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Wang WC, Hou TC, Kuo CY, Lai YC. Amplifications of EVX2 and HOXD9-HOXD13 on 2q31 in mature cystic teratomas of the ovary identified by array comparative genomic hybridization may explain teratoma characteristics in chondrogenesis and osteogenesis. J Ovarian Res 2024; 17:129. [PMID: 38907278 PMCID: PMC11193297 DOI: 10.1186/s13048-024-01458-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/16/2024] [Indexed: 06/23/2024] Open
Abstract
BACKGROUND Teratomas are a common type of germ cell tumor. However, only a few reports on their genomic constitution have been published. The study of teratomas may provide a better understanding of their stepwise differentiation processes and molecular bases, which could prove useful for the development of tissue-engineering technologies. METHODS In the present study, we analyzed the copy number aberrations of nine ovarian mature cystic teratomas using array comparative genomic hybridization in an attempt to reveal their genomic aberrations. RESULTS The many chromosomal aberrations observed on array comparative genomic hybridization analysis reveal the complex genetics of this tumor. Amplifications and deletions of large DNA fragments were observed in some samples, while amplifications of EVX2 and HOXD9-HOXD13 on 2q31.1, NDUFV1 on 11q13.2, and RPL10, SNORA70, DNASE1L1, TAZ, ATP6AP1, and GDI1 on Xq28 were found in all nine mature cystic teratomas. CONCLUSIONS Our results indicated that amplifications of these genes may play an important etiological role in teratoma formation. Moreover, amplifications of EVX2 and HOXD9-HOXD13 on 2q31.1, found on array comparative genomic hybridization, may help to explain the characteristics of teratomas in chondrogenesis and osteogenesis.
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Affiliation(s)
- Wen-Chung Wang
- Department of Obstetrics and Gynecology, Jen-Ai Hospital, Taichung, Taiwan
| | - Tai-Cheng Hou
- Department of Pathology, Jen-Ai Hospital, Taichung, Taiwan
| | - Chen-Yun Kuo
- Department of Pathology, Jen-Ai Hospital, Taichung, Taiwan
| | - Yen-Chein Lai
- Department of Medical Laboratory and Biotechnology, Chung Shan Medical University, No.110, Sec. 1, Chien Kuo N. Road, Taichung, 402, Taiwan, R.O.C..
- Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan.
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2
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Yu T, Sun Z, Cao X, Yang F, Pang Q, Deng H. Identification and characterization of TatD DNase in planarian Dugesia japonica and its antibiofilm effect. ENVIRONMENTAL RESEARCH 2024; 251:118534. [PMID: 38395336 DOI: 10.1016/j.envres.2024.118534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
TatD DNase, a key enzyme in vertebrates and invertebrates, plays a pivotal role in various physiological processes. Dugesia japonica (D. japonica), a flatworm species, has remarkable regenerative capabilities and possesses a simplified immune system. However, the existence and biological functions of TatD DNase in D. japonica require further investigation. Here, we obtained the open reading frame (ORF) of DjTatD and demonstrated its conservation. The three-dimensional structure of DjTatD revealed its active site and binding mechanism. To investigate its enzymological properties, we overexpressed, purified, and characterized recombinant DjTatD (rDjTatD). We observed that DjTatD was primarily expressed in the pharynx and its expression could be significantly challenged upon stimulation with lipopolysaccharide, peptidoglycan, gram-positive and gram-negative bacteria. RNA interference results indicated that both DjTatD and DjDN2s play a role in pharyngeal regeneration and may serve as functional complements to each other. Additionally, we found that rDjTatD and recombinant T7DjTatD effectively reduce biofilm formation regardless of their bacterial origin. Together, our results demonstrated that DjTatD may be involved in the planarian immune response and pharyngeal regeneration. Furthermore, after further optimization in the future, rDjTatD and T7DjTatD can be considered highly effective antibiofilm agents.
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Affiliation(s)
- Tong Yu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Zhe Sun
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Xiangyu Cao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Fengtang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China.
| | - Qiuxiang Pang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China.
| | - Hongkuan Deng
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China; Shandong Jiuyi Biotechnology Co., Ltd, Zibo, 255000, China.
