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Zhang W, Miller CA, Wilson MJ. Assessment of the In Vitro Phosphatidylinositol Glycan Class A (PIG-A) Gene Mutation Assay Using Human TK6 and Mouse Hepa1c1c7 Cell Lines. J Xenobiot 2024; 14:1293-1311. [PMID: 39311152 PMCID: PMC11417843 DOI: 10.3390/jox14030073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 09/08/2024] [Accepted: 09/13/2024] [Indexed: 09/26/2024] Open
Abstract
Gene mutations linked to diseases like cancer may be caused by exposure to environmental chemicals. The X-linked phosphatidylinositol glycan class A (PIG-A) gene, required for glycosylphosphatidylinositol (GPI) anchor biosynthesis, is a key target locus for in vitro genetic toxicity assays. Various organisms and cell lines may respond differently to genotoxic agents. Here, we compared the mutagenic potential of directly genotoxic ethyl methane sulfonate (EMS) to metabolically activated pro-mutagenic polycyclic aromatic hydrocarbons (PAHs). The two classes of mutagens were compared in an in vitro PIG-A gene mutation test using the metabolically active murine hepatoma Hepa1c1c7 cell line and the human TK6 cell line, which has limited metabolic capability. Determination of cell viability is required for quantifying mutagenicity. Two common cell viability tests, the MTT assay and propidium iodide (PI) staining measured by flow cytometry, were evaluated. The MTT assay overestimated cell viability in adherent cells at high benzo[a]pyrene (B[a]P) exposure concentrations, so PI-based cytotoxicity was used in calculations. The spontaneous mutation rates for TK6 and Hepa1c1c7 cells were 1.87 and 1.57 per million cells per cell cycle, respectively. TK6 cells exposed to 600 µM and 800 µM EMS showed significantly higher mutation frequencies (36 and 47 per million cells per cell cycle, respectively). Exposure to the pro-mutagen benzo[a]pyrene (B[a]P, 10 µM) did not increase mutation frequency in TK6 cells. In Hepa1c1c7 cells, mutation frequencies varied across exposure groups (50, 50, 29, and 81 per million cells per cell cycle when exposed to 10 µM B[a]P, 5-methylcholanthrene (5-MC), chrysene, or 16,000 µM EMS, respectively). We demonstrate that the choice of cytotoxicity assay and cell line can determine the outcome of the Pig-A mutagenesis assay when assessing a specific mutagen.
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Affiliation(s)
- Wenhao Zhang
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; (C.A.M.); (M.J.W.)
| | - Charles A. Miller
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; (C.A.M.); (M.J.W.)
| | - Mark J. Wilson
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; (C.A.M.); (M.J.W.)
- Chemical Insights Research Institute of Underwriters Laboratories Research Institutes, Marietta, GA 30067, USA
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2
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Tutanov O, Shefer A, Shefer E, Ruzankin P, Tsentalovich Y, Tamkovich S. DNA-Binding Proteins and Passenger Proteins in Plasma DNA-Protein Complexes: Imprint of Parental Cells or Key Mediators of Carcinogenesis Processes? Int J Mol Sci 2024; 25:5165. [PMID: 38791202 PMCID: PMC11121045 DOI: 10.3390/ijms25105165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Knowledge of the composition of proteins that interact with plasma DNA will provide a better understanding of the homeostasis of circulating nucleic acids and the various modes of interaction with target cells, which may be useful in the development of gene targeted therapy approaches. The goal of the present study is to shed light on the composition and architecture of histone-containing nucleoprotein complexes (NPCs) from the blood plasma of healthy females (HFs) and breast cancer patients (BCPs) and to explore the relationship of proteins with crucial steps of tumor progression: epithelial-mesenchymal transition (EMT), cell proliferation, invasion, cell migration, stimulation of angiogenesis, and immune response. MALDI-TOF mass spectrometric analysis of NPCs isolated from blood samples using affine chromatography was performed. Bioinformatics analysis showed that the shares of DNA-binding proteins in the compositions of NPCs in normal and cancer patients are comparable and amount to 40% and 33%, respectively; in total, we identified 38 types of DNA-binding motifs. Functional enrichment analysis using FunRich 3.13 showed that, in BCP blood, the share of DNA-binding proteins involved in nucleic acid metabolism increased, while the proportion of proteins involved in intercellular communication and signal transduction decreased. The representation of NPC passenger proteins in breast cancer also changes: the proportion of proteins involved in transport increases and the share of proteins involved in energy biological pathways decreases. Moreover, in the HF blood, proteins involved in the processes of apoptosis were more represented in the composition of NPCs and in the BCP blood-in the processes of active secretion. For the first time, bioinformatics approaches were used to visualize the architecture of circulating NPCs in the blood and to show that breast cancer has an increased representation of passenger proteins involved in EMT, cell proliferation, invasion, cell migration, and immune response. Using breast cancer protein data from the Human Protein Atlas (HPA) and DEPC, we found that 86% of NPC proteins in the blood of BCPs were not previously annotated in these databases. The obtained data may indirectly indicate directed protein sorting in NPCs, which, along with extracellular vesicles, can not only be diagnostically significant molecules for liquid biopsy, but can also carry out the directed transfer of genetic material from donor cells to recipient cells.
