1
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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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2
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Tani T, Mathsyaraja H, Campisi M, Li ZH, Haratani K, Fahey CG, Ota K, Mahadevan NR, Shi Y, Saito S, Mizuno K, Thai TC, Sasaki N, Homme M, Yusuf CFB, Kashishian A, Panchal J, Wang M, Wolf BJ, Barbie TU, Paweletz CP, Gokhale PC, Liu D, Uppaluri R, Kitajima S, Cain J, Barbie DA. TREX1 Inactivation Unleashes Cancer Cell STING-Interferon Signaling and Promotes Antitumor Immunity. Cancer Discov 2024; 14:752-765. [PMID: 38227896 PMCID: PMC11062818 DOI: 10.1158/2159-8290.cd-23-0700] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/28/2023] [Accepted: 01/08/2024] [Indexed: 01/18/2024]
Abstract
A substantial fraction of cancers evade immune detection by silencing Stimulator of Interferon Genes (STING)-Interferon (IFN) signaling. Therapeutic reactivation of this program via STING agonists, epigenetic, or DNA-damaging therapies can restore antitumor immunity in multiple preclinical models. Here we show that adaptive induction of three prime exonuclease 1 (TREX1) restrains STING-dependent nucleic acid sensing in cancer cells via its catalytic function in degrading cytosolic DNA. Cancer cell TREX1 expression is coordinately induced with STING by autocrine IFN and downstream STAT1, preventing signal amplification. TREX1 inactivation in cancer cells thus unleashes STING-IFN signaling, recruiting T and natural killer (NK) cells, sensitizing to NK cell-derived IFNγ, and cooperating with programmed cell death protein 1 blockade in multiple mouse tumor models to enhance immunogenicity. Targeting TREX1 may represent a complementary strategy to induce cytosolic DNA and amplify cancer cell STING-IFN signaling as a means to sensitize tumors to immune checkpoint blockade (ICB) and/or cell therapies. SIGNIFICANCE STING-IFN signaling in cancer cells promotes tumor cell immunogenicity. Inactivation of the DNA exonuclease TREX1, which is adaptively upregulated to limit pathway activation in cancer cells, recruits immune effector cells and primes NK cell-mediated killing. Targeting TREX1 has substantial therapeutic potential to amplify cancer cell immunogenicity and overcome ICB resistance. This article is featured in Selected Articles from This Issue, p. 695.
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Affiliation(s)
- Tetsuo Tani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Contributed equally
| | | | - Marco Campisi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ze-Hua Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Koji Haratani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Caroline G. Fahey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keiichi Ota
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Navin R. Mahadevan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Yingxiao Shi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shin Saito
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kei Mizuno
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tran C. Thai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nobunari Sasaki
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mizuki Homme
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Choudhury Fabliha B. Yusuf
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Min Wang
- Gilead Sciences, Foster City, CA, USA
| | | | - Thanh U. Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Cloud P. Paweletz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Prafulla C Gokhale
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ravindra Uppaluri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shunsuke Kitajima
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | - David A. Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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3
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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4
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Han H, Jeung JH, Jang SH, Lee CY, Ahn JK. Peroxidase-Mimicking Activity of Nanoceria for Label-Free Colorimetric Assay for Exonuclease III Activity. Int J Mol Sci 2023; 24:12330. [PMID: 37569706 PMCID: PMC10418927 DOI: 10.3390/ijms241512330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
We present a novel label-free colorimetric method for detecting exonuclease III (Exo III) activity using the peroxidase-mimicking activity of cerium oxide nanoparticles (nanoceria). Exo III, an enzyme that specifically catalyzes the stepwise removal of mononucleotides from the 3'-OH termini of double-stranded DNA, plays a significant role in various cellular and physiological processes, including DNA proofreading and repair. Malfunctions of Exo III have been associated with increased cancer risks. To assay the activity of Exo III, we applied the previous reports in that the peroxidase-mimicking activity of nanoceria is inhibited due to the aggregation induced by the electrostatic attraction between DNA and nanoceria. In the presence of Exo III, the substrate DNA (subDNA), which inhibits nanoceria's activity, is degraded, thereby restoring the peroxidase-mimicking activity of nanoceria. Consequently, the 3,3',5,5'-tetramethylbenzidine (TMB) substrate is oxidized, leading to a color change from colorless to blue, along with an increase in the absorbance intensity. This approach enabled us to reliably detect Exo III at a limit of detection (LOD) of 0.263 units/mL across a broad dynamic range from 3.1 to 400 units/mL, respectively, with an outstanding specificity. Since this approach does not require radiolabels, complex DNA design, or sophisticated experimental techniques, it provides a simpler and more feasible alternative to standard methods.
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Affiliation(s)
- Hyogu Han
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan 15588, Republic of Korea; (H.H.); (J.H.J.); (S.H.J.)
- Department of Chemistry, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Jae Hoon Jeung
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan 15588, Republic of Korea; (H.H.); (J.H.J.); (S.H.J.)
| | - Se Hee Jang
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan 15588, Republic of Korea; (H.H.); (J.H.J.); (S.H.J.)
