1
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Kwak SB, Kim SJ, Kang YJ, Lee WW, Huh J, Park JW. Development of a rectally administrable Dnase1 to treat septic shock by targeting NETs. Life Sci 2024; 342:122526. [PMID: 38417543 DOI: 10.1016/j.lfs.2024.122526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/11/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
AIMS Neutrophil extracellular trap (NET), which is formed by DNA threads, induces septic shock by aggravating systemic inflammation. An intravenous administration of deoxyribonuclease is regarded as a compelling modality for treating septic shock. However, alternative routes should be chosen when cutaneous veins are all collapsed due to hypotension. In this study, we genetically engineered this enzyme to develop a rectal suppository formulation to treat septic shock. MAIN METHODS Dnase1 was mutated at two amino acid residues to increase its stability in the blood and fused with a cell-penetrating peptide CR8 to increase its absorption through the rectal mucosa, which is designated AR-CR8. The life-saving effect of AR-CR8 was evaluated in a LPS-induced shock mouse model. KEY FINDINGS AR-CR8 was shown to remove NETs effectively in human neutrophils. When AR-CR8 was administered to the mouse rectum, the deoxyribonuclease activity in the mouse serum was significantly increased. In the LPS-induced shock model, 90 % of the control mice died over 72 h after LPS injection. In contrast, the rectal administration of AR-CR8 showed a mortality rate of 30 % by 72 h after LPS injection. The Log-rank test revealed that the survival rate is significantly higher in the AR-CR8 group. The NET markers in the mouse serum were enhanced by LPS, and significantly downregulated in the AR-CR8 group. These results suggest that AR-CR8 ameliorates LPS-induced shock by degrading NETs. SIGNIFICANCE The engineered DNASE1 could be developed as a rectal suppository formulation to treat septic shock urgently at out-of-hospital places where no syringe is available.
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Affiliation(s)
- Su-Bin Kwak
- Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea
| | - Sang-Jin Kim
- Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea
| | - Yeon Jun Kang
- Laboratory of Autoimmunity and Inflammation, Department of Biomedical Sciences, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea; Department of Microbiology and Immunology, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea
| | - Won-Woo Lee
- Laboratory of Autoimmunity and Inflammation, Department of Biomedical Sciences, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea; Department of Microbiology and Immunology, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea
| | - June Huh
- Department of Chemical and Biological Engineering, Korea University, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jong-Wan Park
- Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea; Department of Biomedical Science, BK21-plus education program, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Daehak-ro 103, Jongno-gu, Seoul 03080, Republic of Korea.
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2
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Kaur R, McGarry A, Shropshire JD, Leigh BA, Bordenstein SR. Prophage proteins alter long noncoding RNA and DNA of developing sperm to induce a paternal-effect lethality. Science 2024; 383:1111-1117. [PMID: 38452081 DOI: 10.1126/science.adk9469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
The extent to which prophage proteins interact with eukaryotic macromolecules is largely unknown. In this work, we show that cytoplasmic incompatibility factor A (CifA) and B (CifB) proteins, encoded by prophage WO of the endosymbiont Wolbachia, alter long noncoding RNA (lncRNA) and DNA during Drosophila sperm development to establish a paternal-effect embryonic lethality known as cytoplasmic incompatibility (CI). CifA is a ribonuclease (RNase) that depletes a spermatocyte lncRNA important for the histone-to-protamine transition of spermiogenesis. Both CifA and CifB are deoxyribonucleases (DNases) that elevate DNA damage in late spermiogenesis. lncRNA knockdown enhances CI, and mutagenesis links lncRNA depletion and subsequent sperm chromatin integrity changes to embryonic DNA damage and CI. Hence, prophage proteins interact with eukaryotic macromolecules during gametogenesis to create a symbiosis that is fundamental to insect evolution and vector control.
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Affiliation(s)
- Rupinder Kaur
- Pennsylvania State University, Departments of Biology and Entomology, University Park, PA 16802, USA
- One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
| | - Angelina McGarry
- Pennsylvania State University, Departments of Biology and Entomology, University Park, PA 16802, USA
- One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - J Dylan Shropshire
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Brittany A Leigh
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
| | - Seth R Bordenstein
- Pennsylvania State University, Departments of Biology and Entomology, University Park, PA 16802, USA
- One Health Microbiome Center, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, USA
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3
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Garcia G, Labrouche-Colomer S, Duvignaud A, Clequin E, Dussiau C, Trégouët DA, Malvy D, Prevel R, Zouine A, Pellegrin I, Goret J, Mamani-Matsuda M, Dewitte A, James C. Impaired balance between neutrophil extracellular trap formation and degradation by DNases in COVID-19 disease. J Transl Med 2024; 22:246. [PMID: 38454482 PMCID: PMC10919029 DOI: 10.1186/s12967-024-05044-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Thrombo-inflammation and neutrophil extracellular traps (NETs) are exacerbated in severe cases of COVID-19, potentially contributing to disease exacerbation. However, the mechanisms underpinning this dysregulation remain elusive. We hypothesised that lower DNase activity may be associated with higher NETosis and clinical worsening in patients with COVID-19. METHODS Biological samples were obtained from hospitalized patients (15 severe, 37 critical at sampling) and 93 non-severe ambulatory cases. Our aims were to compare NET biomarkers, functional DNase levels, and explore mechanisms driving any imbalance concerning disease severity. RESULTS Functional DNase levels were diminished in the most severe patients, paralleling an imbalance between NET markers and DNase activity. DNase1 antigen levels were higher in ambulatory cases but lower in severe patients. DNase1L3 antigen levels remained consistent across subgroups, not rising alongside NET markers. DNASE1 polymorphisms correlated with reduced DNase1 antigen levels. Moreover, a quantitative deficiency in plasmacytoid dendritic cells (pDCs), which primarily express DNase1L3, was observed in critical patients. Analysis of public single-cell RNAseq data revealed reduced DNase1L3 expression in pDCs from severe COVID-19 patient. CONCLUSION Severe and critical COVID-19 cases exhibited an imbalance between NET and DNase functional activity and quantity. Early identification of NETosis imbalance could guide targeted therapies against thrombo-inflammation in COVID-19-related sepsis, such as DNase administration, to avert clinical deterioration. TRIAL REGISTRATION COVERAGE trial (NCT04356495) and COLCOV19-BX study (NCT04332016).
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Affiliation(s)
- Geoffrey Garcia
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France
| | - Sylvie Labrouche-Colomer
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France
- Laboratory of Hematology, Bordeaux University Hospital, 33600, Pessac, France
| | - Alexandre Duvignaud
- Department of Infectious Diseases and Tropical Medicine, Hôpital Pellegrin, CHU Bordeaux, 33076, Bordeaux, France
- University Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, 33000, Bordeaux, France
| | - Etienne Clequin
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Department of Anaesthesia and Intensive Care, Bordeaux University Hospital, 33600, Pessac, France
| | - Charles Dussiau
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France
- Laboratory of Hematology, Bordeaux University Hospital, 33600, Pessac, France
| | - David-Alexandre Trégouët
- University Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, 33000, Bordeaux, France
| | - Denis Malvy
- Department of Infectious Diseases and Tropical Medicine, Hôpital Pellegrin, CHU Bordeaux, 33076, Bordeaux, France
- University Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, 33000, Bordeaux, France
| | - Renaud Prevel
- Medical Intensive Care Unit, Bordeaux University Hospital, 33000, Bordeaux, France
- Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM, UMR 1045, Bordeaux University, 33000, Bordeaux, France
| | - Atika Zouine
- CNRS, INSERM, TBM-Core, US5, UAR 3427, Flow Cytometry Facility, Bordeaux University, 33000, Bordeaux, France
| | - Isabelle Pellegrin
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Centre de Ressources Biologiques, Bordeaux University Hospital, 33000, Bordeaux, France
| | - Julien Goret
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Department of Immunology and Immunogenetics, Bordeaux University Hospital, Bordeaux, France
| | - Maria Mamani-Matsuda
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
| | - Antoine Dewitte
- CNRS, ImmunoConcEpT, UMR 5164, Inserm ERL1303, Bordeaux University, 33000, Bordeaux, France
- Department of Anaesthesia and Intensive Care, Bordeaux University Hospital, 33600, Pessac, France
| | - Chloe James
- Biology of Cardiovascular Disease, INSERM, UMR 1034, Bordeaux University, CHU Haut-Lévêque, 1 Avenue Magellan, 33600, Pessac, France.
- Laboratory of Hematology, Bordeaux University Hospital, 33600, Pessac, France.
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Yu L, Huang J. Deoxyribonuclease 1-like 3 inhibits colorectal malignancy through antagonizing NEDD4-triggered CDKN1A ubiquitination. Cell Biol Int 2024; 48:325-333. [PMID: 38108119 DOI: 10.1002/cbin.12108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 10/06/2023] [Accepted: 11/28/2023] [Indexed: 12/19/2023]
Abstract
Deoxyribonuclease 1-like 3 (DNASE1L3) has been shown to play nonnegligible roles in several types of carcinomas. Nevertheless, the biological function, clinical relevance, and influence of DNASE1L3 in colorectal cancer (CRC) remain obscure. Immunohistochemistry was adopted to examine DNASE1L3 and CDKN1A expression in CRC tissue, and the clinical significance of DNASE1L3 was assessed. Cell counting kit-8, colony formation, and transwell assays were employed for assessing tumor proliferation and migration. The mechanisms underlying the impact of DNASE1L3 were explored via western blot analysis, co-immunoprecipitation, and ubiquitination assay. It was observed that DNASE1L3 was downregulated in CRC tissues and was tightly associated with patient prognosis. DNASE1L3 impaired CRC cell proliferation and migration through elevating CDKN1A via suppressing CDKN1A ubiquitination. Meanwhile, DNASE1L3 was positively related to CDKN1A. In mechanism, DNASE1L3 and CDKN1A interacted with the E3 ubiquitin ligase NEDD4. Moreover, DNASE1L3 was competitively bound to NEDD4, thus repressing NEDD4-mediated CDKN1A ubiquitination and degradation. These discoveries implied the potential mechanisms of DNASE1L3 during tumorigenesis, suggesting that DNASE1L3 may serve as a new potential therapeutic agent for CRC.
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Affiliation(s)
- Lifei Yu
- Department of Gastroenterology, Changzhou No. 2 People's Hospital, The Affiliated Hospital of Nanjing Medical University, Changzhou, China
| | - Jin Huang
- Department of Gastroenterology, Changzhou No. 2 People's Hospital, The Affiliated Hospital of Nanjing Medical University, Changzhou, China
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5
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Schneider AH, Taira TM, Públio GA, da Silva Prado D, Donate Yabuta PB, Dos Santos JC, Machado CC, de Souza FFL, Rodrigues Venturini LG, de Oliveira RDR, Cunha TM, Alves-Filho JC, Louzada-Júnior P, Aparecida da Silva T, Fukada SY, Cunha FQ. Neutrophil extracellular traps mediate bone erosion in rheumatoid arthritis by enhancing RANKL-induced osteoclastogenesis. Br J Pharmacol 2024; 181:429-446. [PMID: 37625900 DOI: 10.1111/bph.16227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/17/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND AND PURPOSE Rheumatoid arthritis (RA) is a chronic autoimmune disease that can cause bone erosion due to increased osteoclastogenesis. Neutrophils involvement in osteoclastogenesis remains uncertain. Given that neutrophil extracellular traps (NETs) can act as inflammatory mediators in rheumatoid arthritis, we investigated the role of NETs in stimulating bone loss by potentiating osteoclastogenesis during arthritis. EXPERIMENTAL APPROACH The level of NETs in synovial fluid from arthritis patients was assessed. Bone loss was evaluated by histology and micro-CT in antigen-induced arthritis (AIA)-induced WT mice treated with DNase or in Padi4-deficient mice (Padi4flox/flox LysMCRE ). The size and function of osteoclasts and the levels of RANKL and osteoprotegerin (OPG) released by osteoblasts that were incubated with NETs were measured. The expression of osteoclastogenic marker genes and protein levels were evaluated by qPCR and western blotting. To assess the participation of TLR4 and TLR9 in osteoclastogenesis, cells from Tlr4-/- and Tlr9-/- mice were cultured with NETs. KEY RESULTS Rheumatoid arthritis patients had higher levels of NETs in synovial fluid than osteoarthritis patients, which correlated with increased levels of RANKL/OPG. Moreover, patients with bone erosion had higher levels of NETs. Inhibiting NETs with DNase or Padi4 deletion alleviated bone loss in arthritic mice. Consistently, NETs enhanced RANKL-induced osteoclastogenesis that was dependent on TLR4 and TLR9 and increased osteoclast resorptive functions in vitro. In addition, NETs stimulated the release of RANKL and inhibited osteoprotegerin in osteoblasts, favouring osteoclastogenesis. CONCLUSIONS AND IMPLICATIONS Inhibiting NETs could be an alternative strategy to reduce bone erosion in arthritis patients.
