elusive. In this study, we demonstrate that TREX1 D18N catalytic deficiency causes dysregulated IFN-I signaling and autoimmunity in mice. Moreover, we show that bone marrow-derived cells drive this process. We identify both innate immune and, surprisingly, activated T cells as sources of pathological IFN-α production. These findings demonstrate that TREX1 enzymatic activity is crucial to prevent inappropriate DNA sensing and IFN-I production in immune cells, including normally low-level IFN-α-producing cells. These results expand our understanding of DNA sensing and innate immunity in T cells and may have relevance to the pathogenesis of human disease caused by TREX1 mutation.
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Affiliation(s)
- Sean R Simpson
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Stephen L Rego
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Scott E Harvey
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Mingyong Liu
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC 27157; and
| | - Wayne O Hemphill
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Rajkumar Venkatadri
- Center for Immunity, Inflammation and Regenerative Medicine, Division of Nephrology, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Rahul Sharma
- Center for Immunity, Inflammation and Regenerative Medicine, Division of Nephrology, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Jason M Grayson
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC 27157; and
| | - Fred W Perrino
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157;
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30
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Feng X, Liu D, Li Z, Bian J. Bioactive modulators targeting STING adaptor in cGAS-STING pathway. Drug Discov Today 2019; 25:230-237. [PMID: 31758915 DOI: 10.1016/j.drudis.2019.11.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 12/21/2022]
Abstract
The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING)-pathway triggers innate immune responses by recognizing cytosolic DNA. Recent studies revealed that STING adaptor associates with various diseases, and several modulators targeting STING have been identified including three agonists that have entered clinical trials for treating cancer over the past 2 years. In particular, the efficacy of STING agonists and/or antagonists suggests adaptor STING as a potential therapeutic target for diverse diseases. Herein, we summarize the latest advances in understanding STING functioning and provide an overview of recent STING modulator discoveries, including structural details and the potential therapeutic applications of these modulators.
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Affiliation(s)
- Xi Feng
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Dongyu Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
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31
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Motwani M, Pesiridis S, Fitzgerald KA. DNA sensing by the cGAS-STING pathway in health and disease. Nat Rev Genet 2019; 20:657-674. [PMID: 31358977 DOI: 10.1038/s41576-019-0151-1] [Citation(s) in RCA: 766] [Impact Index Per Article: 153.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2019] [Indexed: 12/18/2022]
Abstract
The detection of pathogens through nucleic acid sensors is a defining principle of innate immunity. RNA-sensing and DNA-sensing receptors sample subcellular compartments for foreign nucleic acids and, upon recognition, trigger immune signalling pathways for host defence. Over the past decade, our understanding of how the recognition of nucleic acids is coupled to immune gene expression has advanced considerably, particularly for the DNA-sensing receptor cyclic GMP-AMP synthase (cGAS) and its downstream signalling effector stimulator of interferon genes (STING), as well as the molecular components and regulation of this pathway. Moreover, the ability of self-DNA to engage cGAS has emerged as an important mechanism fuelling the development of inflammation and implicating the cGAS-STING pathway in human inflammatory diseases and cancer. This detailed mechanistic and biological understanding is paving the way for the development and clinical application of pharmacological agonists and antagonists in the treatment of chronic inflammation and cancer.
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Affiliation(s)
- Mona Motwani
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Scott Pesiridis
- Innate Immunity Research Unit, GlaxoSmithKline, Collegeville, PA, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
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Cheng HL, Lin CT, Huang KW, Wang S, Lin YT, Toh SI, Hsiao YY. Structural insights into the duplex DNA processing of TREX2. Nucleic Acids Res 2019; 46:12166-12176. [PMID: 30357414 PMCID: PMC6294518 DOI: 10.1093/nar/gky970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/05/2018] [Indexed: 02/06/2023] Open
Abstract
The three prime repair exonuclease 2 (TREX2) is an essential 3′-to-5′ exonuclease that functions in cell proliferation, genome integrity and skin homeostasis maintenance. The abnormal expression level of TREX2 can result in broken chromosome, increased susceptibility to skin carcinogenesis and Psoriasis. However, the molecular mechanisms of how TREX2 binds and processes its natural substrates, dsDNA or chromosomal DNA, to maintain genome stability remain unclear. In this study, we present four new crystal structures: apo-TREX2, TREX2 in complex with two different dsDNA substrates, and TREX2 in complex with a processed dsDNA product. Analysis of the structures reveals that TREX2 stacks with the 5′-terminal of dsDNA by a Leu20-Pro21-Asn22 cluster for precisely trimming the 3′-overhang. In addition, TREX2 specifically interacts with the non-scissile strand of dsDNA by an α-helix-loop region. The unique interaction patterns of the TREX2–dsDNA complex highlight the requirement of long double-stranded region for TREX2 binding and provide evidence of the functional role of TREX2 in processing chromosomal DNA. Moreover, the non-processive property of TREX2 is elucidated by the structure of TREX2–product complex. Our work discloses the first structural basis of the molecular interactions between TREX2 and its substrates and unravels the mechanistic actions of TREX2.