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3
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Pisetsky DS, Herbert A. The role of DNA in the pathogenesis of SLE: DNA as a molecular chameleon. Ann Rheum Dis 2024; 83:830-837. [PMID: 38749573 PMCID: PMC11168871 DOI: 10.1136/ard-2023-225266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/11/2024] [Indexed: 06/14/2024]
Abstract
Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterised by antibodies to DNA (anti-DNA) and other nuclear macromolecules. Anti-DNA antibodies are markers for classification and disease activity and promote pathogenesis by forming immune complexes that deposit in the tissue or stimulate cytokine production. Studies on the antibody response to DNA have focused primarily on a conformation of DNA known as B-DNA, the classic right-handed double helix. Among other conformations of DNA, Z-DNA is a left-handed helix with a zig-zag backbone; hence, the term Z-DNA. Z-DNA formation is favoured by certain base sequences, with the energetically unfavourable flip from B-DNA to Z-DNA dependent on conditions. Z-DNA differs from B-DNA in its immunogenicity in animal models. Furthermore, anti-Z-DNA antibodies, but not anti-B-DNA antibodies, can be present in otherwise healthy individuals. In SLE, antibodies to Z-DNA can occur in association with antibodies to B-DNA as a cross-reactive response, rising and falling together. While formed transiently in chromosomal DNA, Z-DNA is stably present in bacterial biofilms; biofilms can provide protection against antibiotics and other challenges including elements of host defence. The high GC content of certain bacterial DNA also favours Z-DNA formation as do DNA-binding proteins of bacterial or host origin. Together, these findings suggest that sources of Z-DNA can enhance the immunogenicity of DNA and, in SLE, stimulate the production of cross-reactive antibodies that bind both B-DNA and Z-DNA. As such, DNA can act as a molecular chameleon that, when stabilised in the Z-DNA conformation, can drive autoimmunity.
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Affiliation(s)
- David S Pisetsky
- Duke University Medical Center, Durham, North Carolina, USA
- Medical Research, Durham VA Health Care System, Durham, North Carolina, USA
| | - Alan Herbert
- InsideOutBio Inc, Charlestown, Massachusetts, USA
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4
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Lu Y, Elrod J, Herrmann M, Knopf J, Boettcher M. Neutrophil Extracellular Traps: A Crucial Factor in Post-Surgical Abdominal Adhesion Formation. Cells 2024; 13:991. [PMID: 38891123 PMCID: PMC11171752 DOI: 10.3390/cells13110991] [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: 04/07/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
Post-surgical abdominal adhesions, although poorly understood, are highly prevalent. The molecular processes underlying their formation remain elusive. This review aims to assess the relationship between neutrophil extracellular traps (NETs) and the generation of postoperative peritoneal adhesions and to discuss methods for mitigating peritoneal adhesions. A keyword or medical subject heading (MeSH) search for all original articles and reviews was performed in PubMed and Google Scholar. It included studies assessing peritoneal adhesion reformation after abdominal surgery from 2003 to 2023. After assessing for eligibility, the selected articles were evaluated using the Critical Appraisal Skills Programme checklist for qualitative research. The search yielded 127 full-text articles for assessment of eligibility, of which 7 studies met our criteria and were subjected to a detailed quality review using the Critical Appraisal Skills Programme (CASP) checklist. The selected studies offer a comprehensive analysis of adhesion pathogenesis with a special focus on the role of neutrophil extracellular traps (NETs) in the development of peritoneal adhesions. Current interventional strategies are examined, including the use of mechanical barriers, advances in regenerative medicine, and targeted molecular therapies. In particular, this review emphasizes the potential of NET-targeted interventions as promising strategies to mitigate postoperative adhesion development. Evidence suggests that in addition to their role in innate defense against infections and autoimmune diseases, NETs also play a crucial role in the formation of peritoneal adhesions after surgery. Therefore, therapeutic strategies that target NETs are emerging as significant considerations for researchers. Continued research is vital to fully elucidate the relationship between NETs and post-surgical adhesion formation to develop effective treatments.