- Department of Medical Device Engineering and Management, College of Medicine, Yonsei University, Seoul 03722, Republic of Korea
| | - Chang Yeol Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jun Ki Ahn
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan 15588, Republic of Korea; (H.H.); (J.H.J.); (S.H.J.)
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5
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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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6
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Manils J, Marruecos L, Soler C. Exonucleases: Degrading DNA to Deal with Genome Damage, Cell Death, Inflammation and Cancer. Cells 2022; 11:2157. [PMID: 35883600 PMCID: PMC9316158 DOI: 10.3390/cells11142157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 01/27/2023] Open
Abstract
Although DNA degradation might seem an unwanted event, it is essential in many cellular processes that are key to maintaining genomic stability and cell and organism homeostasis. The capacity to cut out nucleotides one at a time from the end of a DNA chain is present in enzymes called exonucleases. Exonuclease activity might come from enzymes with multiple other functions or specialized enzymes only dedicated to this function. Exonucleases are involved in central pathways of cell biology such as DNA replication, repair, and death, as well as tuning the immune response. Of note, malfunctioning of these enzymes is associated with immune disorders and cancer. In this review, we will dissect the impact of DNA degradation on the DNA damage response and its links with inflammation and cancer.
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Affiliation(s)
- Joan Manils
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Feixa Llarga s/n, 08907 L’Hospitalet de Llobregat, Spain;
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
| | - Laura Marruecos
- Breast Cancer Laboratory, Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Concepció Soler
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
- Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
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7
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Reusable and sensitive exonuclease III activity detection on DNB nanoarrays based on cPAS sequencing technology. Enzyme Microb Technol 2021; 150:109878. [PMID: 34489031 DOI: 10.1016/j.enzmictec.2021.109878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/16/2022]
Abstract
In this article we describe a sensitive exonuclease III detection method using a DNB nanoarray from a BGISEQ-500 sequencing kit and demonstrate a detection limit as low as 0.001 U/mL. The flow cell of the sequencing kit was loaded with billions of DNA nanoballs (DNBs) to form the DNB nanoarray and initially used for massively parallel sequencing. The 3'-end recessed dsDNA structure formed by sequencing was shown to be a perfect substrate for exonuclease III, but not for other nucleases such as exonuclease I, RecJf and nuclease P1. We developed an exonuclease III assay using the DNB nanoarray, together with other reagents within the BGISEQ-500 sequencing kit, which only required one additional cycle of sequencing. The DNB nanoarray can be reused for the exonuclease III assay at least five times. This method demonstrated superior sensitivity, selectivity, and reusability compared with other assay methods and is accompanied by low cost and simple setup.
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8
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Liu TC, Guo KW, Chu JW, Hsiao YY. Understanding APE1 cellular functions by the structural preference of exonuclease activities. Comput Struct Biotechnol J 2021; 19:3682-3691. [PMID: 34285771 PMCID: PMC8258793 DOI: 10.1016/j.csbj.2021.06.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/17/2022] Open
Abstract
Mammalian apurinic/apyrimidinic (AP) endonuclease 1 (APE1) has versatile enzymatic functions, including redox, endonuclease, and exonuclease activities. APE1 is thus broadly associated with pathways in DNA repair, cancer cell growth, and drug resistance. Unlike its AP site-specific endonuclease activity in Base excision repair (BER), the 3′-5′ exonucleolytic cleavage of APE1 using the same active site exhibits complex substrate selection patterns, which are key to the biological functions. This work aims to integrate molecular structural information and biocatalytic properties to deduce the substrate recognition mechanism of APE1 as an exonuclease and make connection to its diverse functionalities in the cell. In particular, an induced space-filling model emerges in which a bridge-like structure is formed by Arg177 and Met270 (RM bridge) upon substrate binding, causing the active site to adopt a long and narrow product pocket for hosting the leaving group of an AP site or the 3′-end nucleotide. Rather than distinguishing bases as other exonucleases, the hydrophobicity and steric hindrance due to the APE1 product pocket provides selectivity for substrate structures, such as matched or mismatched blunt-ended dsDNA, recessed dsDNA, gapped dsDNA, and nicked dsDNA with 3′-end overhang shorter than 2 nucleotides. These dsDNAs are similar to the native substrates in BER proofreading, BER for trinucleotide repeats (TNR), Nucleotide incision repair (NIR), DNA single-strand breaks (SSB), SSB with damaged bases, and apoptosis. Integration of in vivo studies, in vitro biochemical assays, and structural analysis is thus essential for linking the APE1 exonuclease activity to the specific roles in cellular functions.