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Affiliation(s)
- Ayda Henriques Schneider
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Thaise Mayumi Taira
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Bio-Molecular Sciences, School of Pharmaceutical Science, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Gabriel Azevedo Públio
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Douglas da Silva Prado
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Paula Barbim Donate Yabuta
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Jéssica Cristina Dos Santos
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Neurosciences, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Caio Cavalcante Machado
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Medicine, Clinical Immunology Division, Medicine Faculty of Ribeirao Preto, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Flávio Falcão Lima de Souza
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Medicine, Clinical Immunology Division, Medicine Faculty of Ribeirao Preto, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Lucas Gabriel Rodrigues Venturini
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Bio-Molecular Sciences, School of Pharmaceutical Science, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Renê Donizeti Ribeiro de Oliveira
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Medicine, Clinical Immunology Division, Medicine Faculty of Ribeirao Preto, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Thiago Mattar Cunha
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
| | - José Carlos Alves-Filho
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Paulo Louzada-Júnior
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Medicine, Clinical Immunology Division, Medicine Faculty of Ribeirao Preto, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Tarcília Aparecida da Silva
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Oral Surgery and Pathology, Faculty of Dentistry, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sandra Yasuyo Fukada
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Bio-Molecular Sciences, School of Pharmaceutical Science, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Fernando Queiróz Cunha
- Center of Research in Inflammatory Diseases, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
- Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, Brazil
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6
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Guo G, Liu Z, Yu J, You Y, Li M, Wang B, Tang J, Han P, Wu J, Shen H. Neutrophil Function Conversion Driven by Immune Switchpoint Regulator against Diabetes-Related Biofilm Infections. Adv Mater 2024; 36:e2310320. [PMID: 38035713 DOI: 10.1002/adma.202310320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Reinforced biofilm structures and dysfunctional neutrophils induced by excessive oxidative stress contribute to the refractoriness of diabetes-related biofilm infections (DRBIs). Herein, in contrast to traditional antibacterial therapies, an immune switchpoint-driven neutrophil immune function conversion strategy based on a deoxyribonuclease I loaded vanadium carbide MXene (DNase-I@V2 C) nanoregulator is proposed to treat DRBIs via biofilm lysis and redirecting neutrophil functions from NETosis to phagocytosis in diabetes. Owing to its intrinsic superoxide dismutase/catalase-like activities, DNase-I@V2 C effectively scavenges reactive oxygen species (ROS) in a high oxidative stress microenvironment to maintain the biological activity of DNase-I. By increasing the depth of biofilm penetration of DNase-I, DNase-I@V2 C thoroughly degrades extracellular DNA and neutrophil extracellular traps (NETs) in extracellular polymeric substances, thus breaking the physical barrier of biofilms. More importantly, as an immune switchpoint regulator, DNase-I@V2 C can skew neutrophil functions from NETosis toward phagocytosis by intercepting ROS-NE/MPO-PAD4 and activating ROS-PI3K-AKT-mTOR pathways in diabetic microenvironment, thereby eliminating biofilm infections. Biofilm lysis and synergistic neutrophil function conversion exert favorable therapeutic effects on biofilm infections in vitro and in vivo. This study serves as a proof-of-principle demonstration of effectively achieving DRBIs with high therapeutic efficacy by regulating immune switchpoint to reverse neutrophil functions.
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Affiliation(s)
- Geyong Guo
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Zihao Liu
- Department of Ultrasound in Medicine, Shanghai Institute of Ultrasound in Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Jinlong Yu
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Yanan You
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, 200090, P. R. China
| | - Mingzhang Li
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Boyong Wang
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Jin Tang
- Department of Clinical Laboratory, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Pei Han
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Jianrong Wu
- Department of Ultrasound in Medicine, Shanghai Institute of Ultrasound in Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
| | - Hao Shen
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200233, P. R. China
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7
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Antine SP, Johnson AG, Mooney SE, Leavitt A, Mayer ML, Yirmiya E, Amitai G, Sorek R, Kranzusch PJ. Structural basis of Gabija anti-phage defence and viral immune evasion. Nature 2024; 625:360-365. [PMID: 37992757 PMCID: PMC10781630 DOI: 10.1038/s41586-023-06855-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation1-5. Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes1,6,7, but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.
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Affiliation(s)
- Sadie P Antine
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alex G Johnson
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah E Mooney
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Azita Leavitt
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Megan L Mayer
- Harvard Center for Cryo-Electron Microscopy, Harvard Medical School, Boston, MA, USA
| | - Erez Yirmiya
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, USA.
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8
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Yu L, Marchisio MA. dCas12a:Pre-crRNA: A New Tool to Induce mRNA Degradation in Saccharomyces cerevisiae Synthetic Gene Circuits. Methods Mol Biol 2024; 2760:95-114. [PMID: 38468084 DOI: 10.1007/978-1-0716-3658-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
We describe a new way to trigger mRNA degradation in Saccharomyces cerevisiae synthetic gene circuits. Our method demands to modify either the 5'- or the 3'-UTR that flanks a target gene with elements from the pre-crRNA of type V Cas12a proteins and expresses a DNase-deficient Cas12a (dCas12a). dCas12a recognizes and cleaves the pre-crRNA motifs on mRNA sequences. Our tool does not require complex engineering operations and permits an efficient control of protein expression via mRNA degradation.
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Affiliation(s)
- Lifang Yu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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9
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Jiang K, Lim J, Sgrizzi S, Trinh M, Kayabolen A, Yutin N, Bao W, Kato K, Koonin EV, Gootenberg JS, Abudayyeh OO. Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses. Sci Adv 2023; 9:eadk0171. [PMID: 37756409 PMCID: PMC10530073 DOI: 10.1126/sciadv.adk0171] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023]
Abstract
Programmable RNA-guided DNA nucleases perform numerous roles in prokaryotes, but the extent of their spread outside prokaryotes is unclear. Fanzors, the eukaryotic homolog of prokaryotic TnpB proteins, have been detected in genomes of eukaryotes and large viruses, but their activity and functions in eukaryotes remain unknown. Here, we characterize Fanzors as RNA-programmable DNA endonucleases, using biochemical and cellular evidence. We found diverse Fanzors that frequently associate with various eukaryotic transposases. Reconstruction of Fanzors evolution revealed multiple radiations of RuvC-containing TnpB homologs in eukaryotes. Fanzor genes captured introns and proteins acquired nuclear localization signals, indicating extensive, long-term adaptation to functioning in eukaryotic cells. Fanzor nucleases contain a rearranged catalytic site of the RuvC domain, similar to a distinct subset of TnpBs, and lack collateral cleavage activity. We demonstrate that Fanzors can be harnessed for genome editing in human cells, highlighting the potential of these widespread eukaryotic RNA-guided nucleases for biotechnology applications.
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Affiliation(s)
- Kaiyi Jiang
- McGovern Institute for Brain Research at MIT Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Justin Lim
- McGovern Institute for Brain Research at MIT Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samantha Sgrizzi
- McGovern Institute for Brain Research at MIT Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael Trinh
- McGovern Institute for Brain Research at MIT Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alisan Kayabolen
- McGovern Institute for Brain Research at MIT Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Weidong Bao
- Genetic Information Research Institute, 20380 Town Center Ln, Suite 240, Cupertino, CA, USA
| | - Kazuki Kato
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
- Department of Molecular and Mechanistic Immunology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Jonathan S. Gootenberg
- McGovern Institute for Brain Research at MIT Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Omar O. Abudayyeh
- McGovern Institute for Brain Research at MIT Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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10
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Huang W, Wen L, Tian H, Jiang J, Liu M, Ye Y, Gao J, Zhang R, Wang F, Li H, Shen L, Peng F, Tu Y. Self-Propelled Proteomotors with Active Cell-Free mtDNA Clearance for Enhanced Therapy of Sepsis-Associated Acute Lung Injury. Adv Sci (Weinh) 2023; 10:e2301635. [PMID: 37518854 PMCID: PMC10520684 DOI: 10.1002/advs.202301635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/10/2023] [Indexed: 08/01/2023]
Abstract
Acute lung injury (ALI) is a frequent and serious complication of sepsis with limited therapeutic options. Gaining insights into the inflammatory dysregulation that causes sepsis-associated ALI can help develop new therapeutic strategies. Herein, the crucial role of cell-free mitochondrial DNA (cf-mtDNA) in the regulation of alveolar macrophage activation during sepsis-associated ALI is identified. Most importantly, a biocompatible hybrid protein nanomotor (NM) composed of recombinant deoxyribonuclease I (DNase-I) and human serum albumin (HSA) via glutaraldehyde-mediated crosslinking is prepared to obtain an inhalable nanotherapeutic platform targeting pulmonary cf-mtDNA clearance. The synthesized DNase-I/HSA NMs are endowed with self-propulsive capability and demonstrate superior performances in stability, DNA hydrolysis, and biosafety. Pulmonary delivery of DNase-I/HSA NMs effectively eliminates cf-mtDNAs in the lungs, and also improves sepsis survival by attenuating pulmonary inflammation and lung injury. Therefore, pulmonary cf-mtDNA clearance strategy using DNase-I/HSA NMs is considered to be an attractive approach for sepsis-associated ALI.
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Affiliation(s)
- Weichang Huang
- Department of Critical Care MedicineDongguan Institute of Respiratory and Critical Care MedicineAffiliated Dongguan HospitalSouthern Medical UniversityDongguan523059China
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug ScreeningSchool of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Lihong Wen
- Department of Plastic SurgerySun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhou510120China
| | - Hao Tian
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug ScreeningSchool of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Jiamiao Jiang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug ScreeningSchool of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Meihuan Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug ScreeningSchool of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Yicheng Ye
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug ScreeningSchool of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Junbin Gao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug ScreeningSchool of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Ruotian Zhang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug ScreeningSchool of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Fei Wang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug ScreeningSchool of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Huaan Li
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug ScreeningSchool of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Lihan Shen
- Department of Critical Care MedicineDongguan Institute of Respiratory and Critical Care MedicineAffiliated Dongguan HospitalSouthern Medical UniversityDongguan523059China
| | - Fei Peng
- School of Materials Science and EngineeringSun Yat‐Sen UniversityGuangzhou510275China
| | - Yingfeng Tu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug ScreeningSchool of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou510515China
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11
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Talbot H, Madhanagopal BR, Hayden A, Halvorsen K, Chandrasekaran AR. Fluorometric Determination of DNA Nanostructure Biostability. ACS Appl Bio Mater 2023; 6:3074-3078. [PMID: 37262927 PMCID: PMC10999248 DOI: 10.1021/acsabm.3c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The analysis and improvement of DNA nanostructure biostability is one of the keys areas of progress needed in DNA nanotechnology applications. Here, we present a plate-compatible fluorometric assay for measuring DNA nanostructure biostability using the common intercalator ethidium bromide. We demonstrate the assay by testing the biostability of duplex DNA, a double crossover DNA motif, and a DNA origami nanostructure against different nucleases and in fetal bovine serum. This method scales well to measure a large number of samples using a plate reader and can complement existing methods for assessing and developing robust DNA nanostructures.
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Affiliation(s)
- Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
| | - Bharath Raj Madhanagopal
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
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12
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Lerner J, Katznelson A, Zhang J, Zaret KS. Different chromatin-scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2. Cell Rep 2023; 42:112748. [PMID: 37405916 PMCID: PMC10529229 DOI: 10.1016/j.celrep.2023.112748] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/20/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Pioneer transcription factors interact with nucleosomes to scan silent, compact chromatin, enabling cooperative events that modulate gene activity. While at a subset of sites pioneer factors access chromatin by assisted loading with other transcription factors, the nucleosome-binding properties of pioneer factors enable them to initiate zygotic genome activation, embryonic development, and cellular reprogramming. To better understand nucleosome targeting in vivo, we assess whether pioneer factors FoxA1 and Sox2 target stable or unstable nucleosomes and find that they target DNase-resistant, stable nucleosomes, whereas HNF4A, a non-nucleosome binding factor, targets open, DNase-sensitive chromatin. Despite FOXA1 and SOX2 targeting similar proportions of DNase-resistant chromatin, using single-molecule tracking, we find that FOXA1 uses lower nucleoplasmic diffusion and longer residence times while SOX2 uses higher nucleoplasmic diffusion and shorter residence times to scan compact chromatin, while HNF4 scans compact chromatin much less efficiently. Thus, pioneer factors target compact chromatin through distinct processes.