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Affiliation(s)
- Yuqing Lu
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Julia Elrod
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Martin Herrmann
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- 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 (FAU) and Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Jasmin Knopf
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Michael Boettcher
- Department of Pediatric Surgery, University Medical Center Mannheim, University of Heidelberg, 68167 Mannheim, Germany
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5
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Pisetsky DS. Unique Interplay Between Antinuclear Antibodies and Nuclear Molecules in the Pathogenesis of Systemic Lupus Erythematosus. Arthritis Rheumatol 2024. [PMID: 38622070 DOI: 10.1002/art.42863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/19/2024] [Accepted: 04/11/2024] [Indexed: 04/17/2024]
Abstract
Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease that primarily affects young women and causes a wide range of inflammatory manifestations. The hallmark of SLE is the production of antibodies to components of the cell nucleus (antinuclear antibodies [ANAs]). These antibodies can bind to DNA, RNA, and protein complexes with nucleic acids. Among ANAs, antibodies to DNA (anti-DNA) are markers for classification and disease activity, waxing and waning disease activity in many patients. In the blood, anti-DNA antibodies can bind to DNA to form immune complexes with two distinct roles in pathogenesis: (1) renal deposition to provoke nephritis and (2) stimulation of cytokine production following uptake into innate immune cells and interaction with internal nucleic acid sensors. These sensors are part of an internal host defense system in the cell cytoplasm that can respond to DNA from infecting organisms; during cell stress, DNA from nuclear and mitochondrial sources can also trigger these sensors. The formation of immune complexes requires a source of extracellular DNA in an immunologically accessible form. As shown in in vivo and in vitro systems, extracellular DNA can emerge from dead and dying cells in both a free and a particulate form. Neutrophils undergoing the process of NETosis can release DNA in mesh-like structures called neutrophil extracellular traps. In SLE, therefore, the combination of ANAs and immunologically active DNA can create new structures that can promote inflammation throughout the body as well as drive organ inflammation and damage.
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Affiliation(s)
- David S Pisetsky
- Duke University Medical Center and Durham Veterans Administration Medical Center, Durham, North Carolina
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Chimienti G, Russo F, Bianco A, Maqoud F, De Virgilio C, Galeano G, Orlando A, Riezzo G, D’Attoma B, Ignazzi A, Linsalata M, Prospero L, Franco I, Bagnato CB, Curci R, Coletta S. Effect of a 12-Week Walking Program Monitored by Global Physical Capacity Score (GPCS) on Circulating Cell-Free mtDNA and DNase Activity in Patients with Irritable Bowel Syndrome. Int J Mol Sci 2024; 25:4293. [PMID: 38673878 PMCID: PMC11050617 DOI: 10.3390/ijms25084293] [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: 03/27/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Irritable bowel syndrome (IBS) involves low-grade mucosal inflammation. Among the various approaches capable of managing the symptoms, physical activity is still under investigation. Despite its benefits, it promotes oxidative stress and inflammation. Mitochondria impacts gut disorders by releasing damage-associated molecular patterns, such as cell-free mtDNA (cf-mtDNA), which support inflammation. This study evaluated the effects of a 12-week walking program on the cf-mtDNA and DNase in 26 IBS and 17 non-IBS subjects. Pro- and anti-inflammatory cytokines were evaluated by ELISA. Digital droplet PCR was used to quantify cf-mtDNA; DNase activity was assessed using a single radial enzyme diffusion assay. PCR-RFLP was used to genotype DNASE1 rs1053874 SNP. Significantly lower IL-10 levels were found in IBS than in non-IBS individuals. Exercise reduced cf-mtDNA in non-IBS subjects but not in IBS patients. DNase activity did not correlate with the cf-mtDNA levels in IBS patients post-exercise, indicating imbalanced cf-mtDNA clearance. Different rs1053874 SNP frequencies were not found between groups. The study confirms the positive effects of regular moderate-intensity physical activity in healthy subjects and its role in cf-mtDNA release and clearance. Walking alone might not sufficiently reduce subclinical inflammation in IBS, based on imbalanced pro- and anti-inflammatory molecules. Prolonged programs are necessary to investigate their effects on inflammatory markers in IBS.
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Affiliation(s)
- Guglielmina Chimienti
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (G.C.); (C.D.V.)
| | - Francesco Russo
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Antonella Bianco
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Fatima Maqoud
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Caterina De Virgilio
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (G.C.); (C.D.V.)
| | - Grazia Galeano
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Antonella Orlando
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Giuseppe Riezzo
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Benedetta D’Attoma
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Antonia Ignazzi
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Michele Linsalata
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Laura Prospero
- Functional Gastrointestinal Disorders Research Group, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (F.M.); (G.G.); (A.O.); (G.R.); (B.D.); (A.I.); (M.L.); (L.P.)