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Affiliation(s)
- Oleg Tutanov
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA;
| | - Aleksei Shefer
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Evgenii Shefer
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Laboratory of Applied Inverse Problems, Sobolev Institute of Mathematics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Pavel Ruzankin
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Laboratory of Applied Inverse Problems, Sobolev Institute of Mathematics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Yuri Tsentalovich
- Laboratory of Proteomics and Metabolomics, International Tomography Center, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Svetlana Tamkovich
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Novosibirsk State University, 630090 Novosibirsk, Russia
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3
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De La Cruz-Sigüenza DA, Reyes-Grajeda JP, Velasco-Velázquez MA, Trejo-Becerril C, Pérez-Cárdenas E, Chávez-Blanco A, Taja-Chayeb L, Domínguez-Gómez G, Ramos-Godinez MP, González-Fierro A, Dueñas-González A. The non-vesicle cell-free DNA (cfDNA) induces cell transformation associated with horizontal DNA transfer. Mol Biol Rep 2024; 51:174. [PMID: 38252353 PMCID: PMC10803523 DOI: 10.1007/s11033-023-09016-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/25/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Cell-free DNA (cfDNA) is a source for liquid biopsy used for cancer diagnosis, therapy selection, and disease monitoring due to its non-invasive nature and ease of extraction. However, cfDNA also participates in cancer development and progression by horizontal transfer. In humans, cfDNA circulates complexed with extracellular vesicles (EV) and macromolecular complexes such as nucleosomes, lipids, and serum proteins. The present study aimed to demonstrate whether cfDNA not associated with EV induces cell transformation and tumorigenesis. METHODS Supernatant of the SW480 human colon cancer cell line was processed by ultracentrifugation to obtain a soluble fraction (SF) and a fraction associated with EV (EVF). Primary murine embryonic fibroblast cells (NIH3T3) underwent passive transfection with these fractions, and cell proliferation, cell cycle, apoptosis, cell transformation, and tumorigenic assays were performed. Next, cfDNA was analyzed by electronic microscopy, and horizontal transfer was assessed by human mutant KRAS in recipient cells via PCR and recipient cell internalization via fluorescence microscopy. RESULTS The results showed that the SF but not the EVF of cfDNA induced proliferative and antiapoptotic effects, cell transformation, and tumorigenesis in nude mice, which were reduced by digestion with DNAse I and proteinase K. These effects were associated with horizontal DNA transfer and cfDNA internalization into recipient cells. CONCLUSIONS The results suggest pro-tumorigenic effects of cfDNA in the SF that can be offset by enzyme treatment. Further exploration of the horizontal tumor progression phenomenon mediated by cfDNA is needed to determine whether its manipulation may play a role in cancer therapy.
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Affiliation(s)
- D A De La Cruz-Sigüenza
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - J P Reyes-Grajeda
- Protein Structure Laboratory, Instituto Nacional de Medicina Genomica (INMEGEN), Tlalpan, 14610, Mexico City, Mexico
| | - M A Velasco-Velázquez
- Department of Pharmacology, Faculty of Medicine, Universidad Nacional Autónoma de México (UNAM), Coyoacan, 04510, Mexico City, Mexico
| | - C Trejo-Becerril
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - E Pérez-Cárdenas
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - A Chávez-Blanco
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - L Taja-Chayeb
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - G Domínguez-Gómez
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - M P Ramos-Godinez
- Department of Pathology, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - A González-Fierro
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - A Dueñas-González
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico.
- Department of Genomic Medicine and Environmental Toxicology, Institute of Biomedical Research, Universidad Nacional Autonoma de Mexico (UNAM), Av. Universidad 3004, Copilco Universidad, Coyoacan, 04510, Mexico City, Mexico.