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Affiliation(s)
- Jonathan Lerner
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Andrew Katznelson
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Jingchao Zhang
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058, USA.
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13
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Lacey KA, Serpas L, Makita S, Wang Y, Rashidfarrokhi A, Soni C, Gonzalez S, Moreira A, Torres VJ, Reizis B. Secreted mammalian DNases protect against systemic bacterial infection by digesting biofilms. J Exp Med 2023; 220:e20221086. [PMID: 36928522 PMCID: PMC10037111 DOI: 10.1084/jem.20221086] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 01/18/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Extracellular DNase DNASE1L3 maintains tolerance to self-DNA in humans and mice, whereas the role of its homolog DNASE1 remains controversial, and the overall function of secreted DNases in immunity is unclear. We report that deletion of murine DNASE1 neither caused autoreactivity in isolation nor exacerbated lupus-like disease in DNASE1L3-deficient mice. However, combined deficiency of DNASE1 and DNASE1L3 rendered mice susceptible to bloodstream infection with Staphylococcus aureus. DNASE1/DNASE1L3 double-deficient mice mounted a normal innate response to S. aureus and did not accumulate neutrophil extracellular traps (NETs). However, their kidneys manifested severe pathology, increased bacterial burden, and biofilm-like bacterial lesions that contained bacterial DNA and excluded neutrophils. Furthermore, systemic administration of recombinant DNASE1 protein during S. aureus infection rescued the mortality of DNase-deficient mice and ameliorated the disease in wild-type mice. Thus, DNASE1 and DNASE1L3 jointly facilitate the control of bacterial infection by digesting extracellular microbial DNA in biofilms, suggesting the original evolutionary function of secreted DNases as antimicrobial agents.
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Affiliation(s)
- Keenan A. Lacey
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Lee Serpas
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Sohei Makita
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Yueyang Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Ali Rashidfarrokhi
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Sandra Gonzalez
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Andre Moreira
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
| | - Victor J. Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY, USA
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
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14
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Casco A, Johannsen E. EBV Reactivation from Latency Is a Degrading Experience for the Host. Viruses 2023; 15:726. [PMID: 36992435 PMCID: PMC10054251 DOI: 10.3390/v15030726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/15/2023] Open
Abstract
During reactivation from latency, gammaherpesviruses radically restructure their host cell to produce virion particles. To achieve this and thwart cellular defenses, they induce rapid degradation of cytoplasmic mRNAs, suppressing host gene expression. In this article, we review mechanisms of shutoff by Epstein-Barr virus (EBV) and other gammaherpesviruses. In EBV, canonical host shutoff is accomplished through the action of the versatile BGLF5 nuclease expressed during lytic reactivation. We explore how BGLF5 induces mRNA degradation, the mechanisms by which specificity is achieved, and the consequences for host gene expression. We also consider non-canonical mechanisms of EBV-induced host shutoff. Finally, we summarize the limitations and barriers to accurate measurements of the EBV host shutoff phenomenon.
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Affiliation(s)
- Alejandro Casco
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53705, USA
| | - Eric Johannsen
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53705, USA
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin, Madison, WI 53705, USA
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15
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Janovičová Ľ, Kmeťová K, Pribulová N, Janko J, Gromová B, Gardlík R, Celec P. Endogenous DNase Activity in an Animal Model of Acute Liver Failure. Int J Mol Sci 2023; 24:ijms24032984. [PMID: 36769306 PMCID: PMC9918174 DOI: 10.3390/ijms24032984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Deoxyribonucleases (DNases) cleave extracellular DNA (ecDNA) and are under intense research as interventions for diseases associated with high ecDNA, such as acute live injury. DNase I treatment decreases morbidity and mortality in this animal model. Endogenous DNase activity has high interindividual variability. In this study, we tested the hypothesis that high endogenous DNase activity is beneficial in an animal model of acute liver failure. DNase activity was measured in the plasma of adult male mice taken before i.p. injection of thioacetamide to induce acute liver failure. The survival of mice was monitored for 48 h. Mice were retrospectively divided into two groups based on the median DNase activity assessed using the gel-based single-radial enzyme diffusion assay. In acute liver failure, mice with a higher baseline DNase activity had lower mortality after 48 h (by 25%). Different protection of ecDNA against nucleases by vesicles or DNA-binding proteins could play a role and should be further evaluated. Similarly, the role of endogenous DNase activity should be analyzed in other disease models associated with high ecDNA.
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Affiliation(s)
- Ľubica Janovičová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
| | - Katarína Kmeťová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
| | - Nikola Pribulová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
| | - Jakub Janko
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
| | - Barbora Gromová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
| | - Roman Gardlík
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
- Institute of Pathophysiology, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
- Institute of Pathophysiology, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
- Correspondence: or
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16
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Oliveira CB, Byrd AS, Okoye GA, Kaplan MJ, Carmona-Rivera C. Neutralizing Anti‒DNase 1 and ‒DNase 1L3 Antibodies Impair Neutrophil Extracellular Traps Degradation in Hidradenitis Suppurativa. J Invest Dermatol 2023; 143:57-66. [PMID: 35934056 PMCID: PMC9771923 DOI: 10.1016/j.jid.2022.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/13/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022]
Abstract
Hidradenitis suppurativa (HS) is a debilitating inflammatory skin disorder characterized by abscess-like nodules and boils resulting in fistulas and tissue scarring. We previously reported evidence of an autoimmune signature in HS, characterized by enhanced neutrophil extracellular trap (NET) infiltration in HS skin lesions and dysregulation of the adaptive immune system characterized by the presence of autoantibodies. Timely removal of NETs is critical for tissue homeostasis to prevent a dysregulated generation of modified autoantigens and tissue damage. DNases 1 and 1L3 play important roles in proper NET removal. We tested the hypothesis that NETs in patients with HS are not effectively cleared owing to the presence of antibodies against DNase 1 and DNase 1L3. We report that HS serum poorly degraded NETs. Addition of exogenous DNase 1 restored NET degradation capabilities in a subset of HS samples. DNase 1 activity was significantly decreased in HS sera. Anti‒DNase 1 and ‒DNase 1L3 antibodies were detected in serum samples and skin lesions from patients with HS. Purified IgGs from HS decreased DNase 1 activity and NET degradation. Taken together, this identification of neutralizing antibodies against nucleases in HS expands the understanding of the pathogenesis of this disease to support an autoimmune mechanism in its underlying pathogenesis.
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Affiliation(s)
- Christopher B Oliveira
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Angel S Byrd
- Department of Dermatology, College of Medicine, Howard University, Washington, District of Columbia, USA; Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ginette A Okoye
- Department of Dermatology, College of Medicine, Howard University, Washington, District of Columbia, USA; Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Carmelo Carmona-Rivera
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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17
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Sun S, Xu D, Zhu L, Hu B, Huang Z. A Programmable, DNA-Exclusively-Guided Argonaute DNase and Its Higher Cleavage Specificity Achieved by 5′-Hydroxylated Guide. Biomolecules 2022; 12:biom12101340. [PMID: 36291549 PMCID: PMC9599953 DOI: 10.3390/biom12101340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/17/2022] [Accepted: 09/18/2022] [Indexed: 12/03/2022] Open
Abstract
Argonaute proteins exist widely in eukaryotes and prokaryotes, and they are of great potential for molecular cloning, nucleic acid detection, DNA assembly, and gene editing. However, their overall properties are not satisfactory and hinder their broad applications. Herein, we investigated a prokaryotic Argonaute nuclease from a mesophilic bacterium Clostridium disporicum (CdAgo) and explored its overall properties, especially with 5′-hydroxylated (5′-OH) guides. We found that CdAgo can exclusively use single-stranded DNA (ssDNA) as guide to cleave ssDNA and plasmid targets. Further, we found the length of the efficient guide is narrower for the 5′-OH guide (17–20 nt) than for the 5′-phosphorylated guide (5′-P, 14–21 nt). Furthermore, we discovered that the 5′-OH guides can generally offer stronger mismatch discrimination than the 5′-P ones. The 5′-OH guides offer the narrower length range, higher mismatch discrimination and more accurate cleavage than the 5′-P guides. Therefore, 5′-OH-guide-directed CdAgo has great potential in biological and biomedical applications.
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Affiliation(s)
- Shichao Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Dejin Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Lin Zhu
- Study on the Structure-Specific Small Molecule Drug in Sichuan Province College Key Laboratory, Department of Pharmacy, Chengdu Medical College, Chengdu 610500, China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
- Correspondence: (B.H.); (Z.H.)
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu 610041, China
- Correspondence: (B.H.); (Z.H.)
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18
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Komaniecka N, Porras M, Cairn L, Santas JA, Ferreiro N, Penedo JC, Bañuelos S. Conformational Rearrangements Regulating the DNA Repair Protein APE1. Int J Mol Sci 2022; 23:ijms23148015. [PMID: 35887361 PMCID: PMC9324194 DOI: 10.3390/ijms23148015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 02/06/2023] Open
Abstract
Apurinic apyrimidinic endonuclease 1 (APE1) is a key enzyme of the Base Excision Repair (BER) pathway, which primarily manages oxidative lesions of DNA. Once the damaged base is removed, APE1 recognises the resulting abasic site and cleaves the phosphodiester backbone to allow for the correction by subsequent enzymes of the BER machinery. In spite of a wealth of information on APE1 structure and activity, its regulation mechanism still remains to be understood. Human APE1 consists of a globular catalytic domain preceded by a flexible N-terminal extension, which might be involved in the interaction with DNA. Moreover, the binding of the nuclear chaperone nucleophosmin (NPM1) to this region has been reported to impact APE1 catalysis. To evaluate intra- and inter-molecular conformational rearrangements upon DNA binding, incision, and interaction with NPM1, we used Förster resonance energy transfer (FRET), a fluorescence spectroscopy technique sensitive to molecular distances. Our results suggest that the N-terminus approaches the DNA at the downstream side of the abasic site and enables the building of a predictive model of the full-length APE1/DNA complex. Furthermore, the spatial configuration of the N-terminal tail is sensitive to NPM1, which could be related to the regulation of APE1.
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Affiliation(s)
- Nina Komaniecka
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (N.K.); (M.P.); (L.C.); (J.A.S.); (N.F.)
| | - Marta Porras
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (N.K.); (M.P.); (L.C.); (J.A.S.); (N.F.)
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Louis Cairn
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (N.K.); (M.P.); (L.C.); (J.A.S.); (N.F.)
| | - Jon Ander Santas
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (N.K.); (M.P.); (L.C.); (J.A.S.); (N.F.)
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Nerea Ferreiro
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (N.K.); (M.P.); (L.C.); (J.A.S.); (N.F.)
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Juan Carlos Penedo
- Centre of Biophotonics, Laboratory for Biophysics and Biomolecular Dynamics, Scottish Universities Physics Alliance (SUPA) School of Physics and Astronomy, University of St. Andrews, St. Andrews KY16 9SS, UK;
- Centre of Biophotonics, Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. Andrews, St. Andrews KY16 9ST, UK
| | - Sonia Bañuelos
- Biofisika Institute (UPV/EHU, CSIC), University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (N.K.); (M.P.); (L.C.); (J.A.S.); (N.F.)
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Correspondence: ; Tel.: +34-94-601-3347
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Kulbay M, Johnson B, Ricaud G, Séguin-Grignon MN, Bernier J. Energetic metabolic reprogramming in Jurkat DFF40-deficient cancer cells. Mol Cell Biochem 2022; 477:2213-2233. [PMID: 35460011 DOI: 10.1007/s11010-022-04433-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/04/2022] [Indexed: 11/25/2022]
Abstract
DNA fragmentation factor 40 (DFF40), or the caspase-activated DNase (CAD), is an endonuclease specific for double-stranded DNA. Alterations in its function and expression have been linked to apoptosis resistance, a mechanism likely used by cancer cells. However, how the DFF40-related apoptosis resistance pathway occurs remains unclear. Here, we sought to determine if DFF40 expression could be linked to cell metabolism through the regulation of mitochondrial integrity and function. We demonstrated that DFF40-deficient cells are more resistant to staurosporine and tributyltin (TBT)-induced apoptosis, and express higher levels of Mcl-1 at basal state. Treatment with TBT induces higher Bcl-2 and caspase-9 mRNA transcripts in DFF40 KO Jurkat cells, as well as enhanced Bcl-2 phosphorylation. A loss of DFF40 expression induces a higher mitochondrial mass, mtDNA copy number, mitochondrial membrane potential, and glycolysis rates in resting T cells. DFF40-deficient cells exhibit the Warburg effect phenotype, where they rely significantly more on glycolysis than oxidative phosphorylation and have a higher proliferative state, demonstrated by a higher Ki-67 transcription factor expression and AKT phosphorylation. Finally, we demonstrated with cell fractioning that DFF40 can translocate to the mitochondria following apoptosis induction. Our study reveals that DFF40 may act as a regulator of mitochondria during cell death and its loss could compromise mitochondrial integrity and cause an energetic reprogramming in pathologies such as cancer.