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Affiliation(s)
- Tung-Chang Liu
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan
| | - Kai-Wei Guo
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan
| | - Jhih-Wei Chu
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 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, Taiwan
| | - Yu-Yuan Hsiao
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 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, Taiwan.,Drug Development and Value Creation Research Center, Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
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9
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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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10
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Davern M, Lysaght J. Cooperation between chemotherapy and immunotherapy in gastroesophageal cancers. Cancer Lett 2020; 495:89-99. [DOI: 10.1016/j.canlet.2020.09.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/05/2020] [Accepted: 09/12/2020] [Indexed: 02/07/2023]
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11
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Cao X, Sun Y, Lu P, Zhao M. Fluorescence imaging of intracellular nucleases-A review. Anal Chim Acta 2020; 1137:225-237. [PMID: 33153605 DOI: 10.1016/j.aca.2020.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 11/28/2022]
Abstract
Nucleases play crucial roles in maintaining genomic integrity. Visualization of intracellular distribution and translocation of nucleases are of great importance for understanding the in-vivo physiological functions of these enzymes and their roles in DNA repair and other cellular signaling pathways. Here we review the recently developed approaches for fluorescence imaging of nucleases in various eukaryotic cells. We mainly focused on the immunofluorescence techniques, the genetically encoded fluorescent probes and the chemically synthesized fluorescent DNA-substrate probes that enabled in-situ visualization of the subcellular localization of nucleases and their interactions with other protein/DNA molecules within cells. The targeted nucleases included important endonucleases, 3' exonucleases and 5' exonucleases that were involved in the DNA damage repair pathways and the intracellular DNA degradation. The advantages and limitations of the available tools were summarized and discussed.
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Affiliation(s)
- Xiangjian Cao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Ying Sun
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peng Lu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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12
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Krushkal J, Silvers T, Reinhold WC, Sonkin D, Vural S, Connelly J, Varma S, Meltzer PS, Kunkel M, Rapisarda A, Evans D, Pommier Y, Teicher BA. Epigenome-wide DNA methylation analysis of small cell lung cancer cell lines suggests potential chemotherapy targets. Clin Epigenetics 2020; 12:93. [PMID: 32586373 PMCID: PMC7318526 DOI: 10.1186/s13148-020-00876-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/26/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Small cell lung cancer (SCLC) is an aggressive neuroendocrine lung cancer. SCLC progression and treatment resistance involve epigenetic processes. However, links between SCLC DNA methylation and drug response remain unclear. We performed an epigenome-wide study of 66 human SCLC cell lines using the Illumina Infinium MethylationEPIC BeadChip array. Correlations of SCLC DNA methylation and gene expression with in vitro response to 526 antitumor agents were examined. RESULTS We found multiple significant correlations between DNA methylation and chemosensitivity. A potentially important association was observed for TREX1, which encodes the 3' exonuclease I that serves as a STING antagonist in the regulation of a cytosolic DNA-sensing pathway. Increased methylation and low expression of TREX1 were associated with the sensitivity to Aurora kinase inhibitors AZD-1152, SCH-1473759, SNS-314, and TAK-901; the CDK inhibitor R-547; the Vertex ATR inhibitor Cpd 45; and the mitotic spindle disruptor vinorelbine. Compared with cell lines of other cancer types, TREX1 had low mRNA expression and increased upstream region methylation in SCLC, suggesting a possible relationship with SCLC sensitivity to Aurora kinase inhibitors. We also identified multiple additional correlations indicative of potential mechanisms of chemosensitivity. Methylation of the 3'UTR of CEP350 and MLPH, involved in centrosome machinery and microtubule tracking, respectively, was associated with response to Aurora kinase inhibitors and other agents. EPAS1 methylation was associated with response to Aurora kinase inhibitors, a PLK-1 inhibitor and a Bcl-2 inhibitor. KDM1A methylation was associated with PLK-1 inhibitors and a KSP inhibitor. Increased promoter methylation of SLFN11 was correlated with resistance to DNA damaging agents, as a result of low or no SLFN11 expression. The 5' UTR of the epigenetic modifier EZH2 was associated with response to Aurora kinase inhibitors and a FGFR inhibitor. Methylation and expression of YAP1 were correlated with response to an mTOR inhibitor. Among non-neuroendocrine markers, EPHA2 was associated with response to Aurora kinase inhibitors and a PLK-1 inhibitor and CD151 with Bcl-2 inhibitors. CONCLUSIONS Multiple associations indicate potential epigenetic mechanisms affecting SCLC response to chemotherapy and suggest targets for combination therapies. While many correlations were not specific to SCLC lineages, several lineage markers were associated with specific agents.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Dr., Rockville, MD, 20850, USA.
| | - Thomas Silvers
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - Suleyman Vural
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - John Connelly
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Mark Kunkel
- Drug Synthesis and Chemistry Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Annamaria Rapisarda
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - David Evans
- Molecular Pharmacology Group, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Beverly A Teicher
- Molecular Pharmacology Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, 20892, USA.