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Affiliation(s)
- Hiu-Lo Cheng
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan 30050, ROC
| | - Chun-Ting Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC
| | - Kuan-Wei Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC
| | - Shuying Wang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan 70101, ROC.,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan 70101, ROC
| | - Yeh-Tung Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC
| | - Shu-Ing Toh
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC.,Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC
| | - Yu-Yuan Hsiao
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan 30050, ROC.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC.,Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC
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33
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Sheppard EC, Rogers S, Harmer NJ, Chahwan R. A universal fluorescence-based toolkit for real-time quantification of DNA and RNA nuclease activity. Sci Rep 2019; 9:8853. [PMID: 31222049 PMCID: PMC6586798 DOI: 10.1038/s41598-019-45356-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/31/2019] [Indexed: 12/12/2022] Open
Abstract
DNA and RNA nucleases play a critical role in a growing number of cellular processes ranging from DNA repair to immune surveillance. Nevertheless, many nucleases have unknown or poorly characterized activities. Elucidating nuclease substrate specificities and co-factors can support a more definitive understanding of cellular mechanisms in physiology and disease. Using fluorescence-based methods, we present a quick, safe, cost-effective, and real-time versatile nuclease assay, which uniquely studies nuclease enzyme kinetics. In conjunction with a substrate library we can now analyse nuclease catalytic rates, directionality, and substrate preferences. The assay is sensitive enough to detect kinetics of repair enzymes when confronted with DNA mismatches or DNA methylation sites. We have also extended our analysis to study the kinetics of human single-strand DNA nuclease TREX2, DNA polymerases, RNA, and RNA:DNA nucleases. These nucleases are involved in DNA repair, immune regulation, and have been associated with various diseases, including cancer and immune disorders.
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Affiliation(s)
- Emily C Sheppard
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Sally Rogers
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Nicholas J Harmer
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Richard Chahwan
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK. .,Institute of Experimental Immunology, University of Zurich, 8057, Zurich, Switzerland.
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34
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Abstract
Three-prime Repair Exonuclease (TREX1) degrades ssDNA and dsDNA. TREX1 localizes to the perinuclear space in cells and degrades cytosolic DNA to prevent aberrant nucleic acid sensing and immune activation in humans and mice. Mutations in the TREX1 gene cause a spectrum of human autoimmune diseases including Aicardi-Goutières syndrome, familial chilblain lupus, retinal vasculopathy with cerebral leukodystrophy, and are associated with systemic lupus erythematosus. More than 60 disease-causing TREX1 variants have been identified including dominant and recessive, missense, and frameshift mutations that map to the catalytic core region and to the C-terminal cell localization region. The TREX1-disease causing mutations affect exonuclease activity at varied levels. In this chapter, we describe methods to purify variant recombinant TREX1 enzymes and measure the exonuclease activity using ssDNA and dsDNA substrates. The relationships between TREX1 activities, types of TREX1 mutations, and TREX1-associated autoimmune diseases are considered.
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Affiliation(s)
- Wayne O Hemphill
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Fred W Perrino
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States.
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35
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Hansen AL, Mukai K, Schopfer FJ, Taguchi T, Holm CK. STING palmitoylation as a therapeutic target. Cell Mol Immunol 2019; 16:236-241. [PMID: 30796349 PMCID: PMC6460494 DOI: 10.1038/s41423-019-0205-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/18/2019] [Indexed: 01/07/2023] Open
Abstract
Gain-of-function mutations in the STING-encoding gene TMEM173 are central to the pathology of the autoinflammatory disorder STING-associated vasculopathy with onset in infancy (SAVI). Furthermore, excessive activity of the STING signaling pathway is associated with autoinflammatory diseases, including systemic lupus erythematosus and Aicardi–Goutières syndrome (AGS). Two independent studies recently identified pharmacological inhibitors of STING. Strikingly, both types of compounds are reactive nitro-containing electrophiles that target STING palmitoylation, a posttranslational modification necessary for STING signaling. As a consequence, the activation of downstream signaling molecules and the induction of type I interferons were inhibited. The compounds were effective at ameliorating inflammation in a mouse model of AGS and in blocking the production of type I interferons in primary fibroblasts from SAVI patients. This mini-review focuses on the roles of palmitoylation in STING activation and signaling and as a pharmaceutical target for drug development.
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Affiliation(s)
| | - Kojiro Mukai
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578, Miyagi, Japan
| | - Francisco J Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Tomohiko Taguchi
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578, Miyagi, Japan.
| | - Christian K Holm
- Department of Biomedicine, Aarhus University, 8000, Aarhus C, Denmark.