| | - Isabella Franco
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Claudia Beatrice Bagnato
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Ritanna Curci
- Laboratory of Movement and Wellness, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy; (A.B.); (I.F.); (C.B.B.); (R.C.)
| | - Sergio Coletta
- Core Facility Biobank, National Institute of Gastroenterology IRCCS “Saverio de Bellis”, 70013 Castellana Grotte, Italy;
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Morita S, Nakamaru Y, Fukuda A, Fujiwara K, Suzuki M, Hoshino K, Honma A, Nakazono A, Homma A. Neutrophil Extracellular Trap Formation and Deoxyribonuclease I Activity in Patients with Otitis Media with Antineutrophil Cytoplasmic Antibody-Associated Vasculitis. Int Arch Allergy Immunol 2024:1-10. [PMID: 38583424 DOI: 10.1159/000537927] [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: 10/22/2023] [Accepted: 02/14/2024] [Indexed: 04/09/2024] Open
Abstract
INTRODUCTION No previous studies have evaluated the levels of neutrophil extracellular trap (NET) remnants or the importance of deoxyribonuclease (DNase) I activity based on the disease activity of otitis media with antineutrophil cytoplasmic antibody-associated vasculitis (OMAAV). The aim of this study was to explore the formation of NETs in the middle ear of patients with OMAAV during the onset and remission phases of the disease, with a particular focus on the relationships between the quantifiable levels of NET remnants and DNase I activity. METHODS OMAAV patients were eligible for inclusion. Patients with otitis media with effusion (OME) were examined as controls. The levels of cell-free deoxyribonucleic acid (DNA), citrullinated-histone H3 (cit-H3)-DNA complex, and myeloperoxidase (MPO)-DNA complex were quantified using an enzyme-linked immunosorbent assay. DNase I activity was measured using a fluorometric method. RESULTS The quantifiable levels of cell-free DNA, cit-H3-DNA complex, and MPO-DNA complex in the middle ear lavage of patients with OMAAV at onset were significantly higher than those in patients with OMAAV at remission and in patients with OME. DNase I activity in the patients with OMAAV at onset was significantly lower than those in patients with OMAAV at remission and OME and was negatively correlated with the level of MPO-DNA complex. CONCLUSIONS This study suggests that NET remnants and DNase I activity may be potentially useful biomarkers for the diagnosis and disease activity of OMAAV.
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Affiliation(s)
- Shinya Morita
- Department of Otolaryngology ‒ Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Yuji Nakamaru
- Department of Otolaryngology ‒ Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Atsushi Fukuda
- Department of Otolaryngology ‒ Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Keishi Fujiwara
- Department of Otolaryngology ‒ Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Masanobu Suzuki
- Department of Otolaryngology ‒ Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Kimiko Hoshino
- Department of Otolaryngology ‒ Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Aya Honma
- Department of Otolaryngology ‒ Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Akira Nakazono
- Department of Otolaryngology ‒ Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Akihiro Homma
- Department of Otolaryngology ‒ Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
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Gavazzi F, Gonzalez CD, Arnold K, Swantkowski M, Charlton L, Modesti N, Dar AA, Vanderver A, Bennett M, Adang LA. Nucleotide metabolism, leukodystrophies, and CNS pathology. J Inherit Metab Dis 2024. [PMID: 38421058 DOI: 10.1002/jimd.12721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
The balance between a protective and a destructive immune response can be precarious, as exemplified by inborn errors in nucleotide metabolism. This class of inherited disorders, which mimics infection, can result in systemic injury and severe neurologic outcomes. The most common of these disorders is Aicardi Goutières syndrome (AGS). AGS results in a phenotype similar to "TORCH" infections (Toxoplasma gondii, Other [Zika virus (ZIKV), human immunodeficiency virus (HIV)], Rubella virus, human Cytomegalovirus [HCMV], and Herpesviruses), but with sustained inflammation and ongoing potential for complications. AGS was first described in the early 1980s as familial clusters of "TORCH" infections, with severe neurology impairment, microcephaly, and basal ganglia calcifications (Aicardi & Goutières, Ann Neurol, 1984;15:49-54) and was associated with chronic cerebrospinal fluid (CSF) lymphocytosis and elevated type I interferon levels (Goutières et al., Ann Neurol, 1998;44:900-907). Since its first description, the clinical spectrum of AGS has dramatically expanded from the initial cohorts of children with severe impairment to including individuals with average intelligence and mild spastic paraparesis. This broad spectrum of potential clinical manifestations can result in a delayed diagnosis, which families cite as a major stressor. Additionally, a timely diagnosis is increasingly critical with emerging therapies targeting the interferon signaling pathway. Despite the many gains in understanding about AGS, there are still many gaps in our understanding of the cell-type drivers of pathology and characterization of modifying variables that influence clinical outcomes and achievement of timely diagnosis.