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13
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Ellerin BE, Demandante CGN, Martins JT. Pure abscopal effect of radiotherapy in a salivary gland carcinoma: Case report, literature review, and a search for new approaches. Cancer Radiother 2020; 24:226-246. [PMID: 32192840 DOI: 10.1016/j.canrad.2020.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 12/12/2022]
Abstract
We report the case of an 84-year-old woman with poorly differentiated non-small cell carcinoma of the right parotid who presented with headache, was found to have a primary right parotid gland cancer as well as metastatic disease, and underwent palliative radiotherapy to the primary site. The patient received no chemotherapy or immunotherapy, but both the primary site and several non-irradiated foci in the lungs regressed or completely resolved. The patient remained free of disease for about one year before progression. The case is a rare instance of abscopal regression of metastatic disease in the absence of pharmacologic immunomodulation. A literature review surveys the history of the abscopal effect of radiation therapy, attempts to understand the mechanisms of its successes and failures, and points to new approaches that can inform and improve the outcomes of radioimmunotherapy.
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Affiliation(s)
| | | | - J T Martins
- UT Health HOPE Cancer Center, Tyler, TX 75701, USA
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14
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Liu X, Wu Y, Wu X, Zhao JX. A graphene oxide-based fluorescence assay for the sensitive detection of DNA exonuclease enzymatic activity. Analyst 2020; 144:6231-6239. [PMID: 31552930 DOI: 10.1039/c9an01283d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The 3'-5' exonuclease enzyme plays a dominant role in multiple pivotal physiological activities, such as DNA replication and repair processes. In this study, we designed a sensitive graphene oxide (GO)-based probe for the detection of exonuclease enzymatic activity. In the absence of Exo III, the strong π-π interaction between the fluorophore-tagged DNA and GO causes the efficient fluorescence quenching via a fluorescence resonance energy transfer (FRET). In contrast, in the presence of Exo III, the fluorophore-tagged 3'-hydroxyl termini of the DNA probe was digested by Exo III to set the fluorophore free from adsorption when GO was introduced, causing an inefficient fluorescence quenching. As a result, the fluorescence intensity of the sensor was found to be proportional to the concentration of Exo III; towards the detection of Exo III, this simple GO-based probe demonstrated a highly sensitive and selective linear response in the low detection range from 0.01 U mL-1 to 0.5 U mL-1 and with the limit of detection (LOD) of 0.001 U mL-1. Compared with other fluorescent probes, this assay exhibited superior sensitivity and selectivity in both buffer and fetal bovine serum samples, in addition to being cost effective and having a simple setup.
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Affiliation(s)
- Xiao Liu
- Department of Chemistry, University of North Dakota, Grand Forks, ND 58202, USA.
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15
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Chanut R, Petrilli V. [Cytosolic DNA sensing by the cGAS-STING pathway in cancer]. Med Sci (Paris) 2019; 35:527-534. [PMID: 31274082 DOI: 10.1051/medsci/2019095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) is a universal cytosolic DNA sensor that detects nucleic acids of pathogens. Upon DNA sensing, cGAS triggers the formation of the second intracellular messenger, the cyclic GMP-AMP (cGAMP), which activates the adaptor STING. STING engagement induces the secretion of cytokines and type I interferons that contribute to pathogen clearance. However, there is emerging evidence that cGAS is activated by self DNA in cancer cells and in antigen-presenting cells to trigger an antitumoral response. In this review, we will highlight the current understanding of self DNA sensing by cGAS in the context of cancer.
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Affiliation(s)
- Romain Chanut
- Centre de recherche en cancérologie de Lyon, UM5286 U1052, université de Lyon, centre Léon Bérard, 69008 Lyon, France
| | - Virginie Petrilli
- Centre de recherche en cancérologie de Lyon, UM5286 U1052, université de Lyon, centre Léon Bérard, 69008 Lyon, France
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16
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Prati B, da Silva Abjaude W, Termini L, Morale M, Herbster S, Longatto-Filho A, Nunes RAL, Córdoba Camacho LC, Rabelo-Santos SH, Zeferino LC, Aguayo F, Boccardo E. Three Prime Repair Exonuclease 1 (TREX1) expression correlates with cervical cancer cells growth in vitro and disease progression in vivo. Sci Rep 2019; 9:351. [PMID: 30674977 PMCID: PMC6344518 DOI: 10.1038/s41598-018-37064-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
Alterations in specific DNA damage repair mechanisms in the presence of human papillomavirus (HPV) infection have been described in different experimental models. However, the global effect of HPV on the expression of genes involved in these pathways has not been analyzed in detail. In the present study, we compared the expression profile of 135 genes involved in DNA damage repair among primary human keratinocytes (PHK), HPV-positive (SiHa and HeLa) and HPV-negative (C33A) cervical cancer derived cell lines. We identified 9 genes which expression pattern distinguishes HPV-positive tumor cell lines from C33A. Moreover, we observed that Three Prime Repair Exonuclease 1 (TREX1) expression is upregulated exclusively in HPV-transformed cell lines and PHK expressing HPV16 E6 and E7 oncogenes. We demonstrated that TREX1 silencing greatly affects tumor cells clonogenic and anchorage independent growth potential. We showed that this effect is associated with p53 upregulation, accumulation of subG1 cells, and requires the expression of E7 from high-risk HPV types. Finally, we observed an increase in TREX1 levels in precancerous lesions, squamous carcinomas and adenocarcinomas clinical samples. Altogether, our results indicate that TREX1 upregulation is important for cervical tumor cells growth and may contribute with tumor establishment and progression.