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36
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Tsubata T. CD72 is a Negative Regulator of B Cell Responses to Nuclear Lupus Self-antigens and Development of Systemic Lupus Erythematosus. Immune Netw 2019; 19:e1. [PMID: 30838156 PMCID: PMC6399098 DOI: 10.4110/in.2019.19.e1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/04/2019] [Accepted: 02/07/2019] [Indexed: 12/22/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is the prototypic systemic autoimmune disease characterized by production of autoantibodies to various nuclear antigens and overexpression of genes regulated by IFN-I called IFN signature. Genetic studies on SLE patients and mutational analyses of mouse models demonstrate crucial roles of nucleic acid (NA) sensors in development of SLE. Although NA sensors are involved in induction of anti-microbial immune responses by recognizing microbial NAs, recognition of self NAs by NA sensors induces production of autoantibodies to NAs in B cells and production of IFN-I in plasmacytoid dendritic cells. Among various NA sensors, the endosomal RNA sensor TLR7 plays an essential role in development of SLE at least in mouse models. CD72 is an inhibitory B cell co-receptor containing an immunoreceptor tyrosine-based inhibition motif (ITIM) in the cytoplasmic region and a C-type lectin like-domain (CTLD) in the extracellular region. CD72 is known to regulate development of SLE because CD72 polymorphisms associate with SLE in both human and mice and CD72−/− mice develop relatively severe lupus-like disease. CD72 specifically recognizes the RNA-containing endogenous TLR7 ligand Sm/RNP by its extracellular CTLD, and inhibits B cell responses to Sm/RNP by ITIM-mediated signal inhibition. These findings indicate that CD72 inhibits development of SLE by suppressing TLR7-dependent B cell response to self NAs. CD72 is thus involved in discrimination of self-NAs from microbial NAs by specifically suppressing autoimmune responses to self-NAs.
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Affiliation(s)
- Takeshi Tsubata
- Department of Immunology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
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37
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Allen F, Crepaldi L, Alsinet C, Strong AJ, Kleshchevnikov V, De Angeli P, Palenikova P, Khodak A, Kiselev V, Kosicki M, Bassett AR, Harding H, Galanty Y, Muñoz-Martínez F, Metzakopian E, Jackson SP, Parts L. Predicting the mutations generated by repair of Cas9-induced double-strand breaks. Nat Biotechnol 2018; 37:nbt.4317. [PMID: 30480667 PMCID: PMC6949135 DOI: 10.1038/nbt.4317] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022]
Abstract
The DNA mutation produced by cellular repair of a CRISPR-Cas9-generated double-strand break determines its phenotypic effect. It is known that the mutational outcomes are not random, but depend on DNA sequence at the targeted location. Here we systematically study the influence of flanking DNA sequence on repair outcome by measuring the edits generated by >40,000 guide RNAs (gRNAs) in synthetic constructs. We performed the experiments in a range of genetic backgrounds and using alternative CRISPR-Cas9 reagents. In total, we gathered data for >109 mutational outcomes. The majority of reproducible mutations are insertions of a single base, short deletions or longer microhomology-mediated deletions. Each gRNA has an individual cell-line-dependent bias toward particular outcomes. We uncover sequence determinants of the mutations produced and use these to derive a predictor of Cas9 editing outcomes. Improved understanding of sequence repair will allow better design of gene editing experiments.
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Affiliation(s)
| | | | | | | | | | | | | | - Anton Khodak
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | | | - Heather Harding
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Yaron Galanty
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francisco Muñoz-Martínez
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Emmanouil Metzakopian
- Wellcome Sanger Institute, Hinxton, United Kingdom
- UK Dementia Research Institute, Cambridge, United Kingdom
| | - Stephen P. Jackson
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Leopold Parts
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Computer Science, University of Tartu, Tartu, Estonia
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38
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Kothari PH, Kolar GR, Jen JC, Hajj‐Ali R, Bertram P, Schmidt RE, Atkinson JP. TREX1 is expressed by microglia in normal human brain and increases in regions affected by ischemia. Brain Pathol 2018; 28:806-821. [PMID: 30062819 PMCID: PMC6404532 DOI: 10.1111/bpa.12626] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 05/28/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Mutations in the three-prime repair exonuclease 1 (TREX1) gene have been associated with neurological diseases, including Retinal Vasculopathy with Cerebral Leukoencephalopathy (RVCL). However, the endogenous expression of TREX1 in human brain has not been studied. METHODS We produced a rabbit polyclonal antibody (pAb) to TREX1 to characterize TREX1 by Western blotting (WB) of cell lysates from normal controls and subjects carrying an RVCL frame-shift mutation. Dual staining was performed to determine cell types expressing TREX1 in human brain tissue. TREX1 distribution in human brain was further evaluated by immunohistochemical analyses of formalin-fixed, paraffin-embedded samples from normal controls and patients with RVCL and ischemic stroke. RESULTS After validating the specificity of our anti-TREX1 rabbit pAb, WB analysis was utilized to detect the endogenous wild-type and frame-shift mutant of TREX1 in cell lysates. Dual staining in human brain tissues from patients with RVCL and normal controls localized TREX1 to a subset of microglia and macrophages. Quantification of immunohistochemical staining of the cerebral cortex revealed that TREX1+ microglia were primarily in the gray matter of normal controls (22.7 ± 5.1% and 5.5 ± 1.9% of Iba1+ microglia in gray and white matter, respectively) and commonly in association with the microvasculature. In contrast, in subjects with RVCL, the TREX1+ microglia were predominantly located in the white matter of normal appearing cerebral cortex (11.8 ± 3.1% and 38.9 ± 5.8% of Iba1+ microglia in gray and white matter, respectively). The number of TREX1+ microglia was increased in ischemic brain lesions in central nervous system of RVCL and stroke patients. CONCLUSIONS TREX1 is expressed by a subset of microglia in normal human brain, often in close proximity to the microvasculature, and increases in the setting of ischemic lesions. These findings suggest a role for TREX1+ microglia in vessel homeostasis and response to ischemic injury.