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4
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Singh J, Boettcher M, Dölling M, Heuer A, Hohberger B, Leppkes M, Naschberger E, Schapher M, Schauer C, Schoen J, Stürzl M, Vitkov L, Wang H, Zlatar L, Schett GA, Pisetsky DS, Liu ML, Herrmann M, Knopf J. Moonlighting chromatin: when DNA escapes nuclear control. Cell Death Differ 2023; 30:861-875. [PMID: 36755071 PMCID: PMC9907214 DOI: 10.1038/s41418-023-01124-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/05/2022] [Accepted: 09/12/2022] [Indexed: 02/10/2023] Open
Abstract
Extracellular chromatin, for example in the form of neutrophil extracellular traps (NETs), is an important element that propels the pathological progression of a plethora of diseases. DNA drives the interferon system, serves as autoantigen, and forms the extracellular scaffold for proteins of the innate immune system. An insufficient clearance of extruded chromatin after the release of DNA from the nucleus into the extracellular milieu can perform a secret task of moonlighting in immune-inflammatory and occlusive disorders. Here, we discuss (I) the cellular events involved in the extracellular release of chromatin and NET formation, (II) the devastating consequence of a dysregulated NET formation, and (III) the imbalance between NET formation and clearance. We include the role of NET formation in the occlusion of vessels and ducts, in lung disease, in autoimmune diseases, in chronic oral disorders, in cancer, in the formation of adhesions, and in traumatic spinal cord injury. To develop effective therapies, it is of utmost importance to target pathways that cause decondensation of chromatin during exaggerated NET formation and aggregation. Alternatively, therapies that support the clearance of extracellular chromatin are conceivable.
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Affiliation(s)
- Jeeshan Singh
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Michael Boettcher
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Maximilian Dölling
- Department of Surgery, University Hospital Magdeburg, Magdeburg, Germany
| | - Annika Heuer
- Division of Spine Surgery, Department of Trauma and Orthopedic Surgery, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Mildred-Scheel Cancer Career Center Hamburg HaTriCS4, University Cancer Center Hamburg, Hamburg, Germany
| | - Bettina Hohberger
- Department of Ophthalmology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Moritz Leppkes
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Department of Internal Medicine 1, Gastroenterology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Elisabeth Naschberger
- Division of Molecular and Experimental Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universtität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Mirco Schapher
- Department of Otorhinolaryngology, Head and Neck Surgery, Friedrich-Alexander University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, Paracelsus University, Nürnberg, Germany
| | - Christine Schauer
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Janina Schoen
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander Universtität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Ljubomir Vitkov
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, Homburg, Germany
- Department of Environment & Biodiversity, University of Salzburg, Salzburg, 5020, Austria
- Department of Dental Pathology, University of East Sarajevo, East Sarajevo, Republic of Srpska, Bosnia and Herzegovina
| | - Han Wang
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Leticija Zlatar
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Georg A Schett
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - David S Pisetsky
- Department of Medicine and Immunology and Medical Research Service, Duke University Medical Center and Veterans Administration Medical Center, Durham, NC, USA
| | - Ming-Lin Liu
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Corporal Michael J. Crescenz VAMC, Philadelphia, PA, 19104, USA
| | - Martin Herrmann
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany.
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany.
| | - Jasmin Knopf
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
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5
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He J, Gao X, Huang H, Hao J. Proposal and Verification of the Theory of Layer-by-Layer Elimination of Biofilm in Listeria monocytogenes. Foods 2023; 12:foods12071361. [PMID: 37048183 PMCID: PMC10093742 DOI: 10.3390/foods12071361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Biofilms are microbial communities that represent a high abundance of microbial life forms on Earth. Within biofilms, structural changes during clearance processes occur in three spatial and temporal dimensions; therefore, microscopy and quantitative image analysis are essential in elucidating their function. Here, we present confocal laser scanning microscopy (CLSM) in conjunction with ISA-2 software analysis for the automated and high-throughput quantification, analysis, and visualisation of biofilm interiors and overall biofilm properties in three spatial and temporal dimensions. This paper discusses the removal process of Listeria monocytogenes (LM) biofilms using slightly acidic electrolytic water, non-electrolytic hypochlorite water, and alternating the use of strongly acidic and strongly alkaline electrolytic water. The results show that the biofilm gradually thins and gutters from the initial viscous dense and thick morphology under the action of either biocide. This process is consistent with first-level kinetics. After CLSM filming to observe the biofilm structure, analysis software was used to process and quantify the biovolume, average biofilm thickness, biofilm roughness and other indicators; fluorescence enzyme markers were used to verify the remaining amount of extracellular nucleic acid. In this study, we proposed and validated the theory of layer-by-layer elimination of LM biofilm.