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Affiliation(s)
- Bruna Prati
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes 1374, 05508-900, São Paulo, SP, Brazil
| | - Walason da Silva Abjaude
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes 1374, 05508-900, São Paulo, SP, Brazil
| | - Lara Termini
- Centro de Investigação Translacional em Oncologia (LIM24), Instituto do Câncer do Estado de São Paulo (ICESP), São Paulo, Brazil
| | - Mirian Morale
- Department of Biochemistry, Institute of Chemistry, USP, São Paulo, Brazil
| | - Suellen Herbster
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes 1374, 05508-900, São Paulo, SP, Brazil
| | - Adhemar Longatto-Filho
- Laboratory of Medical Investigation (LIM 14), Department of Pathology, School of Medicine, USP, Av. Dr. Arnaldo 455, São Paulo, 01246-903, Brazil.,Life and Health Sciences Research Institute, School of Health Sciences, ICVS/3B's - PT Government Associate Laboratory, University of Minho, Braga, Guimarães, Portugal.,Molecular Oncology Research Center, Barretos Cancer Hospital, Pio XII Foundation, Barretos, Rua Antenor Duarte Villela, 1331, Barretos, 14784-400, Brazil
| | - Rafaella Almeida Lima Nunes
- Centro de Investigação Translacional em Oncologia (LIM24), Instituto do Câncer do Estado de São Paulo (ICESP), São Paulo, Brazil
| | - Lizeth Carolina Córdoba Camacho
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes 1374, 05508-900, São Paulo, SP, Brazil.,Laboratório de Oncologia Experimental, Departamento de Radiologia, Faculdade de Medicina, USP, São Paulo, SP, Brazil.,Centro de Investigação Translacional em Oncologia, ICESP, São Paulo, SP, Brazil
| | | | - Luiz Carlos Zeferino
- School of Medical Sciences, State University of Campinas (UNICAMP), Rua Alexander Fleming 101, 13083-881, Campinas, SP, Brazil
| | - Francisco Aguayo
- Basic and Clinical Oncology Department, Faculty of Medicine, University of Chile, Santiago, Chile.,Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Enrique Boccardo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo (USP), Av. Prof. Lineu Prestes 1374, 05508-900, São Paulo, SP, Brazil.
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17
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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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18
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Xie J, Wu YY, Zhang TY, Zhang MY, Zhu WW, Gullen EA, Wang ZJ, Cheng YC, Zhang YX. New and bioactive natural products from an endophyte of Panax notoginseng. RSC Adv 2017. [DOI: 10.1039/c7ra07060h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Secondary metabolites with cytotoxic activity, antiviral activity and antimicrobial activity from the endophytic fungi of Panax notoginseng.
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Affiliation(s)
- Jun Xie
- School of Life Science and Biopharmaceutics
- Shenyang Pharmaceutical University
- Shenyang
- People's Republic of China
| | - Ying-Ying Wu
- School of Life Science and Biopharmaceutics
- Shenyang Pharmaceutical University
- Shenyang
- People's Republic of China
| | - Tian-Yuan Zhang
- School of Life Science and Biopharmaceutics
- Shenyang Pharmaceutical University
- Shenyang
- People's Republic of China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics
- Shenyang Pharmaceutical University
- Shenyang
- People's Republic of China
| | - Wei-Wei Zhu
- School of Life Science and Biopharmaceutics
- Shenyang Pharmaceutical University
- Shenyang
- People's Republic of China
| | | | - Zhao-Jie Wang
- Yunnan Provincial Academy of Science and Technology
- Kunming
- People's Republic of China
| | - Yung-Chi Cheng
- Department of Pharmacology
- Yale University School of Medicine
- New Haven
- USA
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics
- Shenyang Pharmaceutical University
- Shenyang
- People's Republic of China
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19
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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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20
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Li F, Wang Y, Zhang G, Zhou J, Yang L, Guan H. Expression and methylation of DNA repair genes in lens epithelium cells of age-related cataract. Mutat Res 2014; 766-767:31-6. [PMID: 25847269 DOI: 10.1016/j.mrfmmm.2014.05.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 05/21/2014] [Accepted: 05/30/2014] [Indexed: 02/05/2023]
Abstract
The development of age-related cataract (ARC) is associated with DNA damage of the lens epithelial cells (LECs). This study aimed to investigate the expression level of DNA repair genes in LECs of ARC and examine whether any altered expression observed could result from DNA methylation of the promoter region of the genes. The expression levels of DNA repair genes were evaluated by microarray analysis. The results were further confirmed by qRT-PCR. DNA methylation of genes with altered expression was determined by bisulfite-specific (BSP) PCR. The mRNA levels of 10 DNA repair genes were decreased and the level of 1 DNA repair gene was increased in LECs of ARC patients compared with controls. The promoter region of the MGMT gene was hypermethylated in ARC tissue compared to controls. The data provide evidence that altered expression of DNA repair genes is associated with pathogenesis of ARC. DNA methylation of MGMT may regulate the expression of the gene and be involved in the development of ARC.