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Affiliation(s)
- Parul H. Kothari
- Department of Biology and Biomedical Sciences Human & Statistical Genetics ProgramWashington University School of MedicineSt. LouisMO
- Division of Rheumatology, Immunology and Allergy, Department of MedicineBrigham and Women's Hospital, Harvard Medical SchoolBostonMA
- Channing Division of Network Medicine, Department of MedicineBrigham and Women's Hospital, Harvard Medical SchoolBostonMA
| | - Grant R. Kolar
- Department of Pathology & ImmunologyWashington University School of MedicineSt. LouisMO
- Department of Pathology and Department of OphthalmologySaint Louis University School of MedicineSt. LouisMO
| | - Joanna C. Jen
- Departments of Neurology and NeurobiologyUCLA School of MedicineLos AngelesCA
- Departments of Neurology, Otolaryngology, NeurosurgeryIcahn School of Medicine at Mount SinaiNew YorkNY
| | - Rula Hajj‐Ali
- Center for Vasculitis Care and ResearchCleveland Clinic Lerner College of Medicine, Orthopaedic and Rheumatologic InstituteClevelandOH
| | - Paula Bertram
- Department of Medicine, Division of RheumatologyWashington University School of MedicineSt. LouisMO
| | - Robert E. Schmidt
- Department of Pathology and Immunology, Division of NeuropathologyWashington University School of MedicineSt. LouisMO
| | - John P. Atkinson
- Department of Medicine, Division of RheumatologyWashington University School of MedicineSt. LouisMO
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39
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Matz KM, Guzman RM, Goodman AG. The Role of Nucleic Acid Sensing in Controlling Microbial and Autoimmune Disorders. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 345:35-136. [PMID: 30904196 PMCID: PMC6445394 DOI: 10.1016/bs.ircmb.2018.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Innate immunity, the first line of defense against invading pathogens, is an ancient form of host defense found in all animals, from sponges to humans. During infection, innate immune receptors recognize conserved molecular patterns, such as microbial surface molecules, metabolites produces during infection, or nucleic acids of the microbe's genome. When initiated, the innate immune response activates a host defense program that leads to the synthesis proteins capable of pathogen killing. In mammals, the induction of cytokines during the innate immune response leads to the recruitment of professional immune cells to the site of infection, leading to an adaptive immune response. While a fully functional innate immune response is crucial for a proper host response and curbing microbial infection, if the innate immune response is dysfunctional and is activated in the absence of infection, autoinflammation and autoimmune disorders can develop. Therefore, it follows that the innate immune response must be tightly controlled to avoid an autoimmune response from host-derived molecules, yet still unencumbered to respond to infection. In this review, we will focus on the innate immune response activated from cytosolic nucleic acids, derived from the microbe or host itself. We will depict how viruses and bacteria activate these nucleic acid sensing pathways and their mechanisms to inhibit the pathways. We will also describe the autoinflammatory and autoimmune disorders that develop when these pathways are hyperactive. Finally, we will discuss gaps in knowledge with regard to innate immune response failure and identify where further research is needed.
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Affiliation(s)
- Keesha M Matz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - R Marena Guzman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - Alan G Goodman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States; Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States.