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Affiliation(s)
- Francesco Gavazzi
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Kaley Arnold
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Meghan Swantkowski
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lauren Charlton
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nicholson Modesti
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Asif A Dar
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mariko Bennett
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Laura A Adang
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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9
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Kandouz M. Cell Death, by Any Other Name…. Cells 2024; 13:325. [PMID: 38391938 PMCID: PMC10886887 DOI: 10.3390/cells13040325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Studies trying to understand cell death, this ultimate biological process, can be traced back to a century ago. Yet, unlike many other fashionable research interests, research on cell death is more alive than ever. New modes of cell death are discovered in specific contexts, as are new molecular pathways. But what is "cell death", really? This question has not found a definitive answer yet. Nevertheless, part of the answer is irreversibility, whereby cells can no longer recover from stress or injury. Here, we identify the most distinctive features of different modes of cell death, focusing on the executive final stages. In addition to the final stages, these modes can differ in their triggering stimulus, thus referring to the initial stages. Within this framework, we use a few illustrative examples to examine how intercellular communication factors in the demise of cells. First, we discuss the interplay between cell-cell communication and cell death during a few steps in the early development of multicellular organisms. Next, we will discuss this interplay in a fully developed and functional tissue, the gut, which is among the most rapidly renewing tissues in the body and, therefore, makes extensive use of cell death. Furthermore, we will discuss how the balance between cell death and communication is modified during a pathological condition, i.e., colon tumorigenesis, and how it could shed light on resistance to cancer therapy. Finally, we briefly review data on the role of cell-cell communication modes in the propagation of cell death signals and how this has been considered as a potential therapeutic approach. Far from vainly trying to provide a comprehensive review, we launch an invitation to ponder over the significance of cell death diversity and how it provides multiple opportunities for the contribution of various modes of intercellular communication.
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Affiliation(s)
- Mustapha Kandouz
- Department of Pathology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA;
- Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
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10
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Federici S, Cinicola BL, La Torre F, Castagnoli R, Lougaris V, Giardino G, Volpi S, Caorsi R, Leonardi L, Corrente S, Soresina A, Cancrini C, Insalaco A, Gattorno M, De Benedetti F, Marseglia GL, Del Giudice MM, Cardinale F. Vasculitis and vasculopathy associated with inborn errors of immunity: an overview. Front Pediatr 2024; 11:1258301. [PMID: 38357265 PMCID: PMC10866297 DOI: 10.3389/fped.2023.1258301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/29/2023] [Indexed: 02/16/2024] Open
Abstract
Systemic autoinflammatory diseases (SAIDs) are disorders of innate immunity, which are characterized by unprovoked recurrent flares of systemic inflammation often characterized by fever associated with clinical manifestations mainly involving the musculoskeletal, mucocutaneous, gastrointestinal, and nervous systems. Several conditions also present with varied, sometimes prominent, involvement of the vascular system, with features of vasculitis characterized by variable target vessel involvement and organ damage. Here, we report a systematic review of vasculitis and vasculopathy associated with inborn errors of immunity.