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Affiliation(s)
- Fei Li
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Yong Wang
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Guowei Zhang
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Jing Zhou
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Ling Yang
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Huaijin Guan
- Eye Institute, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China.
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21
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Han G, Tian Y, Duan B, Sheng H, Gao H, Huang J. Association of nuclear annexin A1 with prognosis of patients with esophageal squamous cell carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:751-759. [PMID: 24551299 PMCID: PMC3925923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 12/31/2013] [Indexed: 06/03/2023]
Abstract
Although recent progress has been made in the diagnosis and treatment of cancer, the prognosis of esophageal squamous cell carcinoma (ESCC) remains poor. The identification of biomarkers for ESCC prognosis is important for treatment decisions. The aim of this study was to evaluate the relationship between the expressions of Annexin A1 (ANXA1), three prime repair exonuclease 1 (TREX1) and apurinic/apyrimidinic endonuclease-1 (APE1) and clinical outcome of patients with ESCC. The expressions of ANXA1, TREX1 and APE1 in 93 pairs of ESCC and paracancerous tissues were tested using immunohistochemistry. ANX1, TREX1 and APE1 were dysregulated in ESCC. Nuclear expressions of ANXA1 and APE1 were significantly associated with pathologic type (P = 0.004 and 0.040, respectively). Patients with low expression of nuclear ANXA1 had a better prognosis than those with high expression of nuclear ANXA1 (HR = 0. 448, 95% CI 0.236-0.849, P = 0.014), especially for those with histologic grade 1 and 2 (HR = 0.303, 95% CI: 0.155-0.593, P < 0.001). In conclusion, nuclear ANXA1 may be potentially used as a prognostic biomarker for ESCC.
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Affiliation(s)
- Gaohua Han
- Department of Oncology, The Affiliated Second Hospital of Suzhou UniversitySuzhou, Jiangsu, China
- Department of Oncology, Taizhou People’s HospitalTaizhou, Jiangsu, China
| | - Ye Tian
- Department of Oncology, The Affiliated Second Hospital of Suzhou UniversitySuzhou, Jiangsu, China
| | - Bensong Duan
- Institute of Digestive Disease, Department of Gastroenterology, Tongji Hospital, Tongji UniversityShanghai, China
- National Engineering Center for Biochip at ShanghaiShanghai, China
| | - Haihui Sheng
- National Engineering Center for Biochip at ShanghaiShanghai, China
| | - Hengjun Gao
- Institute of Digestive Disease, Department of Gastroenterology, Tongji Hospital, Tongji UniversityShanghai, China
- National Engineering Center for Biochip at ShanghaiShanghai, China
| | - Junxing Huang
- Department of Oncology, Taizhou People’s HospitalTaizhou, Jiangsu, China
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22
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Christmann M, Kaina B. Transcriptional regulation of human DNA repair genes following genotoxic stress: trigger mechanisms, inducible responses and genotoxic adaptation. Nucleic Acids Res 2013; 41:8403-20. [PMID: 23892398 PMCID: PMC3794595 DOI: 10.1093/nar/gkt635] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
DNA repair is the first barrier in the defense against genotoxic stress. In recent years, mechanisms that recognize DNA damage and activate DNA repair functions through transcriptional upregulation and post-translational modification were the focus of intensive research. Most DNA repair pathways are complex, involving many proteins working in discrete consecutive steps. Therefore, their balanced expression is important for avoiding erroneous repair that might result from excessive base removal and DNA cleavage. Amelioration of DNA repair requires both a fine-tuned system of lesion recognition and transcription factors that regulate repair genes in a balanced way. Transcriptional upregulation of DNA repair genes by genotoxic stress is counteracted by DNA damage that blocks transcription. Therefore, induction of DNA repair resulting in an adaptive response is only visible through a narrow window of dose. Here, we review transcriptional regulation of DNA repair genes in normal and cancer cells and describe mechanisms of promoter activation following genotoxic exposures through environmental carcinogens and anticancer drugs. The data available to date indicate that 25 DNA repair genes are subject to regulation following genotoxic stress in rodent and human cells, but for only a few of them, the data are solid as to the mechanism, homeostatic regulation and involvement in an adaptive response to genotoxic stress.