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40
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Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1. PLoS Biol 2018; 16:e2005653. [PMID: 29734329 PMCID: PMC5957452 DOI: 10.1371/journal.pbio.2005653] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/17/2018] [Accepted: 04/03/2018] [Indexed: 01/12/2023] Open
Abstract
Three prime repair exonuclease 1 (TREX1) is an essential exonuclease in mammalian cells, and numerous in vivo and in vitro data evidenced its participation in immunity regulation and in genotoxicity remediation. In these very complicated cellular functions, the molecular mechanisms by which duplex DNA substrates are processed are mostly elusive because of the lack of structure information. Here, we report multiple crystal structures of TREX1 complexed with various substrates to provide the structure basis for overhang excision and terminal unwinding of DNA duplexes. The substrates were designed to mimic the intermediate structural DNAs involved in various repair pathways. The results showed that the Leu24-Pro25-Ser26 cluster of TREX1 served to cap the nonscissile 5′-end of the DNA for precise removal of the short 3′-overhang in L- and Y-structural DNA or to wedge into the double-stranded region for further digestion along the duplex. Biochemical assays were also conducted to demonstrate that TREX1 can indeed degrade double-stranded DNA (dsDNA) to a full extent. Overall, this study provided unprecedented knowledge at the molecular level on the enzymatic substrate processing involved in prevention of immune activation and in responses to genotoxic stresses. For example, Arg128, whose mutation in TREX1 was linked to a disease state, were shown to exhibit consistent interaction patterns with the nonscissile strand in all of the structures we solved. Such structure basis is expected to play an indispensable role in elucidating the functional activities of TREX1 at the cellular level and in vivo. Three prime repair exonuclease 1 (TREX1) was shown to participate in various cellular events such as DNA repair, immunity regulation, and viral infection. In addition to relating to autoimmune diseases, this exonuclease also acts as a potential protein target for anticancer or antiviral therapies. A key for such broad attendance of TREX1 is the activities of precise trimming of the 3′-overhang in a double-stranded (dsDNA) and breaking of the terminal base pairing of the duplex. Here, we designed a series of structural DNA substrates and activity assays to delineate the underlying mechanisms. The structures newly resolved in this work indicated that the Leu24-Pro25-Ser26 cluster of TREX1 is essential for the enzyme to carry out the aforementioned activities. Together, our results established an integrated structure view into the versatile exonuclease functions of TREX1 and illuminated the molecular origin for the unique catalytic properties of TREX1 in processing various DNA intermediates in DNA repair and in cytosolic immunity regulation.
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41
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Manils J, Fischer H, Climent J, Casas E, García-Martínez C, Bas J, Sukseree S, Vavouri T, Ciruela F, de Anta JM, Tschachler E, Eckhart L, Soler C. Double deficiency of Trex2 and DNase1L2 nucleases leads to accumulation of DNA in lingual cornifying keratinocytes without activating inflammatory responses. Sci Rep 2017; 7:11902. [PMID: 28928425 PMCID: PMC5605544 DOI: 10.1038/s41598-017-12308-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/06/2017] [Indexed: 01/19/2023] Open
Abstract
The cornification of keratinocytes on the surface of skin and oral epithelia is associated with the degradation of nuclear DNA. The endonuclease DNase1L2 and the exonuclease Trex2 are expressed specifically in cornifying keratinocytes. Deletion of DNase1L2 causes retention of nuclear DNA in the tongue epithelium but not in the skin. Here we report that lack of Trex2 results in the accumulation of DNA fragments in the cytoplasm of cornifying lingual keratinocytes and co-deletion of DNase1L2 and Trex2 causes massive accumulation of DNA fragments throughout the cornified layers of the tongue epithelium. By contrast, cornification-associated DNA breakdown was not compromised in the epidermis. Aberrant retention of DNA in the tongue epithelium was associated neither with enhanced expression of DNA-driven response genes, such as Ifnb, Irf7 and Cxcl10, nor with inflammation. Of note, the expression of Tlr9, Aim2 and Tmem173, key DNA sensor genes, was markedly lower in keratinocytes and keratinocyte-built tissues than in macrophages and immune tissues, and DNA-driven response genes were not induced by introduction of DNA in keratinocytes. Altogether, our results indicate that DNase1L2 and Trex2 cooperate in the breakdown and degradation of DNA during cornification of lingual keratinocytes and aberrant DNA retention is tolerated in the oral epithelium.
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Affiliation(s)
- Joan Manils
- Departament de Patologia i Terapèutica Experimental, Facultat de Medicina i Ciències de la Salut, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain.,The Francis Crick Institute-Mill Hill Laboratory, London, NW7 1AA, United Kingdom
| | - Heinz Fischer
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Unit of Pathology of Laboratory Animals, University of Veterinary Medicine, Vienna, Austria
| | - Joan Climent
- Departament de Patologia i Terapèutica Experimental, Facultat de Medicina i Ciències de la Salut, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain.,Departament d'Immunologia, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Eduard Casas
- Program of Predictive and Personalized Medicine of Cancer (PMPPC) - Institute Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Celia García-Martínez
- Departament de Patologia i Terapèutica Experimental, Facultat de Medicina i Ciències de la Salut, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jordi Bas
- Departament de Patologia i Terapèutica Experimental, Facultat de Medicina i Ciències de la Salut, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain.,Departament d'Immunologia, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Supawadee Sukseree
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Tanya Vavouri
- Program of Predictive and Personalized Medicine of Cancer (PMPPC) - Institute Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain.,Josep Carreras Leukaemia Research Institute (IJC), ICO-Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Francisco Ciruela
- Departament de Patologia i Terapèutica Experimental, Facultat de Medicina i Ciències de la Salut, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Josep Maria de Anta
- Departament de Patologia i Terapèutica Experimental, Facultat de Medicina i Ciències de la Salut, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Erwin Tschachler
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Leopold Eckhart
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Vienna, Austria.
| | - Concepció Soler
- Departament de Patologia i Terapèutica Experimental, Facultat de Medicina i Ciències de la Salut, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain.