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Affiliation(s)
- Jialin He
- College of Food Science and Biology, Hebei University of Science and Technology, No. 26 Yuxiang Street, Shijiazhuang 050018, China
| | - Xiangyu Gao
- College of Food Science and Biology, Hebei University of Science and Technology, No. 26 Yuxiang Street, Shijiazhuang 050018, China
| | - Hanbing Huang
- College of Food Science and Biology, Hebei University of Science and Technology, No. 26 Yuxiang Street, Shijiazhuang 050018, China
| | - Jianxiong Hao
- College of Food Science and Biology, Hebei University of Science and Technology, No. 26 Yuxiang Street, Shijiazhuang 050018, China
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6
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Wang H, Stehr AM, Singh J, Zlatar L, Hartmann A, Evert K, Naschberger E, von Stillfried S, Boor P, Muñoz LE, Knopf J, Stürzl M, Herrmann M. Anti-DNA-IgM Favors the Detection of NET-Associated Extracellular DNA. Int J Mol Sci 2023; 24:ijms24044101. [PMID: 36835515 PMCID: PMC9958910 DOI: 10.3390/ijms24044101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/25/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
During inflammatory responses, neutrophils enter the sites of attack where they execute various defense mechanisms. They (I) phagocytose microorganisms, (II) degranulate to release cytokines, (III) recruit various immune cells by cell-type specific chemokines, (IV) secrete anti-microbials including lactoferrin, lysozyme, defensins and reactive oxygen species, and (V) release DNA as neutrophil extracellular traps (NETs). The latter originates from mitochondria as well as from decondensed nuclei. This is easily detected in cultured cells by staining of DNA with specific dyes. However, in tissues sections the very high fluorescence signals emitted from the condensed nuclear DNA hamper the detection of the widespread, extranuclear DNA of the NETs. In contrast, when we employ anti-DNA-IgM antibodies, they are unable to penetrate deep into the tightly packed DNA of the nucleus, and we observe a robust signal for the extended DNA patches of the NETs. To validate anti-DNA-IgM, we additionally stained the sections for the NET-markers histone H2B, myeloperoxidase, citrullinated histone H3, and neutrophil elastase. Altogether, we have described a fast one-step procedure for the detection of NETs in tissue sections, which provides new perspectives to characterize neutrophil-associated immune reactions in disease.
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Affiliation(s)
- Han Wang
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Antonia Margarethe Stehr
- Division of Molecular and Experimental Surgery, Friedrich-Alexander Universtität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Jeeshan Singh
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Leticija Zlatar
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Arndt Hartmann
- Institut für Pathologie, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Katja Evert
- Institut für Pathologie, Universität Regensburg, 93053 Regensburg, Germany
| | - Elisabeth Naschberger
- Division of Molecular and Experimental Surgery, Friedrich-Alexander Universtität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | | | - Peter Boor
- Institute of Pathology, University Clinic of the RWTH Aachen, 52074 Aachen, Germany
| | - Luis E. Muñoz
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Jasmin Knopf
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Friedrich-Alexander Universtität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Martin Herrmann
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Correspondence:
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7
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Schoen J, Euler M, Schauer C, Schett G, Herrmann M, Knopf J, Yaykasli KO. Neutrophils' Extracellular Trap Mechanisms: From Physiology to Pathology. Int J Mol Sci 2022; 23:12855. [PMID: 36361646 PMCID: PMC9653572 DOI: 10.3390/ijms232112855] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 07/30/2023] Open
Abstract
Neutrophils are an essential part of the innate immune system and the first line of defense against invading pathogens. They phagocytose, release granular contents, produce reactive oxygen species, and form neutrophil extracellular traps (NETs) to fight pathogens. With the characterization of NETs and their components, neutrophils were identified as players of the innate adaptive crosstalk. This has placed NETs at the center not only of physiological but also pathological processes. Aside from their role in pathogen uptake and clearance, NETs have been demonstrated to contribute to the resolution of inflammation by forming aggregated NETs able to degrade inflammatory mediators. On the other hand, NETs have the potential to foster severe pathological conditions. When homeostasis is disrupted, they occlude vessels and ducts, serve as sources of autoantigens and danger or damage associated molecular patterns, directly damage tissues, and exaggerate complement activity and inflammation. This review focusses on the understanding of NETs from their formation to their functions in both physiological and pathological processes.