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Affiliation(s)
- Merve Kulbay
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
- Department of Medicine, Université de Montréal, 2900 Blvd. Edouard Montpetit, Montréal, QC, Canada
| | - Bruno Johnson
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Guillaume Ricaud
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | | | - Jacques Bernier
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada.
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Berry N, Suspène R, Caval V, Khalfi P, Beauclair G, Rigaud S, Blanc H, Vignuzzi M, Wain-Hobson S, Vartanian JP. Herpes Simplex Virus Type 1 Infection Disturbs the Mitochondrial Network, Leading to Type I Interferon Production through the RNA Polymerase III/RIG-I Pathway. mBio 2021; 12:e0255721. [PMID: 34809467 PMCID: PMC8609356 DOI: 10.1128/mbio.02557-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/19/2021] [Indexed: 11/20/2022] Open
Abstract
Viruses have evolved a plethora of mechanisms to impair host innate immune responses. Herpes simplex virus type 1 (HSV-1), a double-stranded linear DNA virus, impairs the mitochondrial network and dynamics predominantly through the UL12.5 gene. We demonstrated that HSV-1 infection induced a remodeling of mitochondrial shape, resulting in a fragmentation of the mitochondria associated with a decrease in their volume and an increase in their sphericity. This damage leads to the release of mitochondrial DNA (mtDNA) to the cytosol. By generating a stable THP-1 cell line expressing the DNase I-mCherry fusion protein and a THP-1 cell line specifically depleted of mtDNA upon ethidium bromide treatment, we showed that cytosolic mtDNA contributes to type I interferon and APOBEC3A upregulation. This was confirmed by using an HSV-1 strain (KOS37 UL98-SPA) with a deletion of the UL12.5 gene that impaired its ability to induce mtDNA stress. Furthermore, by using an inhibitor of RNA polymerase III, we demonstrated that upon HSV-1 infection, cytosolic mtDNA enhanced type I interferon induction through the RNA polymerase III/RIG-I pathway. APOBEC3A was in turn induced by interferon. Deep sequencing analyses of cytosolic mtDNA mutations revealed an APOBEC3A signature predominantly in the 5'TpCpG context. These data demonstrate that upon HSV-1 infection, the mitochondrial network is disrupted, leading to the release of mtDNA and ultimately to its catabolism through APOBEC3-induced mutations. IMPORTANCE Herpes simplex virus 1 (HSV-1) impairs the mitochondrial network through the viral protein UL12.5. This leads to the fusion of mitochondria and simultaneous release of mitochondrial DNA (mtDNA) in a mouse model. We have shown that released mtDNA is recognized as a danger signal, capable of stimulating signaling pathways and inducing the production of proinflammatory cytokines. The expression of the human cytidine deaminase APOBEC3A is highly upregulated by interferon responses. This enzyme catalyzes the deamination of cytidine to uridine in single-stranded DNA substrates, resulting in the catabolism of edited DNA. Using human cell lines deprived of mtDNA and viral strains deficient in UL12, we demonstrated the implication of mtDNA in the production of interferon and APOBEC3A expression during viral infection. We have shown that HSV-1 induces mitochondrial network fragmentation in a human model and confirmed the implication of RNA polymerase III/RIG-I signaling in the capture of cytosolic mtDNA.
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Affiliation(s)
- Noémie Berry
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
- Sorbonne Université, Complexité du Vivant, Paris, France
| | | | - Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
| | - Pierre Khalfi
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
- Sorbonne Université, Complexité du Vivant, Paris, France
| | | | | | - Hervé Blanc
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, Paris, France
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Abstract
Many studies have reported an increase in the level of circulating cell-free DNA (cfDNA) in the blood of patients with cancer. cfDNA mainly comes from tumor cells and, therefore, carries features of its genomic profile. Moreover, tumor-derived cfDNA can act like oncoviruses, entering the cells of vulnerable organs, transforming them and forming metastatic nodes. Another source of cfDNA is immune cells, including neutrophils that generate neutrophil extracellular traps (NETs). Despite the potential eliminative effect of NETs on tumors, in some cases, their excessive generation provokes tumor growth as well as invasion. Considering both possible pathological contributions of cfDNA, as an agent of oncotransformation and the main component of NETs, the study of deoxyribonucleases (DNases) as anticancer and antimetastatic agents is important and promising. This review considers the pathological role of cfDNA in cancer development and the role of DNases as agents to prevent and/or prohibit tumor progression and the development of metastases.
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Affiliation(s)
| | - Nadezhda Mironova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia;
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Angeletti A, Volpi S, Bruschi M, Lugani F, Vaglio A, Prunotto M, Gattorno M, Schena F, Verrina E, Ravelli A, Ghiggeri GM. Neutrophil Extracellular Traps-DNase Balance and Autoimmunity. Cells 2021; 10:cells10102667. [PMID: 34685647 PMCID: PMC8534732 DOI: 10.3390/cells10102667] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/26/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022] Open
Abstract
Neutrophil extracellular traps (NETs) are macromolecular structures programmed to trap circulating bacteria and viruses. The accumulation of NETs in the circulation correlates with the formation of anti-double-stranded (ds) DNA antibodies and is considered a causative factor for systemic lupus erythematosus (SLE). The digestion of DNA by DNase1 and DNases1L3 is the rate- limiting factor for NET accumulation. Mutations occurring in one of these two DNase genes determine anti-DNA formation and are associated with severe Lupus-like syndromes and lupus nephritis (LN). A second mechanism that may lead to DNase functional impairment is the presence of circulating DNase inhibitors in patients with low DNase activity, or the generation of anti-DNase antibodies. This phenomenon has been described in a relevant number of patients with SLE and may represent an important mechanism determining autoimmunity flares. On the basis of the reviewed studies, it is tempting to suppose that the blockade or selective depletion of anti-DNase autoantibodies could represent a potential novel therapeutic approach to prevent or halt SLE and LN. In general, strategies aimed at reducing NET formation might have a similar impact on the progression of SLE and LN.
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Affiliation(s)
- Andrea Angeletti
- Division of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, GenoaLargo Gaslini, 16148 Genoa, Italy; (A.A.); (E.V.)
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, GenoaLargo Gaslini, 16148 Genoa, Italy; (M.B.); (F.L.)
| | - Stefano Volpi
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.V.); (M.G.); (F.S.); (A.R.)
- Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno Infantili, University of Genoa, 16132 Genoa, Italy
| | - Maurizio Bruschi
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, GenoaLargo Gaslini, 16148 Genoa, Italy; (M.B.); (F.L.)
| | - Francesca Lugani
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, GenoaLargo Gaslini, 16148 Genoa, Italy; (M.B.); (F.L.)
| | - Augusto Vaglio
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Firenze, 50121 Firenze, Italy;
| | - Marco Prunotto
- Institute of Pharmaceutical Sciences of Western Switzerland, School of Pharmaceutical Sciences, University of Geneva, 1205 Geneva, Switzerland;
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.V.); (M.G.); (F.S.); (A.R.)
- Clinics of Pediatrics and Rheumatology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Francesca Schena
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.V.); (M.G.); (F.S.); (A.R.)
| | - Enrico Verrina
- Division of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, GenoaLargo Gaslini, 16148 Genoa, Italy; (A.A.); (E.V.)
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, GenoaLargo Gaslini, 16148 Genoa, Italy; (M.B.); (F.L.)
| | - Angelo Ravelli
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy; (S.V.); (M.G.); (F.S.); (A.R.)
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, GenoaLargo Gaslini, 16148 Genoa, Italy; (A.A.); (E.V.)
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, GenoaLargo Gaslini, 16148 Genoa, Italy; (M.B.); (F.L.)
- Correspondence:
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Luque Paz D, Bayeh B, Chauvin P, Poizeau F, Lederlin M, Kerjouan M, Lefevre C, de Latour B, Letheulle J, Tattevin P, Jouneau S. Intrapleural use of urokinase and DNase in pleural infections managed with repeated thoracentesis: A comparative cohort study. PLoS One 2021; 16:e0257339. [PMID: 34547022 PMCID: PMC8454966 DOI: 10.1371/journal.pone.0257339] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/30/2021] [Indexed: 01/13/2023] Open
Abstract
Introduction Evacuation of infected fluid in pleural infections is essential. To date, the use of an intrapleural fibrinolytic agent such as urokinase and DNase has not yet been assessed in infections managed by repeated therapeutic thoracentesis (RTT). Methods We performed a retrospective comparative study of two successive cohorts of consecutive patients with pleural infections from 2001 to 2018. Between 2001 and 2010, patients had RTT with intrapleural urokinase (RTT-U). After 2011, patients received intrapleural urokinase and DNase with RTT (RTT-UD). Data were collected through a standardized questionnaire. Results One hundred and thirty-three patients were included: 93 were men and the mean age was 59 years (standard deviation 17.2). Eighty-one patients were treated with a combination of intrapleural urokinase and DNase, and 52 were treated with intrapleural urokinase only. In the RTT-UD, RTT failure occurred in 14 patients (17%) compared to 10 (19%) in the RTT-U group (P = 0.82). There was no difference between the two groups in intensive care unit admission, surgical referrals or in-hospital mortality. RTT-UD was associated with faster time to apyrexia (aOR = 0.51, 95%CI [0.37–0.72]), a reduced length of hospital stay (aOR = 0.61, 95%CI [0.52–0.73]) and a higher volume of total pleural fluid retrieved (aOR = 1.38, 95%CI [1.02–1.88]). Complications were rare with only one hemothorax in the RTT-UD group and no pneumothorax requiring drainage in either group. Conclusion Compared to urokinase only, intrapleural use of urokinase and DNase in RTT was associated with quicker defervescence, shorter hospital stay and increased volumes of pleural fluid drained. Randomized controlled trials evaluating urokinase and DNase with RTT technique would be required to confirm these results.
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Affiliation(s)
- David Luque Paz
- Department of Respiratory Diseases, Rennes University Hospital, Rennes, France
- Infectious Diseases and Intensive Care Unit, Pontchaillou University Hospital, Rennes, France
- University of Rennes, Inserm, BRM (Bacterial Regulatory RNAs and Medicine), UMR 1230, Rennes, France
- * E-mail:
| | - Betsega Bayeh
- Department of Pneumology and Respiratory Functional Exploration, University Hospital of Tours, Tours, France
| | - Pierre Chauvin
- Department of Respiratory Diseases, Rennes University Hospital, Rennes, France
| | - Florence Poizeau
- EA 7449 (Pharmacoepidemiology and Health Services Research) REPERES, Univ Rennes, CHU Rennes, Rennes, France
- PEPS Research Consortium (Pharmacoepidemiology for Health Product Safety), Rennes, France
- Department of Dermatology, CHU Rennes, Rennes, France
| | - Mathieu Lederlin
- Department of Radiology, Pontchaillou University Hospital, Rennes, France
| | - Mallorie Kerjouan
- Department of Respiratory Diseases, Rennes University Hospital, Rennes, France
| | - Charles Lefevre
- Biochemistry Laboratory, Pontchaillou Hospital CHU Rennes, Rennes, France
| | - Bertrand de Latour
- Department of Thoracic and Cardiovascular Surgery, Rennes University Hospital, Rennes, France
| | - Julien Letheulle
- Department of Internal Medicine, Laval Center Hospital, Laval, France
| | - Pierre Tattevin
- Infectious Diseases and Intensive Care Unit, Pontchaillou University Hospital, Rennes, France
- University of Rennes, Inserm, BRM (Bacterial Regulatory RNAs and Medicine), UMR 1230, Rennes, France
| | - Stéphane Jouneau
- Department of Respiratory Diseases, Rennes University Hospital, Rennes, France
- University of Rennes, CHU Rennes, Inserm, EHESP, IRSET (Institut de recherche en santé, environnement et travail)—UMR_S 1085, Rennes, France
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Vlková B, Janovičová Ľ, Pšenková P, Melníková L, Balažovjechová B, Záhumenský J, Celec P. Deoxyribonuclease activity negative correlates with extracellular DNA in uncomplicated singleton pregnancies in the third trimester. J Perinat Med 2021; 49:755-758. [PMID: 33768760 DOI: 10.1515/jpm-2020-0526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 02/19/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES It is not clear, which factors affect extracellular DNA (ecDNA) concentrations in healthy women with singleton uncomplicated pregnancies, although deoxyribonucleases (DNases) are hypothesized to be responsible for the cleavage of plasma ecDNA. The aim of this study was to analyze potential determinants of total ecDNA including plasma DNase activity. METHODS Plasma samples were collected from 48 healthy women with singleton uncomplicated pregnancies in the third trimester (gestation week 37). DNA was isolated and quantified using fluorometry and real time PCR. DNase activity was assessed using the single radial enzyme-diffusion method. RESULTS Neither ecDNA, nor DNase activity were affected by maternal age or BMI. DNase activity negatively correlated with total plasma ecDNA (r=-0.40, p=0.007). Similar associations were found for ecDNA of nuclear and mitochondrial origin, but not with fetal DNA quantified using Y-targeted PCR in male fetus-bearing pregnancies. CONCLUSIONS The role of plasma ecDNA of fetal and maternal origin is studied in the pathogenesis of pregnancy-complications. The results indicate that plasma DNase activity could negatively regulate ecDNA concentrations and should, thus, be analyzed in preeclampsia, preterm birth and other ecDNA-related pregnancy complications.