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42
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Li P, Du J, Goodier JL, Hou J, Kang J, Kazazian HH, Zhao K, Yu XF. Aicardi-Goutières syndrome protein TREX1 suppresses L1 and maintains genome integrity through exonuclease-independent ORF1p depletion. Nucleic Acids Res 2017; 45:4619-4631. [PMID: 28334850 PMCID: PMC5416883 DOI: 10.1093/nar/gkx178] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/11/2017] [Indexed: 12/22/2022] Open
Abstract
Maintaining genome integrity is important for cells and damaged DNA triggers autoimmunity. Previous studies have reported that Three-prime repair exonuclease 1(TREX1), an endogenous DNA exonuclease, prevents immune activation by depleting damaged DNA, thus preventing the development of certain autoimmune diseases. Consistently, mutations in TREX1 are linked with autoimmune diseases such as systemic lupus erythematosus, Aicardi–Goutières syndrome (AGS) and familial chilblain lupus. However, TREX1 mutants competent for DNA exonuclease activity are also linked to AGS. Here, we report a nuclease-independent involvement of TREX1 in preventing the L1 retrotransposon-induced DNA damage response. TREX1 interacted with ORF1p and altered its intracellular localization. Furthermore, TREX1 triggered ORF1p depletion and reduced the L1-mediated nicking of genomic DNA. TREX1 mutants related to AGS were deficient in inducing ORF1p depletion and could not prevent L1-mediated DNA damage. Therefore, our findings not only reveal a new mechanism for TREX1-mediated L1 suppression and uncover a new function for TREX1 in protein destabilization, but they also suggest a novel mechanism for TREX1-mediated suppression of innate immune activation through maintaining genome integrity.
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Affiliation(s)
- Peng Li
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Juan Du
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - John L Goodier
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jingwei Hou
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Jian Kang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Haig H Kazazian
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ke Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Xiao-Fang Yu
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin 130061, China.,Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Achleitner M, Kleefisch M, Hennig A, Peschke K, Polikarpova A, Oertel R, Gabriel B, Schulze L, Lindeman D, Gerbaulet A, Fiebig U, Lee-Kirsch MA, Roers A, Behrendt R. Lack of Trex1 Causes Systemic Autoimmunity despite the Presence of Antiretroviral Drugs. THE JOURNAL OF IMMUNOLOGY 2017; 199:2261-2269. [PMID: 28835460 DOI: 10.4049/jimmunol.1700714] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/26/2017] [Indexed: 01/25/2023]
Abstract
Biallelic mutations of three prime repair exonuclease 1 (TREX1) cause the lupus-like disease Aicardi-Goutières syndrome in which accumulation of a yet unknown endogenous DNA substrate of TREX1 triggers a cyclic GMP-AMP synthase-dependent type I IFN response and systemic autoimmunity. Products of reverse transcription originating from endogenous retroelements have been suggested to be a major substrate for TREX1, and reverse transcriptase inhibitors (RTIs) were proposed as a therapeutic option in autoimmunity ensuing from defects of TREX1. In this study, we treated Trex1-/- mice with RTIs. The serum RTI levels reached were sufficient to block retrotransposition of endogenous retroelements. However, the treatment did not reduce the spontaneous type I IFN response and did not ameliorate lethal inflammation. Furthermore, long interspersed nuclear elements 1 retrotransposition was not enhanced in the absence of Trex1. Our data do not support the concept of retroelement-derived cDNA as key triggers of systemic autoimmunity in Trex1-deficient humans and mice and motivate the continuing search for the pathogenic IFN-inducing Trex1 substrate.
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Affiliation(s)
- Martin Achleitner
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Martin Kleefisch
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Alexander Hennig
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Katrin Peschke
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Anastasia Polikarpova
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Reinhard Oertel
- Institute of Clinical Pharmacology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Benjamin Gabriel
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Livia Schulze
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Dirk Lindeman
- Institute of Virology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany; and
| | - Alexander Gerbaulet
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Uwe Fiebig
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Min Ae Lee-Kirsch
- Molecular Pediatrics, Department of Pediatrics, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Rayk Behrendt
- Institute for Immunology, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany;
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44
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Crowl JT, Gray EE, Pestal K, Volkman HE, Stetson DB. Intracellular Nucleic Acid Detection in Autoimmunity. Annu Rev Immunol 2017; 35:313-336. [PMID: 28142323 DOI: 10.1146/annurev-immunol-051116-052331] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protective immune responses to viral infection are initiated by innate immune sensors that survey extracellular and intracellular space for foreign nucleic acids. The existence of these sensors raises fundamental questions about self/nonself discrimination because of the abundance of self-DNA and self-RNA that occupy these same compartments. Recent advances have revealed that enzymes that metabolize or modify endogenous nucleic acids are essential for preventing inappropriate activation of the innate antiviral response. In this review, we discuss rare human diseases caused by dysregulated nucleic acid sensing, focusing primarily on intracellular sensors of nucleic acids. We summarize lessons learned from these disorders, we rationalize the existence of these diseases in the context of evolution, and we propose that this framework may also apply to a number of more common autoimmune diseases for which the underlying genetics and mechanisms are not yet fully understood.