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Affiliation(s)
- Markus Christmann
- Department of Toxicology, University Medical Center, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany
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23
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Tomicic MT, Aasland D, Nikolova T, Kaina B, Christmann M. Human three prime exonuclease TREX1 is induced by genotoxic stress and involved in protection of glioma and melanoma cells to anticancer drugs. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:1832-43. [PMID: 23578789 DOI: 10.1016/j.bbamcr.2013.03.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 03/15/2013] [Accepted: 03/29/2013] [Indexed: 11/25/2022]
Abstract
To counteract genotoxic stress, DNA repair functions are in effect. Most of them are constitutively expressed while some of them can be up-regulated depending on the level of DNA damage. In human cells, only few DNA repair functions are subject of induction following DNA damage, and thus there is a need to identify and characterize inducible repair functions more thoroughly. Here, we provide evidence that the "three prime exonuclease I" (TREX1) is up-regulated in human fibroblasts and cancer cells on mRNA and protein level. Transcriptional upregulation of TREX1 was observed upon exposure to ultraviolet light and various anticancer drugs in glioma and malignant melanoma cells. Induction of TREX1 was found following treatment with the crosslinking alkylating agents nimustine, carmustine, fotemustine and the topoisomerase I inhibitor topotecan, but not following temozolomide, etoposide and ionizing radiation. Induction of TREX1 following DNA damage requires the AP-1 components c-Jun and c-Fos, as shown by siRNA knockdown, EMSA experiments, ChIP analysis and reporter assays with the TREX1 promoter and constructs harboring mutations in the AP-1 binding site. To analyze whether TREX1 expression impacts the sensitivity of cancer cells to therapeutics, TREX1 expression was down-regulated by siRNA in malignant glioma and melanoma cells. TREX1 knockdown resulted in enhanced cell death following nimustine, fotemustine and topotecan and to a reduced recovery from the anticancer drug induced block to replication. The data revealed that induction of TREX1 is a survival response evoked by various genotoxic anticancer drugs and identified TREX1 as a potential therapeutic target for anticancer therapy.
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Affiliation(s)
- Maja T Tomicic
- Department of Toxicology, University Medical Center, Mainz, Germany
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Dong X, Li Y, Chang P, Hess KR, Abbruzzese JL, Li D. DNA mismatch repair network gene polymorphism as a susceptibility factor for pancreatic cancer. Mol Carcinog 2011; 51:491-9. [PMID: 21681824 DOI: 10.1002/mc.20817] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 05/18/2011] [Accepted: 05/21/2011] [Indexed: 12/20/2022]
Abstract
DNA repair plays a critical role in human cancers. We hypothesized that DNA mismatch repair gene variants are associated with risk of pancreatic cancer. We retrospectively genotyped 102 single-nucleotide polymorphisms (SNPs) of 13 mismatch repair related genes in 706 patients with pancreatic cancer and 706 cancer-free controls using the mass spectroscopy-based MassArray method. Association of genotype with pancreatic cancer risk was tested by multivariate logistic regression models. A significance level of P ≤ 0.0015 was set at the false discovery rate (FDR) <1% using the Beta-Uniform Mixture method. We found 28 SNPs related to altered pancreatic cancer risk (P < 0.05). Adjusting for multiple comparisons, MGMT I143V AG/GG, PMS2 IVS1-1121C > T TC/TT, and PMS2L3 Ex1 + 118C > T CT/TT genotypes showed significant main effects on pancreatic cancer risk at FDR <1% with OR (95% CI) of 0.60 (0.46-0.80), 1.44 (1.14-1.81), and 5.54 (2.10-14.61), respectively (P ≤ 0.0015). To demonstrate genotype-phenotype association, we measured O(6)-ethylguanosine (O(6)-EtGua) adduct levels in vitro by immunoslot blot assay in lymphocytes treated with N-ethyl-N-nitrosourea (ENU) in 297 case/control subjects. MGMT I143V GG, MGMT K178R GG, MSH6 G39E AG/AA, PMS2L3 IVS3 + 9A > G GA and TP73 IVS1-7449G > C CG/CC genotypes correlated with a higher level of ENU-induced DNA adducts. Haplotypes of MGMT, MSH6, PMS2, PMS2L3, and TP73 were significantly associated with pancreatic cancer risk (P ≤ 0.0015). Our findings suggest that mismatch repair gene variants may affect susceptibility to pancreatic cancer.
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Affiliation(s)
- Xiaoqun Dong
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030-4009, USA
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Leung CH, Chan DSH, Man BYW, Wang CJ, Lam W, Cheng YC, Fong WF, Hsiao WWL, Ma DL. Simple and convenient G-quadruplex-based turn-on fluorescence assay for 3' → 5' exonuclease activity. Anal Chem 2011; 83:463-6. [PMID: 21114271 PMCID: PMC3021625 DOI: 10.1021/ac1025896] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A selective, oligonucleotide-based, label-free, turn-on fluorescence detection method for 3' → 5' exonuclease activity has been developed using crystal violet as a G-quadruplex-binding probe. The assay is highly simple and rapid, does not require the use of gel-based equipment or radioisotopic labeling, and is amenable to high-throughput and real-time detection. A proof-of-concept of this assay has been demonstrated for prokaryotic Exonuclease III (ExoIII) and human TREX1.