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Affiliation(s)
- Barbora Vlková
- Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia
| | - Ľubica Janovičová
- Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia
| | - Petra Pšenková
- 2nd Department of Gynecology and Obstetrics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Lívia Melníková
- 2nd Department of Gynecology and Obstetrics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Barbora Balažovjechová
- 2nd Department of Gynecology and Obstetrics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Jozef Záhumenský
- 2nd Department of Gynecology and Obstetrics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Peter Celec
- Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia
- Institute of Pathophysiology, Comenius University, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
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25
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Lee J, Jo I, Ahn J, Hong S, Jeong S, Kwon A, Ha NC. Crystal structure of the nuclease and capping domain of SbcD from Staphylococcus aureus. J Microbiol 2021; 59:584-589. [PMID: 33877576 DOI: 10.1007/s12275-021-1012-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 10/21/2022]
Abstract
The SbcCD complex is an essential component of the DNA double-strand break (DSB) repair system in bacteria. The bacterial SbcCD complex recognizes and cleaves the DNA ends in DSBs by ATP-dependent endo- and exonuclease activities as an early step of the DNA repair process. SbcD consists of nuclease, capping, and helix-loop-helix domains. Here, we present the crystal structure of a SbcD fragment from Staphylococcus aureus, which contained nuclease and capping domains, at a resolution of 2.9 Å. This structure shows a dimeric assembly similar to that of the corresponding domains of SbcD from Escherichia coli. The S. aureus SbcD fragment exhibited endonuclease activities on supercoiled DNA and exonuclease activity on linear and nicked DNA. This study contributes to the understanding of the molecular basis for how bacteria can resist sterilizing treatment, causing DNA damage.
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Affiliation(s)
- Jinwook Lee
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Inseong Jo
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
- Current address: KoBioLabs, Inc., Seoul, 08826, Republic of Korea
| | - Jinsook Ahn
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seokho Hong
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soyeon Jeong
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea
| | - Aeran Kwon
- Department of Beauty Care, College of Medical Science, Daegu Haany University, Gyeongsan, 38610, Republic of Korea
| | - Nam-Chul Ha
- Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Department of Agricultural Biotechnology, CALS, Seoul National University, Seoul, 08826, Republic of Korea.
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Shevtsov-Tal S, Best C, Matan R, Chandran SA, Brown GG, Ostersetzer-Biran O. nMAT3 is an essential maturase splicing factor required for holo-complex I biogenesis and embryo development in Arabidopsis thaliana plants. Plant J 2021; 106:1128-1147. [PMID: 33683754 DOI: 10.1111/tpj.15225] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 05/21/2023]
Abstract
Group-II introns are self-splicing mobile genetic elements consisting of catalytic intron-RNA and its related intron-encoded splicing maturase protein cofactor. Group-II sequences are particularly plentiful within the mitochondria of land plants, where they reside within many critical gene loci. During evolution, the plant organellar introns have degenerated, such as they lack regions that are are required for splicing, and also lost their evolutionary related maturase proteins. Instead, for their splicing the organellar introns in plants rely on different host-acting protein cofactors, which may also provide a means to link cellular signals with respiratory functions. The nuclear genome of Arabidopsis thaliana encodes four maturase-related factors. Previously, we showed that three of the maturases, nMAT1, nMAT2 and nMAT4, function in the excision of different group-II introns in Arabidopsis mitochondria. The function of nMAT3 (encoded by the At5g04050 gene locus) was found to be essential during early embryogenesis. Using a modified embryo-rescue method, we show that nMAT3-knockout plants are strongly affected in the splicing of nad1 introns 1, 3 and 4 in Arabidopsis mitochondria, resulting in complex-I biogenesis defects and altered respiratory activities. Functional complementation of nMAT3 restored the organellar defects and embryo-arrested phenotypes associated with the nmat3 mutant line. Notably, nMAT3 and nMA4 were found to act on the same RNA targets but have no redundant functions in the splicing of nad1 transcripts. The two maturases, nMAT3 and nMAT4 are likely to cooperate together in the maturation of nad1 pre-RNAs. Our results provide important insights into the roles of maturases in mitochondria gene expression and the biogenesis of the respiratory system during early plant life.
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Affiliation(s)
- Sofia Shevtsov-Tal
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, 91904, Israel
| | - Corinne Best
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, 91904, Israel
| | - Roei Matan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, 91904, Israel
| | - Sam A Chandran
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613 401, India
| | - Gregory G Brown
- Department of Biology, McGill University, Montreal, Quebec, H3A 1B1, Canada
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem, 91904, Israel
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Meier B, Volkova NV, Hong Y, Bertolini S, González-Huici V, Petrova T, Boulton S, Campbell PJ, Gerstung M, Gartner A. Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation. PLoS One 2021; 16:e0250291. [PMID: 33905417 PMCID: PMC8078821 DOI: 10.1371/journal.pone.0250291] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
Maintaining genome integrity is particularly important in germ cells to ensure faithful transmission of genetic information across generations. Here we systematically describe germ cell mutagenesis in wild-type and 61 DNA repair mutants cultivated over multiple generations. ~44% of the DNA repair mutants analysed showed a >2-fold increased mutagenesis with a broad spectrum of mutational outcomes. Nucleotide excision repair deficiency led to higher base substitution rates, whereas polh-1(Polη) and rev-3(Polζ) translesion synthesis polymerase mutants resulted in 50-400 bp deletions. Signatures associated with defective homologous recombination fall into two classes: 1) brc-1/BRCA1 and rad-51/RAD51 paralog mutants showed increased mutations across all mutation classes, 2) mus-81/MUS81 and slx-1/SLX1 nuclease, and him-6/BLM, helq-1/HELQ or rtel-1/RTEL1 helicase mutants primarily accumulated structural variants. Repetitive and G-quadruplex sequence-containing loci were more frequently mutated in specific DNA repair backgrounds. Tandem duplications embedded in inverted repeats were observed in helq-1 helicase mutants, and a unique pattern of 'translocations' involving homeologous sequences occurred in rip-1 recombination mutants. atm-1/ATM checkpoint mutants harboured structural variants specifically enriched in subtelomeric regions. Interestingly, locally clustered mutagenesis was only observed for combined brc-1 and cep-1/p53 deficiency. Our study provides a global view of how different DNA repair pathways contribute to prevent germ cell mutagenesis.
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Affiliation(s)
- Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | - Nadezda V. Volkova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Ye Hong
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | - Simone Bertolini
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | | | - Tsvetana Petrova
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | | | - Peter J. Campbell
- Cancer, Ageing and Somatic Mutation Program, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
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Tesser A, Piperno GM, Pin A, Piscianz E, Boz V, Benvenuti F, Tommasini A. Priming of the cGAS-STING-TBK1 Pathway Enhances LPS-Induced Release of Type I Interferons. Cells 2021; 10:785. [PMID: 33916318 PMCID: PMC8067196 DOI: 10.3390/cells10040785] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Cytoplasmic nucleic acids sensing through cGAS-STING-TBK1 pathway is crucial for the production of antiviral interferons (IFNs). IFN production can also be induced by lipopolysaccharide (LPS) stimulation through Toll-like receptor 4 (TLR4) in appropriate conditions. Of note, both IFN production and dysregulated LPS-response could play a role in the pathogenesis of Systemic Lupus Erythematosus (SLE). Indeed, LPS can trigger SLE in lupus-prone mice and bacterial infections can induce disease flares in human SLE. However, the interactions between cGAS and TLR4 pathways to IFNs have been poorly investigated. To address this issue, we studied LPS-stimulation in cellular models with a primed cGAS-STING-TBK1 pathway. cGAS-stimulation was naturally sustained by undigested self-nucleic acids in fibroblasts from DNase2-deficiency interferonopathy, whilst it was pharmacologically obtained by cGAMP-stimulation in THP1 cells and murine bone marrow-derived dendritic cells. We showed that cells with a primed cGAS-STING-TBK1 pathway displayed enhanced IFNs production after TLR4-challenge. STING-inhibition did not affect IFN production after LPS alone, but prevented the amplified IFN production in cGAMP-primed cells, suggesting that functional STING is required for priming-dependent enhancement. Furthermore, we speculated that an increased PIK3AP1 expression in DNase2-deficient fibroblasts may link cGAMP-priming with increased LPS-induced IFN production. We showed that both the hyper-expression of PIK3API and the enhanced LPS-induced IFN production can be contrasted by STING inhibitors. Our results may explain how bacterial LPS can synergize with cGAS-pathway in promoting the development of SLE-like autoimmunity.
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Affiliation(s)
- Alessandra Tesser
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (A.T.); (A.P.); (E.P.)
| | - Giulia Maria Piperno
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy; (G.M.P.); (F.B.)
| | - Alessia Pin
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (A.T.); (A.P.); (E.P.)
| | - Elisa Piscianz
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (A.T.); (A.P.); (E.P.)
| | - Valentina Boz
- Department of Medicine, Surgery, and Health Sciences, University of Trieste, 34149 Trieste, Italy;
| | - Federica Benvenuti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy; (G.M.P.); (F.B.)
| | - Alberto Tommasini
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy; (A.T.); (A.P.); (E.P.)
- Department of Medicine, Surgery, and Health Sciences, University of Trieste, 34149 Trieste, Italy;
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29
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Zhang K, Jiang N, Chen H, Zhang N, Sang X, Feng Y, Chen R, Chen Q. TatD DNases of African trypanosomes confer resistance to host neutrophil extracellular traps. Sci China Life Sci 2021; 64:621-632. [PMID: 33420923 DOI: 10.1007/s11427-020-1854-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 11/19/2020] [Indexed: 01/07/2023]
Abstract
African trypanosomatid parasites escape host acquired immune responses through periodic antigenic variation of their surface coat. In this study, we describe a mechanism by which the parasites counteract innate immune responses. Two TatD DNases were identified in each of Trypanosoma evansi and Trypanosoma brucei. These DNases are bivalent metal-dependent endonucleases localized in the cytoplasm and flagella of the parasites that can also be secreted by the parasites. These enzymes possess conserved functional domains and have efficient DNA hydrolysis activity. Host neutrophil extracellular traps (NETs) induced by the parasites could be hydrolyzed by native and recombinant TatD DNases. NET disruption was prevented, and the survival rate of parasites was decreased, in the presence of the DNase inhibitor aurintricarboxylic acid. These data suggest that trypanosomes can counteract host innate immune responses by active secretion of TatD DNases to degrade NETs.
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Affiliation(s)
- Kai Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
- The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, 110866, China
| | - Ning Jiang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
- The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, 110866, China
| | - Hongyu Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
- The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, 110866, China
| | - Naiwen Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
- The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, 110866, China
| | - Xiaoyu Sang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
- The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, 110866, China
| | - Ying Feng
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
- The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, 110866, China
| | - Ran Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
- The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, 110866, China
| | - Qijun Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
- The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, Shenyang, 110866, China.