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Affiliation(s)
- Janina Schoen
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Maximilien Euler
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Christine Schauer
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Georg Schett
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Martin Herrmann
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Jasmin Knopf
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Kursat Oguz Yaykasli
- Department of Internal Medicine 3—Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
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8
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Mizuno Y, Shibata S, Miyagaki T, Ito Y, Taira H, Omori I, Hisamoto T, Oka K, Matsuda KM, Boki H, Takahashi-Shishido N, Sugaya M, Sato S. Serum cell-free DNA as a new biomarker in cutaneous T-cell lymphoma. J Dermatol 2022; 49:1124-1130. [PMID: 35821652 DOI: 10.1111/1346-8138.16520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/26/2022]
Abstract
In recent years, circulating cell-free DNA (cfDNA) has received a great attention as a biomarker for various cancers. Many reports have shown that serum cfDNA levels are elevated in cancer patients and their levels correlate with prognosis and disease activity. The aim of this study was to measure serum cfDNA levels in patients with cutaneous T-cell lymphoma (CTCL) and to evaluate their correlations with hematological and clinical findings. Serum cfDNA levels in CTCL patients were significantly higher than those in healthy controls, and their levels gradually increased with the progression of the disease stage. Positive correlations were detected between serum cfDNA levels and those of lactate dehydrogenase, thymus and activation-regulated chemokine and soluble IL-2 receptor as well as neutrophil and eosinophil count in peripheral blood and neutrophil-to-lymphocyte ratio. Furthermore, CTCL patients with higher serum cfDNA levels exhibited a significantly worse prognosis. Taken together, these results suggest the potential of cfDNA as a new biomarker reflecting prognosis and disease activity in CTCL. CfDNA levels may serve as an indicator for considering the intensity and timing of subsequent therapeutic intervention.
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Affiliation(s)
- Yuka Mizuno
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Sayaka Shibata
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Tomomitsu Miyagaki
- Department of Dermatology, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Yukiko Ito
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Haruka Taira
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Issei Omori
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Teruyoshi Hisamoto
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Kenta Oka
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Kazuki M Matsuda
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Hikari Boki
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | | | - Makoto Sugaya
- Department of Dermatology, International University of Health and Welfare, Chiba, Japan
| | - Shinichi Sato
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
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9
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Tutanov O, Tamkovich S. The Influence of Proteins on Fate and Biological Role of Circulating DNA. Int J Mol Sci 2022; 23:7224. [PMID: 35806228 PMCID: PMC9266439 DOI: 10.3390/ijms23137224] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Circulating DNA has already proven itself as a valuable tool in translational medicine. However, one of the overlooked areas of circulating DNA research is its association with different proteins, despite considerable evidence that this association might impact DNA's fate in circulation and its biological role. In this review, we attempt to shed light on current ideas about circulating DNA origins and forms of circulation, known biological effects, and the clinical potential of circulating tumor deoxyribonucleoprotein complexes.
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Affiliation(s)
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
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10
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Tutanov O, Shtam T, Grigor’eva A, Tupikin A, Tsentalovich Y, Tamkovich S. Blood Plasma Exosomes Contain Circulating DNA in Their Crown. Diagnostics (Basel) 2022; 12:diagnostics12040854. [PMID: 35453902 PMCID: PMC9027845 DOI: 10.3390/diagnostics12040854] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 01/13/2023] Open
Abstract
It is known that circulating DNA (cirDNA) is protected from nuclease activity by proteins that form macromolecular complexes with DNA. In addition, it was previously shown that cirDNA can bind to the outer surface of exosomes. NTA analysis and real-time PCR show that exosomes from healthy females (HF) or breast cancer patients (BCP) plasma contain less than 1.4 × 10−8 pg of DNA. Thus, only a minor part of cirDNA is attached to the outer side of the exosome as part of the vesicle crown: the share of exosomal DNA does not exceed 0.025% HF plasma DNA and 0.004% BCP plasma DNA. Treatment of plasma exosomes with DNase I with subsequent dot immunoassay reveals that H2a, H2b, and H3 histones are not part of the exosomal membrane, but are part of the cirDNA–protein macromolecular complex associated with the surface of the exosome either through interaction with DNA-binding proteins or with histone-binding proteins. Using bioinformatics approaches after identification by MALDI-TOF mass spectrometry, 16 exosomal DNA-binding proteins were identified. It was shown that four proteins—AIFM1, IGHM, CHD5, and KCNIP3—are candidates for DNA binding on the outer membrane of exosomes; the crown of exosomes may include five DNA-binding proteins: H2a, H2b, H3, IGHM, and ALB. Of note, AIFM1, IGHM, and CHD5 proteins are found only in HF plasma exosomes; KCNIP3 protein is identified only in BCP plasma exosomes; and H2a, H2b, H3, and ALB are revealed in all samples of plasma exosomes. Two histone-binding proteins, CHD5 and KDM6B, have been found in exosomes from HF plasma. The data obtained indicate that cirDNA preferentially binds to the outer membrane of exosomes by association with DNA-binding proteins.