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Affiliation(s)
- John T Crowl
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109;
| | - Elizabeth E Gray
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109;
| | - Kathleen Pestal
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109;
| | - Hannah E Volkman
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109;
| | - Daniel B Stetson
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109;
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45
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Manils J, Casas E, Viña-Vilaseca A, López-Cano M, Díez-Villanueva A, Gómez D, Marruecos L, Ferran M, Benito C, Perrino FW, Vavouri T, de Anta JM, Ciruela F, Soler C. The Exonuclease Trex2 Shapes Psoriatic Phenotype. J Invest Dermatol 2016; 136:2345-2355. [DOI: 10.1016/j.jid.2016.05.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 05/10/2016] [Accepted: 05/31/2016] [Indexed: 02/07/2023]
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46
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Peschke K, Achleitner M, Frenzel K, Gerbaulet A, Ada SR, Zeller N, Lienenklaus S, Lesche M, Poulet C, Naumann R, Dahl A, Ravens U, Günther C, Müller W, Knobeloch KP, Prinz M, Roers A, Behrendt R. Loss of Trex1 in Dendritic Cells Is Sufficient To Trigger Systemic Autoimmunity. THE JOURNAL OF IMMUNOLOGY 2016; 197:2157-66. [DOI: 10.4049/jimmunol.1600722] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/12/2016] [Indexed: 01/14/2023]
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47
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The danger model approach to the pathogenesis of the rheumatic diseases. J Immunol Res 2015; 2015:506089. [PMID: 25973436 PMCID: PMC4417989 DOI: 10.1155/2015/506089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 12/12/2014] [Indexed: 12/19/2022] Open
Abstract
The danger model was proposed by Polly Matzinger as complement to the traditional self-non-self- (SNS-) model to explain the immunoreactivity. The danger model proposes a central role of the tissular cells' discomfort as an element to prime the immune response processes in opposition to the traditional SNS-model where foreignness is a prerequisite. However recent insights in the proteomics of diverse tissular cells have revealed that under stressful conditions they have a significant potential to initiate, coordinate, and perpetuate autoimmune processes, in many cases, ruling over the adaptive immune response cells; this ruling potential can also be confirmed by observations in several genetically manipulated animal models. Here, we review the pathogenesis of rheumatic diseases such as systemic lupus erythematous, rheumatoid arthritis, spondyloarthritis including ankylosing spondylitis, psoriasis, and Crohn's disease and provide realistic approaches based on the logic of the danger model. We assume that tissular dysfunction is a prerequisite for chronic autoimmunity and propose two genetically conferred hypothetical roles for the tissular cells causing the disease: (A) the Impaired cell and (B) the paranoid cell. Both roles are not mutually exclusive. Some examples in human disease and in animal models are provided based on current evidence.
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48
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Yuan F, Dutta T, Wang L, Song L, Gu L, Qian L, Benitez A, Ning S, Malhotra A, Deutscher MP, Zhang Y. Human DNA Exonuclease TREX1 Is Also an Exoribonuclease That Acts on Single-stranded RNA. J Biol Chem 2015; 290:13344-53. [PMID: 25855793 DOI: 10.1074/jbc.m115.653915] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Indexed: 01/22/2023] Open
Abstract
3' repair exonuclease 1 (TREX1) is a known DNA exonuclease involved in autoimmune disorders and the antiviral response. In this work, we show that TREX1 is also a RNA exonuclease. Purified TREX1 displays robust exoribonuclease activity that degrades single-stranded, but not double-stranded, RNA. TREX1-D200N, an Aicardi-Goutieres syndrome disease-causing mutant, is defective in degrading RNA. TREX1 activity is strongly inhibited by a stretch of pyrimidine residues as is a bacterial homolog, RNase T. Kinetic measurements indicate that the apparent Km of TREX1 for RNA is higher than that for DNA. Like RNase T, human TREX1 is active in degrading native tRNA substrates. Previously reported TREX1 crystal structures have revealed that the substrate binding sites are open enough to accommodate the extra hydroxyl group in RNA, further supporting our conclusion that TREX1 acts on RNA. These findings indicate that its RNase activity needs to be taken into account when evaluating the physiological role of TREX1.