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Maronek M, Gromova B, Liptak R, Konecna B, Pastorek M, Cechova B, Harsanyova M, Budis J, Smolak D, Radvanszky J, Szemes T, Harsanyiova J, Kralova Trancikova A, Gardlik R. Extracellular DNA Correlates with Intestinal Inflammation in Chemically Induced Colitis in Mice. Cells 2021; 10:E81. [PMID: 33418977 PMCID: PMC7825321 DOI: 10.3390/cells10010081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/25/2020] [Accepted: 12/31/2020] [Indexed: 12/12/2022] Open
Abstract
Circulating extracellular DNA (ecDNA) is known to worsen the outcome of many diseases. ecDNA released from neutrophils during infection or inflammation is present in the form of neutrophil extracellular traps (NETs). It has been shown that higher ecDNA concentration occurs in a number of inflammatory diseases including inflammatory bowel disease (IBD). Enzymes such as peptidyl arginine deiminases (PADs) are crucial for NET formation. We sought to describe the dynamics of ecDNA concentrations and fragmentation, along with NETosis during a mouse model of chemically induced colitis. Plasma ecDNA concentration was highest on day seven of dextran sulfate sodium (DSS) intake and the increase was time-dependent. This increase correlated with the percentage of cells undergoing NETosis and other markers of disease activity. Relative proportion of nuclear ecDNA increased towards more severe colitis; however, absolute amount decreased. In colon explant medium, the highest concentration of ecDNA was on day three of DSS consumption. Early administration of PAD4 inhibitors did not alleviate disease activity, but lowered the ecDNA concentration. These results uncover the biological characteristics of ecDNA in IBD and support the role of ecDNA in intestinal inflammation. The therapeutic intervention aimed at NETs and/or nuclear ecDNA has yet to be fully investigated.
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Affiliation(s)
- Martin Maronek
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, 81108 Bratislava, Slovakia; (M.M.); (B.G.); (B.K.); (M.P.)
| | - Barbora Gromova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, 81108 Bratislava, Slovakia; (M.M.); (B.G.); (B.K.); (M.P.)
| | - Robert Liptak
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, 81372 Bratislava, Slovakia;
| | - Barbora Konecna
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, 81108 Bratislava, Slovakia; (M.M.); (B.G.); (B.K.); (M.P.)
| | - Michal Pastorek
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, 81108 Bratislava, Slovakia; (M.M.); (B.G.); (B.K.); (M.P.)
| | - Barbora Cechova
- Department of Physiology, Third Faculty of Medicine, Charles University, 10000 Prague, Czech Republic;
| | - Maria Harsanyova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia; (M.H.); (D.S.); (T.S.)
- Geneton Ltd., 84104 Bratislava, Slovakia; (J.B.); (J.R.)
| | - Jaroslav Budis
- Geneton Ltd., 84104 Bratislava, Slovakia; (J.B.); (J.R.)
- Comenius University Science Park, Univerzita Komenského, 84104 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 81104 Bratislava, Slovakia
| | - David Smolak
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia; (M.H.); (D.S.); (T.S.)
- Geneton Ltd., 84104 Bratislava, Slovakia; (J.B.); (J.R.)
| | - Jan Radvanszky
- Geneton Ltd., 84104 Bratislava, Slovakia; (J.B.); (J.R.)
- Comenius University Science Park, Univerzita Komenského, 84104 Bratislava, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia; (M.H.); (D.S.); (T.S.)
- Geneton Ltd., 84104 Bratislava, Slovakia; (J.B.); (J.R.)
- Comenius University Science Park, Univerzita Komenského, 84104 Bratislava, Slovakia
| | - Jana Harsanyiova
- Department of Pathophysiology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Alzbeta Kralova Trancikova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Roman Gardlik
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, 81108 Bratislava, Slovakia; (M.M.); (B.G.); (B.K.); (M.P.)
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31
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Moore CL, Savenka AV, Basnakian AG. TUNEL Assay: A Powerful Tool for Kidney Injury Evaluation. Int J Mol Sci 2021; 22:ijms22010412. [PMID: 33401733 PMCID: PMC7795088 DOI: 10.3390/ijms22010412] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023] Open
Abstract
Terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) assay is a long-established assay used to detect cell death-associated DNA fragmentation (3'-OH DNA termini) by endonucleases. Because these enzymes are particularly active in the kidney, TUNEL is widely used to identify and quantify DNA fragmentation and cell death in cultured kidney cells and animal and human kidneys resulting from toxic or hypoxic injury. The early characterization of TUNEL as an apoptotic assay has led to numerous misinterpretations of the mechanisms of kidney cell injury. Nevertheless, TUNEL is becoming increasingly popular for kidney injury assessment because it can be used universally in cultured and tissue cells and for all mechanisms of cell death. Furthermore, it is sensitive, accurate, quantitative, easily linked to particular cells or tissue compartments, and can be combined with immunohistochemistry to allow reliable identification of cell types or likely mechanisms of cell death. Traditionally, TUNEL analysis has been limited to the presence or absence of a TUNEL signal. However, additional information on the mechanism of cell death can be obtained from the analysis of TUNEL patterns.
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Affiliation(s)
- Christopher L. Moore
- Department of Pharmacology & Toxicology, University of Arkansas for Medical Sciences, 4301 West Markham Street, #638, Little Rock, AR 72205, USA; (C.L.M.); (A.V.S.)
| | - Alena V. Savenka
- Department of Pharmacology & Toxicology, University of Arkansas for Medical Sciences, 4301 West Markham Street, #638, Little Rock, AR 72205, USA; (C.L.M.); (A.V.S.)
| | - Alexei G. Basnakian
- Department of Pharmacology & Toxicology, University of Arkansas for Medical Sciences, 4301 West Markham Street, #638, Little Rock, AR 72205, USA; (C.L.M.); (A.V.S.)
- John L. McClellan Memorial VA Hospital, Central Arkansas Veterans Healthcare System, 4300 West 7th Street, Little Rock, AR 72205, USA
- Correspondence: ; Tel.: +1-501-352-2870
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32
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Wong N, John S, Nussenzweig A, Canela A. END-seq: An Unbiased, High-Resolution, and Genome-Wide Approach to Map DNA Double-Strand Breaks and Resection in Human Cells. Methods Mol Biol 2021; 2153:9-31. [PMID: 32840769 DOI: 10.1007/978-1-0716-0644-5_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA double-strand breaks (DSBs) represent the most toxic form of DNA damage and can arise in either physiological or pathological conditions. If left unrepaired, these DSBs can lead to genome instability which serves as a major driver to tumorigenesis and other pathologies. Consequently, localizing DSBs and understanding the dynamics of break formation and the repair process are of great interest for dissecting underlying mechanisms and in the development of targeted therapies. Here, we describe END-seq, a highly sensitive next-generation sequencing technique for quantitatively mapping DNA double-strand breaks (DSB) at nucleotide resolution across the genome in an unbiased manner. END-seq is based on the direct ligation of a sequencing adapter to the ends of DSBs and provides information about DNA processing (end resection) at DSBs, a critical determinant in the selection of repair pathways. The absence of cell fixation and the use of agarose for embedding cells and exonucleases for blunting the ends of DSBs are key advances that contribute to the technique's increased sensitivity and robustness over previously established methods. Overall, END-seq has provided a major technical advance for mapping DSBs and has also helped inform the biology of complex biological processes including genome organization, replication fork collapse and chromosome fragility, off-target identification of RAG recombinase and gene-editing nucleases, and DNA end resection at sites of DSBs.
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Affiliation(s)
- Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sam John
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
| | - Andrés Canela
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
- The Hakubi Center for Advanced Research and Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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33
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Abstract
Homologous recombination (HR) has been extensively studied in response to DNA double-strand breaks (DSBs). In contrast, much less is known about how HR deals with DNA lesions other than DSBs (e.g., at single-stranded DNA) and replication forks, despite the fact that these DNA structures are associated with most spontaneous recombination events. A major handicap for studying the role of HR at non-DSB DNA lesions and replication forks is the difficulty of discriminating whether a recombination protein is associated with the non-DSB lesion per se or rather with a DSB generated during their processing. Here, we describe a method to follow the in vivo binding of recombination proteins to non-DSB DNA lesions and replication forks. This approach is based on the cleavage and subsequent electrophoretic analysis of the target DNA by the recombination protein fused to the micrococcal nuclease.
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Affiliation(s)
- Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - María J Cabello-Lobato
- Division of Cancer Sciences, Manchester Cancer Research Center, University of Manchester, Manchester, UK
| | - Félix Prado
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC-University of Seville-UPO, Seville, Spain.
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34
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Zabolotnaya E, Mela I, Henderson RM, Robinson NP. Turning the Mre11/Rad50 DNA repair complex on its head: lessons from SMC protein hinges, dynamic coiled-coil movements and DNA loop-extrusion? Biochem Soc Trans 2020; 48:2359-2376. [PMID: 33300987 PMCID: PMC7752040 DOI: 10.1042/bst20170168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
The bacterial SbcC/SbcD DNA repair proteins were identified over a quarter of a century ago. Following the subsequent identification of the homologous Mre11/Rad50 complex in the eukaryotes and archaea, it has become clear that this conserved chromosomal processing machinery is central to DNA repair pathways and the maintenance of genomic stability in all forms of life. A number of experimental studies have explored this intriguing genome surveillance machinery, yielding significant insights and providing conceptual advances towards our understanding of how this complex operates to mediate DNA repair. However, the inherent complexity and dynamic nature of this chromosome-manipulating machinery continue to obfuscate experimental interrogations, and details regarding the precise mechanisms that underpin the critical repair events remain unanswered. This review will summarize our current understanding of the dramatic structural changes that occur in Mre11/Rad50 complex to mediate chromosomal tethering and accomplish the associated DNA processing events. In addition, undetermined mechanistic aspects of the DNA enzymatic pathways driven by this vital yet enigmatic chromosomal surveillance and repair apparatus will be discussed. In particular, novel and putative models of DNA damage recognition will be considered and comparisons will be made between the modes of action of the Rad50 protein and other related ATPases of the overarching SMC superfamily.
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Affiliation(s)
| | - Ioanna Mela
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, U.K
| | | | - Nicholas P. Robinson
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, U.K
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35
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Eaglesham JB, McCarty KL, Kranzusch PJ. Structures of diverse poxin cGAMP nucleases reveal a widespread role for cGAS-STING evasion in host-pathogen conflict. eLife 2020; 9:e59753. [PMID: 33191912 PMCID: PMC7688311 DOI: 10.7554/elife.59753] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/12/2020] [Indexed: 02/06/2023] Open
Abstract
DNA viruses in the family Poxviridae encode poxin enzymes that degrade the immune second messenger 2'3'-cGAMP to inhibit cGAS-STING immunity in mammalian cells. The closest homologs of poxin exist in the genomes of insect viruses suggesting a key mechanism of cGAS-STING evasion may have evolved outside of mammalian biology. Here we use a biochemical and structural approach to discover a broad family of 369 poxins encoded in diverse viral and animal genomes and define a prominent role for 2'3'-cGAMP cleavage in metazoan host-pathogen conflict. Structures of insect poxins reveal unexpected homology to flavivirus proteases and enable identification of functional self-cleaving poxins in RNA-virus polyproteins. Our data suggest widespread 2'3'-cGAMP signaling in insect antiviral immunity and explain how a family of cGAS-STING evasion enzymes evolved from viral proteases through gain of secondary nuclease activity. Poxin acquisition by poxviruses demonstrates the importance of environmental connections in shaping evolution of mammalian pathogens.