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Affiliation(s)
- Chung-Hang Leung
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Daniel Shiu-Hin Chan
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Bradley Yat-Wah Man
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Chuan-Jen Wang
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, U.S.A
| | - Wing Lam
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, U.S.A
| | - Yung-Chi Cheng
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, U.S.A
| | - Wang-Fun Fong
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Wendy Wen-Luan Hsiao
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, U.S.A
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
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Yamamoto Y, Craggs L, Baumann M, Kalimo H, Kalaria RN. Review: Molecular genetics and pathology of hereditary small vessel diseases of the brain. Neuropathol Appl Neurobiol 2011; 37:94-113. [DOI: 10.1111/j.1365-2990.2010.01147.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Christmann M, Tomicic MT, Aasland D, Berdelle N, Kaina B. Three prime exonuclease I (TREX1) is Fos/AP-1 regulated by genotoxic stress and protects against ultraviolet light and benzo(a)pyrene-induced DNA damage. Nucleic Acids Res 2010; 38:6418-32. [PMID: 20511593 PMCID: PMC2965218 DOI: 10.1093/nar/gkq455] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Cells respond to genotoxic stress with the induction of DNA damage defence functions. Aimed at identifying novel players in this response, we analysed the genotoxic stress-induced expression of DNA repair genes in mouse fibroblasts proficient and deficient for c-Fos or c-Jun. The experiments revealed a clear up-regulation of the three prime exonuclease I (trex1) mRNA following ultraviolet (UV) light treatment. This occurred in the wild-type but not c-fos and c-jun null cells, indicating the involvement of AP-1 in trex1 induction. Trex1 up-regulation was also observed in human cells and was found on promoter, RNA and protein level. Apart from UV light, TREX1 is induced by other DNA damaging agents such as benzo(a)pyrene and hydrogen peroxide. The mouse and human trex1 promoter harbours an AP-1 binding site that is recognized by c-Fos and c-Jun, and its mutational inactivation abrogated trex1 induction. Upon genotoxic stress, TREX1 is not only up-regulated but also translocated into the nucleus. Cells deficient in TREX1 show reduced recovery from the UV and benzo(a)pyrene-induced replication inhibition and increased sensitivity towards the genotoxins compared to the isogenic control. The data revealed trex1 as a novel DNA damage-inducible repair gene that plays a protective role in the genotoxic stress response.
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Affiliation(s)
- Markus Christmann
- Department of Toxicology, University Medical Center, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany.
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Defective resection at DNA double-strand breaks leads to de novo telomere formation and enhances gene targeting. PLoS Genet 2010; 6:e1000948. [PMID: 20485519 PMCID: PMC2869328 DOI: 10.1371/journal.pgen.1000948] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 04/12/2010] [Indexed: 11/19/2022] Open
Abstract
The formation of single-stranded DNA (ssDNA) at double-strand break (DSB) ends is essential in repair by homologous recombination and is mediated by DNA helicases and nucleases. Here we estimated the length of ssDNA generated during DSB repair and analyzed the consequences of elimination of processive resection pathways mediated by Sgs1 helicase and Exo1 nuclease on DSB repair fidelity. In wild-type cells during allelic gene conversion, an average of 2–4 kb of ssDNA accumulates at each side of the break. Longer ssDNA is formed during ectopic recombination or break-induced replication (BIR), reflecting much slower repair kinetics. This relatively extensive resection may help determine sequences involved in homology search and prevent recombination within short DNA repeats next to the break. In sgs1Δ exo1Δ mutants that form only very short ssDNA, allelic gene conversion decreases 5-fold and DSBs are repaired by BIR or de novo telomere formation resulting in loss of heterozygosity. The absence of the telomerase inhibitor, PIF1, increases de novo telomere pathway usage to about 50%. Accumulation of Cdc13, a protein recruiting telomerase, at the break site increases in sgs1Δ exo1Δ, and the requirement of the Ku complex for new telomere formation is partially bypassed. In contrast to this decreased and alternative DSB repair, the efficiency and accuracy of gene targeting increases dramatically in sgs1Δ exo1Δ cells, suggesting that transformed DNA is very stable in these mutants. Altogether these data establish a new role for processive resection in the fidelity of DSB repair. Chromosomal breaks occur spontaneously or are induced by ionizing radiation and many chemotherapeutic drugs. DNA double-strand breaks are processed by nucleases and helicases in yeast and human to generate single-stranded DNA that is then used for repair by recombination with homologous chromosome. Single-stranded DNA at chromosomal breaks also constitutes a signal for cells to arrest cell cycle progression until the DNA damage is repaired. This study examines the consequences of elimination of enzymes that process chromosomal breaks to single-stranded DNA on the fidelity of repair and genome stability in the model organism yeast. Mutants deficient in these enzymes often fail to repair the breaks by homologous recombination and instead add new telomeres at the breaks. Formation of new telomeres is associated with partial loss of the chromosome arm distal from the break. Such chromosomal aberrations were frequently observed in tumor cells and are responsible for about 10% of human genomic disorders resulting from chromosomal abnormalities. We also observed that elimination of enzymes that process chromosomal breaks into single-stranded DNA greatly stimulates genome manipulation by gene targeting, suggesting that transformed DNA is also a substrate for degradation by these enzymes. We discuss the possibility of using a similar approach in mammalian cells where gene targeting is inaccurate and less efficient when compared to yeast.
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