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Affiliation(s)
- Oleg Tutanov
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Tatiana Shtam
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia;
| | - Alina Grigor’eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.G.); (A.T.)
| | - Alexey Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.G.); (A.T.)
| | - Yuri Tsentalovich
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
- Correspondence:
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11
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Ershova ES, Shmarina GV, Porokhovnik LN, Zakharova NV, Kostyuk GP, Umriukhin PE, Kutsev SI, Sergeeva VA, Veiko NN, Kostyuk SV. In Vitro Analysis of Biological Activity of Circulating Cell-Free DNA Isolated from Blood Plasma of Schizophrenic Patients and Healthy Controls. Genes (Basel) 2022; 13:genes13030551. [PMID: 35328103 PMCID: PMC8955124 DOI: 10.3390/genes13030551] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/09/2022] [Accepted: 03/17/2022] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia is associated with low-grade systemic inflammation. Circulating cell-free DNA (c-cfDNA) belongs to the DAMP class. The major research question was: can the c-cfDNA of schizophrenic patients (sz-cfDNA) stimulate the DNA sensor genes, which control the innate immunity? We investigated the in vitro response of ten human skin fibroblast (HSF) lines to five DNA probes containing different amounts of a GC-rich marker (the ribosomal repeat) and a DNA oxidation marker (8-oxodG) including sz-cfDNA and healthy control c-cfDNA (hc-cfDNA) probes. After 1 h, 3 h, and 24 h of incubation, the expression of 6 protein genes responsible for cfDNA transport into the cell (EEA1 and HMGB1) and the recognition of cytosolic DNA (TLR9, AIM2, STING and RIG-I) was analyzed at the transcriptional (RT-qPCR) and protein level (flow cytometry and fluorescence microscopy). Additionally, we analyzed changes in the RNA amount of 32 genes (RT-qPCR), which had been previously associated with different cellular responses to cell-free DNA with different characteristics. Adding sz-cfDNA and hc-cfDNA to the HSF medium in equal amounts (50 ng/mL) blocked endocytosis and stimulated TLR9 and STING gene expression while blocking RIG-I and AIM2 expression. Sz-cfDNA and hc-cfDNA, compared to gDNA, demonstrated much stronger stimulated transcription of genes that control cell proliferation, cytokine synthesis, apoptosis, autophagy, and mitochondrial biogenesis. No significant difference was observed in the response of the cells to sz-cfDNA and hc-cfDNA. Sz-cfDNA and hc-cfDNA showed similarly high biological activity towards HSFs, stimulating the gene activity of TLR9 and STING DNA sensor proteins and blocking the activity of the AIM2 protein gene. Since the sz-cfDNA content in the patients’ blood is several times higher than the hc-cfDNA content, sz-cfDNA may upregulate pro-inflammatory cytokines in schizophrenia.
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Affiliation(s)
- Elizaveta S. Ershova
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Galina V. Shmarina
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Lev N. Porokhovnik
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
- Correspondence:
| | - Natalia V. Zakharova
- N.A. Alekseev Clinical Psychiatric Hospital No. 1, 117152 Moscow, Russia; (N.V.Z.); (G.P.K.)
| | - George P. Kostyuk
- N.A. Alekseev Clinical Psychiatric Hospital No. 1, 117152 Moscow, Russia; (N.V.Z.); (G.P.K.)
| | - Pavel E. Umriukhin
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
- Department of Physiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Sergey I. Kutsev
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Vasilina A. Sergeeva
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Natalia N. Veiko
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Svetlana V. Kostyuk
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
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