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Affiliation(s)
- James B Eaglesham
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
- Department of Cancer Immunology and Virology, Dana-Farber Cancer InstituteBostonUnited States
- Harvard PhD Program in Virology, Division of Medical Sciences, Harvard UniversityBostonUnited States
| | - Kacie L McCarty
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
- Department of Cancer Immunology and Virology, Dana-Farber Cancer InstituteBostonUnited States
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
- Department of Cancer Immunology and Virology, Dana-Farber Cancer InstituteBostonUnited States
- Harvard PhD Program in Virology, Division of Medical Sciences, Harvard UniversityBostonUnited States
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer InstituteBostonUnited States
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36
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Van der Gucht M, Aktan MK, Hendrix H, Velde GV, Paeshuyse J, Braem A, Lavigne R. qDNase assay: A quantitative method for real-time assessment of DNase activity on coated surfaces. Biochem Biophys Res Commun 2020; 534:1003-1006. [PMID: 33121680 DOI: 10.1016/j.bbrc.2020.10.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 10/17/2020] [Indexed: 11/17/2022]
Abstract
DNase coatings show great potential to prevent biofilm formation in various applications of the medical implant, food and marine industry. However, straightforward and quantitative methods to characterize the enzymatic activity of these coatings are currently not available. We here introduce the qDNase assay, a quantitative, real-time method to characterize the activity of DNase coatings. The assay combines (1) the use of an oligonucleotide probe, which fluoresces upon cleavage by coated DNases, and (2) the continuous read-out of the fluorescent signal within a microplate fluorometer format. The combination of these two properties results in a real-time fluorescent signal that is used to directly quantify the activity of DNase coatings. As a proof of concept, bovine DNase I coatings were immobilized on titanium by means of chemical grafting and their activity was estimated at 3.87 × 10-4 U. To our knowledge, the qDNase assay provides the first approach to report the activity of a DNase coating in absolute DNase activity units. This assay will not only serve to compare existing DNase coating methods more accurately, but will also enable the rational design of new DNase coating methods in the future.
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Affiliation(s)
- Marie Van der Gucht
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Kasteelpark Arenberg 21 - box 2462, B-3001, Leuven, Belgium
| | - Merve Kübra Aktan
- KU Leuven, Department of Materials Engineering (MTM), Biomaterials and Tissue Engineering Research Group, Kasteelpark Arenberg 44 - box 2450, B-3001, Leuven, Belgium
| | - Hanne Hendrix
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Kasteelpark Arenberg 21 - box 2462, B-3001, Leuven, Belgium
| | - Greetje Vande Velde
- KU Leuven, Department of Imaging & Pathology, Biomedical MRI / MoSAIC, Herestraat 49, building O&N1 - box 505, B-3000, Leuven, Belgium
| | - Jan Paeshuyse
- KU Leuven, Department of Biosystems, Laboratory of Host Pathogen Interaction in Livestock, Kasteelpark Arenberg 30 - box 2472, B-3001, Leuven, Belgium
| | - Annabel Braem
- KU Leuven, Department of Materials Engineering (MTM), Biomaterials and Tissue Engineering Research Group, Kasteelpark Arenberg 44 - box 2450, B-3001, Leuven, Belgium
| | - Rob Lavigne
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Kasteelpark Arenberg 21 - box 2462, B-3001, Leuven, Belgium.
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37
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Ogloblina AM, Iaccarino N, Capasso D, Di Gaetano S, Garzarella EU, Dolinnaya NG, Yakubovskaya MG, Pagano B, Amato J, Randazzo A. Toward G-Quadruplex-Based Anticancer Agents: Biophysical and Biological Studies of Novel AS1411 Derivatives. Int J Mol Sci 2020; 21:E7781. [PMID: 33096752 PMCID: PMC7590035 DOI: 10.3390/ijms21207781] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Certain G-quadruplex forming guanine-rich oligonucleotides (GROs), including AS1411, are endowed with cancer-selective antiproliferative activity. They are known to bind to nucleolin protein, resulting in the inhibition of nucleolin-mediated phenomena. However, multiple nucleolin-independent biological effects of GROs have also been reported, allowing them to be considered promising candidates for multi-targeted cancer therapy. Herein, with the aim of optimizing AS1411 structural features to find GROs with improved anticancer properties, we have studied a small library of AS1411 derivatives differing in the sequence length and base composition. The AS1411 derivatives were characterized by using circular dichroism and nuclear magnetic resonance spectroscopies and then investigated for their enzymatic resistance in serum and nuclear extract, as well as for their ability to bind nucleolin, inhibit topoisomerase I, and affect the viability of MCF-7 human breast adenocarcinoma cells. All derivatives showed higher thermal stability and inhibitory effect against topoisomerase I than AS1411. In addition, most of them showed an improved antiproliferative activity on MCF-7 cells compared to AS1411 despite a weaker binding to nucleolin. Our results support the hypothesis that the antiproliferative properties of GROs are due to multi-targeted effects.
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Affiliation(s)
- Anna M. Ogloblina
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Domenica Capasso
- Center for Life Sciences and Technologies (CESTEV), University of Naples Federico II, Via A. De Amicis 95, 80145 Naples, Italy;
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy;
| | - Emanuele U. Garzarella
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Marianna G. Yakubovskaya
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
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Foster K, Grüschow S, Bailey S, White MF, Terns MP. Regulation of the RNA and DNA nuclease activities required for Pyrococcus furiosus Type III-B CRISPR-Cas immunity. Nucleic Acids Res 2020; 48:4418-4434. [PMID: 32198888 PMCID: PMC7192623 DOI: 10.1093/nar/gkaa176] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/28/2020] [Accepted: 03/19/2020] [Indexed: 12/25/2022] Open
Abstract
Type III CRISPR-Cas prokaryotic immune systems provide anti-viral and anti-plasmid immunity via a dual mechanism of RNA and DNA destruction. Upon target RNA interaction, Type III crRNP effector complexes become activated to cleave both target RNA (via Cas7) and target DNA (via Cas10). Moreover, trans-acting endoribonucleases, Csx1 or Csm6, can promote the Type III immune response by destroying both invader and host RNAs. Here, we characterize how the RNase and DNase activities associated with Type III-B immunity in Pyrococcus furiosus (Pfu) are regulated by target RNA features and second messenger signaling events. In vivo mutational analyses reveal that either the DNase activity of Cas10 or the RNase activity of Csx1 can effectively direct successful anti-plasmid immunity. Biochemical analyses confirmed that the Cas10 Palm domains convert ATP into cyclic oligoadenylate (cOA) compounds that activate the ribonuclease activity of Pfu Csx1. Furthermore, we show that the HEPN domain of the adenosine-specific endoribonuclease, Pfu Csx1, degrades cOA signaling molecules to provide an auto-inhibitory off-switch of Csx1 activation. Activation of both the DNase and cOA generation activities require target RNA binding and recognition of distinct target RNA 3' protospacer flanking sequences. Our results highlight the complex regulatory mechanisms controlling Type III CRISPR immunity.
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Affiliation(s)
- Kawanda Foster
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Scott Bailey
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Michael P Terns
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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Ueki R, Uchida S, Kanda N, Yamada N, Ueki A, Akiyama M, Toh K, Cabral H, Sando S. A chemically unmodified agonistic DNA with growth factor functionality for in vivo therapeutic application. Sci Adv 2020; 6:eaay2801. [PMID: 32270033 PMCID: PMC7112757 DOI: 10.1126/sciadv.aay2801] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 12/19/2019] [Indexed: 05/25/2023]
Abstract
Although growth factors have great therapeutic potential because of their regenerative functions, they often have intrinsic drawbacks, such as low thermal stability and high production cost. Oligonucleotides have recently emerged as promising chemical entities for designing synthetic alternatives to growth factors. However, their applications in vivo have been recognized as a challenge because of their susceptibility to nucleases and limited distribution to a target tissue. Here, we present the first example of oligonucleotide-based growth factor mimetics that exerts therapeutic effects at a target tissue after systemic injection. The aptamer was designed to dimerize a growth factor receptor for its activation and mitigated the progression of Fas-induced fulminant hepatitis in a mouse model. This unprecedented functionality of the aptamer can be reasonably explained by its high nuclease stability and migration to the liver parenchyma. These mechanistic analyses provided insights for the successful application of aptamer-based receptor agonists.
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Affiliation(s)
- Ryosuke Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satoshi Uchida
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Naoto Kanda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Naoki Yamada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ayaka Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Momoko Akiyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazuko Toh
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Horacio Cabral
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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East KW, Newton JC, Morzan UN, Narkhede Y, Acharya A, Skeens E, Jogl G, Batista VS, Palermo G, Lisi GP. Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics. J Am Chem Soc 2020; 142:1348-1358. [PMID: 31885264 PMCID: PMC7497131 DOI: 10.1021/jacs.9b10521] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
CRISPR-Cas9 is a widely employed genome-editing tool with functionality reliant on the ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA. In this system, an intriguing allosteric communication has been suggested to control its DNA cleavage activity through flexibility of the catalytic HNH domain. Here, solution NMR experiments and a novel Gaussian-accelerated molecular dynamics (GaMD) simulation method are used to capture the structural and dynamic determinants of allosteric signaling within the HNH domain. We reveal the existence of a millisecond time scale dynamic pathway that spans HNH from the region interfacing the adjacent RuvC nuclease and propagates up to the DNA recognition lobe in full-length CRISPR-Cas9. These findings reveal a potential route of signal transduction within the CRISPR-Cas9 HNH nuclease, advancing our understanding of the allosteric pathway of activation. Further, considering the role of allosteric signaling in the specificity of CRISPR-Cas9, this work poses the mechanistic basis for novel engineering efforts aimed at improving its genome-editing capability.
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Affiliation(s)
- Kyle W. East
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Jocelyn C. Newton
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Uriel N. Morzan
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Yogesh Narkhede
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - Atanu Acharya
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Erin Skeens
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, CT 06520 , United States
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA 52512, United States
| | - George P. Lisi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, United States
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Cantón PE, Bonning BC. Proteases and nucleases across midgut tissues of Nezara viridula (Hemiptera:Pentatomidae) display distinct activity profiles that are conserved through life stages. J Insect Physiol 2019; 119:103965. [PMID: 31610185 DOI: 10.1016/j.jinsphys.2019.103965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
The southern green stink bug, Nezara viridula is a polyphagous pest of commercially important crops during both nymph and adult stages. This insect has recently transitioned from a secondary agricultural pest to one of primary concern. Novel management solutions are needed due to the limited effectiveness of current control strategies. We performed biochemical and transcriptomic analyses to characterize digestive enzymes in the salivary glands and along midgut tissues of N. viridula nymphs and adults fed on sweet corn. The digestive profiles were more distinct between midgut regions (M1 to M3) than between life stages. Aminopeptidase and chymotrypsin activities declined from the M1 (anterior) toward the M3 midgut region. Cysteine protease activity was higher in the M2 and M3 regions than in M1. Differences in sensitivity to chymotrypsin inhibitors between midgut regions suggest that distinct genes or isoforms are expressed in different regions of the gut. In nymphs, DNA and RNA degradation was higher in M1 than in M3. Adult nuclease activity was low across all midgut regions, but high in salivary glands. The differences in protease activities are reflected by transcriptomic data and functional enrichment of GO terms. Together, our results show that different regions of the digestive tract of N. viridula have specific and distinct digestive properties, and increase our understanding of the physiology of this organism.
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Affiliation(s)
- Pablo Emiliano Cantón
- Department of Entomology and Nematology, University of Florida, PO Box 110620, Gainesville, FL 32611, USA
| | - Bryony C Bonning
- Department of Entomology and Nematology, University of Florida, PO Box 110620, Gainesville, FL 32611, USA.
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Chen H, Ronau JA, Beckmann JF, Hochstrasser M. A Wolbachia nuclease and its binding partner provide a distinct mechanism for cytoplasmic incompatibility. Proc Natl Acad Sci U S A 2019; 116:22314-22321. [PMID: 31615889 PMCID: PMC6825299 DOI: 10.1073/pnas.1914571116] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wolbachia are endosymbiotic bacteria that infect nearly half of all arthropod species. This pandemic is due in part to their ability to increase their transmission through the female germline, most commonly by a mechanism called cytoplasmic incompatibility (CI). The Wolbachia cid operon, encoding 2 proteins, CidA and CidB, the latter a deubiquitylating enzyme (DUB), recapitulates CI in transgenic Drosophila melanogaster However, some CI-inducing Wolbachia strains lack a DUB-encoding cid operon; it was therefore proposed that the related cin operon codes for an alternative CI system. Here we show that the Wolbachia cin operon encodes a nuclease, CinB, and a second protein, CinA, that tightly binds CinB. Recombinant CinB has nuclease activity against both single-stranded and double-stranded DNA but not RNA under the conditions tested. Expression of the cin operon in transgenic male flies induces male sterility and embryonic defects typical of CI. Importantly, transgenic CinA can rescue defects in egg-hatch rates when expressed in females. Expression of CinA also rescues CinB-induced growth defects in yeast. CinB has 2 PD-(D/E)xK nuclease domains, and both are required for nuclease activity and for toxicity in yeast and flies. Our data suggest a distinct mechanism for CI involving a nuclease toxin and highlight the central role of toxin-antidote operons in Wolbachia-induced cytoplasmic incompatibility.