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Affiliation(s)
- Fenghua Yuan
- From the Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136
| | - Tanmay Dutta
- From the Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136
| | - Ling Wang
- the Department of Medicine, Center for Inflammation, Infectious Diseases, and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614, and
| | - Lei Song
- From the Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136
| | - Liya Gu
- the Graduate Center for Toxicology, University of Kentucky College of Medicine, Lexington, Kentucky 40536
| | - Liangyue Qian
- From the Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136
| | - Anaid Benitez
- From the Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136
| | - Shunbin Ning
- the Department of Medicine, Center for Inflammation, Infectious Diseases, and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614, and
| | - Arun Malhotra
- From the Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136
| | - Murray P Deutscher
- From the Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136
| | - Yanbin Zhang
- From the Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136,
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49
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Exonuclease TREX1 degrades double-stranded DNA to prevent spontaneous lupus-like inflammatory disease. Proc Natl Acad Sci U S A 2015; 112:5117-22. [PMID: 25848017 DOI: 10.1073/pnas.1423804112] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The TREX1 gene encodes a potent DNA exonuclease, and mutations in TREX1 cause a spectrum of lupus-like autoimmune diseases. Most lupus patients develop autoantibodies to double-stranded DNA (dsDNA), but the source of DNA antigen is unknown. The TREX1 D18N mutation causes a monogenic, cutaneous form of lupus called familial chilblain lupus, and the TREX1 D18N enzyme exhibits dysfunctional dsDNA-degrading activity, providing a link between dsDNA degradation and nucleic acid-mediated autoimmune disease. We determined the structure of the TREX1 D18N protein in complex with dsDNA, revealing how this exonuclease uses a novel DNA-unwinding mechanism to separate the polynucleotide strands for single-stranded DNA (ssDNA) loading into the active site. The TREX1 D18N dsDNA interactions coupled with catalytic deficiency explain how this mutant nuclease prevents dsDNA degradation. We tested the effects of TREX1 D18N in vivo by replacing the TREX1 WT gene in mice with the TREX1 D18N allele. The TREX1 D18N mice exhibit systemic inflammation, lymphoid hyperplasia, vasculitis, and kidney disease. The observed lupus-like inflammatory disease is associated with immune activation, production of autoantibodies to dsDNA, and deposition of immune complexes in the kidney. Thus, dysfunctional dsDNA degradation by TREX1 D18N induces disease in mice that recapitulates many characteristics of human lupus. Failure to clear DNA has long been linked to lupus in humans, and these data point to dsDNA as a key substrate for TREX1 and a major antigen source in mice with dysfunctional TREX1 enzyme.
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50
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Miyazaki T, Kim YS, Yoon J, Wang H, Suzuki T, Morse HC. The 3'-5' DNA exonuclease TREX1 directly interacts with poly(ADP-ribose) polymerase-1 (PARP1) during the DNA damage response. J Biol Chem 2014; 289:32548-58. [PMID: 25278026 DOI: 10.1074/jbc.m114.547331] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The main function of the 3'-5' DNA exonuclease TREX1 is to digest cytosolic single-stranded DNA to prevent activation of cell-intrinsic responses to immunostimulatory DNA. TREX1 translocates to the nucleus following DNA damage with its nuclear activities being less well defined. Although mutations in human TREX1 have been linked to autoimmune/inflammatory diseases, the mechanisms contributing to the pathogenesis of these diseases remain incompletely understood. Here, using mass spectrometry and co-immunoprecipitation assays and in vivo overexpression models, we show that TREX1 interacts with poly(ADP-ribose) polymerase-1 (PARP1), a nuclear enzyme involved in the DNA damage response. Two zinc finger domains at the amino terminus of PARP1 were required for the interaction with TREX1 that occurs after nuclear translocation of TREX1 in response to DNA damage. Functional studies suggested that TREX1 may contribute to stabilization of PARP1 levels in the DNA damage response and its activity. These results provide new insights into the mechanisms of single-stranded DNA repair following DNA damage and alterations induced by gene mutations.
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Affiliation(s)
- Takuya Miyazaki
- From the Virology and Cellular Immunology Section, Laboratory of Immunogenetics, NIAID, National Institutes of Health, Rockville, Maryland 20852 and
| | - Yong-Soo Kim
- From the Virology and Cellular Immunology Section, Laboratory of Immunogenetics, NIAID, National Institutes of Health, Rockville, Maryland 20852 and
| | - Jeongheon Yoon
- From the Virology and Cellular Immunology Section, Laboratory of Immunogenetics, NIAID, National Institutes of Health, Rockville, Maryland 20852 and
| | - Hongsheng Wang
- From the Virology and Cellular Immunology Section, Laboratory of Immunogenetics, NIAID, National Institutes of Health, Rockville, Maryland 20852 and
| | - Teruhiko Suzuki
- Stem Cell Project Group, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506 Japan
| | - Herbert C Morse
- From the Virology and Cellular Immunology Section, Laboratory of Immunogenetics, NIAID, National Institutes of Health, Rockville, Maryland 20852 and
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