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Affiliation(s)
- Hongli Chen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - Judith A Ronau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
| | - John F Beckmann
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 26849
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511;
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511
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Reuven N, Adler J, Broennimann K, Myers N, Shaul Y. Recruitment of DNA Repair MRN Complex by Intrinsically Disordered Protein Domain Fused to Cas9 Improves Efficiency of CRISPR-Mediated Genome Editing. Biomolecules 2019; 9:E584. [PMID: 31597252 PMCID: PMC6843829 DOI: 10.3390/biom9100584] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 is a powerful tool for genome editing in cells and organisms. Nevertheless, introducing directed templated changes by homology-directed repair (HDR) requires the cellular DNA repair machinery, such as the MRN complex (Mre11/Rad50/Nbs1). To improve the process, we tailored chimeric constructs of Cas9, in which SpCas9 was fused at its N- or C-terminus to a 126aa intrinsically disordered domain from HSV-1 alkaline nuclease (UL12) that recruits the MRN complex. The chimeric Cas9 constructs were two times more efficient in homology-directed editing of endogenous loci in tissue culture cells. This effect was dependent upon the MRN-recruiting activity of the domain and required lower amounts of the chimeric Cas9 in comparison with unmodified Cas9. The new constructs improved the yield of edited cells when making endogenous point mutations or inserting small tags encoded by oligonucleotide donor DNA (ssODN), and also with larger insertions encoded by plasmid DNA donor templates. Improved editing was achieved with both transfected plasmid-encoded Cas9 constructs as well as recombinant Cas9 protein transfected as ribonucleoprotein complexes. Our strategy was highly efficient in restoring a genetic defect in a cell line, exemplifying the possible implementation of our strategy in gene therapy. These constructs provide a simple approach to improve directed editing.
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Affiliation(s)
- Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Julia Adler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Karin Broennimann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Nadav Myers
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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Abstract
RNA samples prepared using monophasic lysis reagents may contain small amounts of contaminating genomic DNA, which must be removed if the RNA will be used in subsequent analyses such as reverse transcriptase-polymerase chain reaction (RT-PCR) or quantitative real-time RT-PCR. In addition, the presence of contaminating DNA can render the quantitative determination of RNA in a sample inaccurate. The most common and effective method for removing trace to moderate amounts of DNA contamination from RNA samples is digestion with DNase I, as described here.
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Abstract
G-quadruplexes are four-stranded guanine-rich structures that have been demonstrated to occur across the genome in humans and other organisms. They provide regulatory functions during transcription, translation and immunoglobulin gene rearrangement, but there is also a large amount of evidence that they can present a potent barrier to the DNA replication machinery. This mini-review will summarize recent advances in understanding the many strategies nature has evolved to overcome G-quadruplex-mediated replication blockage, including removal of the structure by helicases or nucleases, or circumventing the deleterious effects on the genome through homologous recombination, alternative end-joining or synthesis re-priming. Paradoxically, G-quadruplexes have also recently been demonstrated to provide a positive role in stimulating the initiation of DNA replication. These recent studies have not only illuminated the many roles and consequences of G-quadruplexes, but have also provided fundamental insights into the general mechanisms of DNA replication and its links with genetic and epigenetic stability.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia.
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Sharma P, Garg N, Sharma A, Capalash N, Singh R. Nucleases of bacterial pathogens as virulence factors, therapeutic targets and diagnostic markers. Int J Med Microbiol 2019; 309:151354. [PMID: 31495663 DOI: 10.1016/j.ijmm.2019.151354] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/12/2019] [Accepted: 08/29/2019] [Indexed: 12/25/2022] Open
Abstract
New frontiers of therapy are being explored against the upcoming bacterial diseases rendered untreatable due to multiple, extreme and pan- antibiotic resistance. Nucleases are ubiquitous in bacterial pathogens performing various functions like acquiring nucleotide nutrients, allowing or preventing uptake of foreign DNA, controlling biofilm formation/dispersal/architecture, invading host by tissue damage, evading immune defence by degrading DNA matrix of neutrophil extracellular traps (NETs) and immunomodulating the host immune response. Secretory nucleases also provide means of survival to other bacteria like iron-reducing Shewanella and such functions help them adapt and survive proficiently. Other than their pro-pathogen roles in survival, nucleases can be used directly as therapeutics. One of the powerful armours of pathogens is the formation of biofilms, thus helping them resist and persist in the harshest of environments. As eDNA forms the structural and binding component of biofilm, nucleases can be used against the adhering component, thus increasing the permeability of antimicrobial agents. Nucleases have recently become a model system of intense study for their biological functions and medical applications in diagnosis, immunoprophylaxis and therapy. Rational implications of these enzymes can impact human medicine positively in future by opening new ways for therapeutics which have otherwise reached saturation due to multi drug resistance.
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Affiliation(s)
- Prince Sharma
- Department of Microbiology, Panjab University, Chandigarh, India.
| | - Nisha Garg
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Anshul Sharma
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Ravinder Singh
- Department of Microbiology, Panjab University, Chandigarh, India
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Pandith A, Kim HY, Shin T, Seo YJ. Unprecedented green-emissive boranyl-hydrazone supramolecular assemblies and their in vitro diagnostic applications. J Photochem Photobiol B 2019; 197:111553. [PMID: 31326845 DOI: 10.1016/j.jphotobiol.2019.111553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/29/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
This paper describes a novel symmetric N,N'-diethylsalicylaldehyde boranyl hydrazone (1) and its in situ-generated assemblies displaying opto-analytical capabilities for the diagnosis of nucleic acids under physiological conditions. The sensing capabilities of these unprecedented supramolecular assemblies were characterized using UV-Vis spectroscopy, fluorescence spectroscopy, 1D and 2D NMR spectroscopy, dynamic light scattering, and zeta potential measurements. Model compounds lacking boranyl units (2, 3) were prepared to correlate and evaluate the sensing mechanism. The rationally designed probe 1 displays unusual aggregation-induced emissive (AIE) properties, with an average particle size of 1096 nm exhibiting green emission upon excitation at 377 nm in pH-7.2 TRIZMA buffer. A selective switch on response toward organic PO43- accompanied through specific nano-aggregations patterns and sizes, thereby causing a significant red-shift through AIE. Exploiting such switch on in green channel behavior has allowed the monitoring of DNase I activities and polymerase chain reactions.
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Affiliation(s)
- Anup Pandith
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Hye-Yeon Kim
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Taeho Shin
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Young Jun Seo
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea; Department of Bioactive Materials, Chonbuk National University, Jeonju 54398, Republic of Korea.
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Shimbo T, Kawamura M, Wijaya E, Takaki E, Kaneda Y, Tamai K. Cut-C: cleavage under tethered nuclease for conformational capture. BMC Genomics 2019; 20:614. [PMID: 31357933 PMCID: PMC6664727 DOI: 10.1186/s12864-019-5989-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Deciphering the 3D structure of the genome is essential for elucidating the regulatory mechanisms of gene expression in detail. Existing methods, such as chromosome conformation capture (3C) and Hi-C have enabled the identification of novel aspects of chromatin structure. Further identification of protein-centric chromatin conformation is enabled by coupling the Hi-C procedure with a conventional chromatin immunoprecipitation assay. However, these methods are time-consuming and require independent methods for validation. RESULTS To simultaneously identify protein-centric chromatin conformation and target protein localization, we have developed Cut-C, a method that combines antibody-mediated cleavage by tethered nuclease with chromosome conformation capture to identify chromatin interactions mediated by a protein of interest. Applying Cut-C to H3K4me3, a histone modification enriched at active gene promoters, we have successfully identified chromatin loops mediated by H3K4me3 along with the genome-wide distribution of H3K4me3. Cut-C also identified chromatin loops mediated by CTCF, validating the general applicability of the method. CONCLUSIONS Cut-C identifies protein-centric chromatin conformations along with the genome-wide distribution of target proteins using simple procedures. The simplified protocol will improve the efficiency of analysing chromatin conformation using precious materials, such as clinical samples.
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Affiliation(s)
- Takashi Shimbo
- Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, Suita, Osaka, 5650871 Japan
| | - Machika Kawamura
- Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, Suita, Osaka, 5650871 Japan
- StemRIM Co., Ltd., Ibaraki, Osaka, 5670085 Japan
| | - Edward Wijaya
- Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, Suita, Osaka, 5650871 Japan
- StemRIM Co., Ltd., Ibaraki, Osaka, 5670085 Japan
| | - Eiichi Takaki
- Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, Suita, Osaka, 5650871 Japan
- StemRIM Co., Ltd., Ibaraki, Osaka, 5670085 Japan
| | - Yasufumi Kaneda
- Division of Gene Therapy Science, Graduate School of Medicine, Osaka University, Suita, Osaka, 5650871 Japan
| | - Katsuto Tamai
- Department of Stem Cell Therapy Science, Graduate School of Medicine, Osaka University, Suita, Osaka, 5650871 Japan
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Wang Y, Zhao Y, Sarkar A, Wang X. Optical sensor revealed abnormal nuclease spatial activity on cancer cell membrane. J Biophotonics 2019; 12:e201800351. [PMID: 30488667 PMCID: PMC6550314 DOI: 10.1002/jbio.201800351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/11/2018] [Accepted: 11/21/2018] [Indexed: 05/22/2023]
Abstract
Nucleases are important enzymes that cleave nucleic acids and play critical roles in DNA repair, immune defense and potentially in cancer invasion. However, their spatial dynamics at subcellular level is much less studied. Here, we developed a surface-tethered nuclease sensor (SNS) which directly converts membrane-bound nuclease (MN) activity to fluorescent signal, therefore, mapping MN activity on cell adhesion sites with high resolution and sensitivity. With SNS, we studied MN activity on the ventral membrane of cancer cells, where MN activity initially occurs in punctate regions and advances in a coral-shaped pattern. In six tested cell-lines, the MN activity levels in cancer cells are significantly higher than those in non-cancer cells. We then tested SNS as a sensitive approach to detect cancer cells at single cell level. Single breast cancer cells were successfully detected from thousands of adherent non-cancer cells and from millions of non-adherent blood cells.
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Affiliation(s)
- Yongliang Wang
- Department of Physics and AstronomyIowa State UniversityAmesIowa
| | - Yuanchang Zhao
- Department of Physics and AstronomyIowa State UniversityAmesIowa
| | - Anwesha Sarkar
- Department of Physics and AstronomyIowa State UniversityAmesIowa
| | - Xuefeng Wang
- Department of Physics and AstronomyIowa State UniversityAmesIowa
- Molecular, Cellular, and Developmental Biology Interdepartmental ProgramMolecular Biology BuildingAmesIowa
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Paska C, Barta I, Drozdovszky O, Antus B. Elimination of bacterial DNA during RNA isolation from sputum: Bashing bead vortexing is preferable over prolonged DNase treatment. PLoS One 2019; 14:e0214609. [PMID: 30921416 PMCID: PMC6438495 DOI: 10.1371/journal.pone.0214609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/17/2019] [Indexed: 11/18/2022] Open
Abstract
Sputum often contains large amounts of contaminating bacterial DNA that, if not eliminated during RNA isolation, may interfere with gene expression studies. During RNA isolation only repeated DNase treatment can effectively remove contaminating bacterial DNA from samples, but this compromises RNA quality. In this study we tested alternative methods to facilitate the removal of DNA and improve the quality of RNA obtained. Sputum samples obtained from patients with chronic obstructive pulmonary disease were processed with dithiothreitol and subjected to various RNA isolation methods, yet with modified protocols. Modifications included prolonged DNase treatment or vortexing of sputum cells in the presence of beads prior to RNA isolation. Bacterial DNA contamination was tested by PCR using universal bacterial primers, while RNA quality was assessed by real-time PCR using GAPDH primers for amplicons of different length. We found that the RNeasy Plus Mini kit equipped with the gDNA eliminator spin column was able to completely eliminate bacterial DNA, if sputum cells were lysed in the presence of bashing beads. Notably, compared with the standard protocol, the modified procedure yielded better quality RNA as well, as indicated by improved threshold profiles of qPCR. Bead vortexing of cells was less effective when combined with other RNA isolation methods, and the repeated DNase treatment needed to completely remove contaminating DNA from the samples reduced the quality of RNA markedly. Bead vortexing in combination with certain RNA extraction methods greatly facilitates the isolation of sputum RNA that is free of contaminating bacterial DNA, and is suitable for downstream applications.
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Affiliation(s)
- Csilla Paska
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Imre Barta
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Orsolya Drozdovszky
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Balazs Antus
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Pulmonology, National Koranyi Institute of Pulmonology, Budapest, Hungary
- * E-mail:
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