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Affiliation(s)
- Silvia Federici
- Division of Rheumatology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Bianca Laura Cinicola
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Francesco La Torre
- Department of Pediatrics, Giovanni XXIII Pediatric Hospital, University of Bari, Bari, Italy
| | - Riccardo Castagnoli
- Pediatric Unit, Department of Clinical, Surgical, Diagnostic, and Pediatric Sciences, University of Pavia, Pavia, Italy
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Vassilios Lougaris
- Department of Clinical and Experimental Sciences, Pediatrics Clinic and Institute for Molecular Medicine A. Nocivelli, University of Brescia and ASST-Spedali Civili di Brescia, Brescia, Italy
| | - Giuliana Giardino
- Pediatric Section, Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - Stefano Volpi
- Center for Autoinflammatory Diseases and Immunodeficiency, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Roberta Caorsi
- Center for Autoinflammatory Diseases and Immunodeficiency, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Lucia Leonardi
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Annarosa Soresina
- Unit of Pediatric Immunology, Pediatrics Clinic, University of Brescia, ASST-Spedali Civili Brescia, Brescia, Italy
| | - Caterina Cancrini
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Academic Department of Pediatrics, Immune and Infectious Diseases Division, Research Unit of Primary Immunodeficiencies, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Antonella Insalaco
- Division of Rheumatology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Marco Gattorno
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Gian Luigi Marseglia
- Pediatric Unit, Department of Clinical, Surgical, Diagnostic, and Pediatric Sciences, University of Pavia, Pavia, Italy
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Michele Miraglia Del Giudice
- Department of Woman, Child and of General and Specialized Surgery, University of Campania ‘Luigi Vanvitelli’, Naples, Italy
| | - Fabio Cardinale
- Department of Pediatrics, Giovanni XXIII Pediatric Hospital, University of Bari, Bari, Italy
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11
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Koga T, Kida H, Yamasaki Y, Feril LB, Endo H, Itaka K, Abe H, Tachibana K. Intracranial Gene Delivery Mediated by Albumin-Based Nanobubbles and Low-Frequency Ultrasound. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:285. [PMID: 38334557 PMCID: PMC10856598 DOI: 10.3390/nano14030285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/27/2024] [Accepted: 01/28/2024] [Indexed: 02/10/2024]
Abstract
Research in the field of high-intensity focused ultrasound (HIFU) for intracranial gene therapy has greatly progressed over the years. However, limitations of conventional HIFU still remain. That is, genes are required to cross the blood-brain barrier (BBB) in order to reach the neurological disordered lesion. In this study, we introduce a novel direct intracranial gene delivery method, bypassing the BBB using human serum albumin-based nanobubbles (NBs) injected through a less invasive intrathecal route via lumbar puncture, followed by intracranial irradiation with low-frequency ultrasound (LoFreqUS). Focusing on both plasmid DNA (pDNA) and messenger RNA (mRNA), our approach utilizes LoFreqUS for deeper tissue acoustic penetration and enhancing gene transfer efficiency. This drug delivery method could be dubbed as the "Spinal Back-Door Approach", an alternative to the "front door" BBB opening method. Experiments showed that NBs effectively responded to LoFreqUS, significantly improving gene transfer in vitro using U-87 MG cell lines. In vivo experiments in mice demonstrated significantly increased gene expression with pDNA; however, we were unable to obtain conclusive results using mRNA. This novel technique, combining albumin-based NBs and LoFreqUS offers a promising, efficient, targeted, and non-invasive solution for central nervous system gene therapy, potentially transforming the treatment landscape for neurological disorders.
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Affiliation(s)
- Takayuki Koga
- Department of Neurosurgery, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan; (T.K.); (H.A.)
- Department of Anatomy, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan; (H.K.); (Y.Y.); (L.B.F.J.); (H.E.)
| | - Hiroshi Kida
- Department of Anatomy, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan; (H.K.); (Y.Y.); (L.B.F.J.); (H.E.)
| | - Yutaro Yamasaki
- Department of Anatomy, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan; (H.K.); (Y.Y.); (L.B.F.J.); (H.E.)
| | - Loreto B. Feril
- Department of Anatomy, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan; (H.K.); (Y.Y.); (L.B.F.J.); (H.E.)
| | - Hitomi Endo
- Department of Anatomy, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan; (H.K.); (Y.Y.); (L.B.F.J.); (H.E.)
| | - Keiji Itaka
- Department of Biofunction Research, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Tokyo 101-0062, Japan;
| | - Hiroshi Abe
- Department of Neurosurgery, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan; (T.K.); (H.A.)
| | - Katsuro Tachibana
- Department of Anatomy, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan; (H.K.); (Y.Y.); (L.B.F.J.); (H.E.)
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12
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Qu X, Meng LC, Lu X, Chen X, Li Y, Zhou R, Zhu YJ, Luo YC, Huang JT, Shi XL, Zhang HB. Prognostic and metabolic characteristics of a novel cuproptosis-related signature in patients with hepatocellular carcinoma. Heliyon 2024; 10:e23686. [PMID: 38259960 PMCID: PMC10801206 DOI: 10.1016/j.heliyon.2023.e23686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 11/29/2023] [Accepted: 12/09/2023] [Indexed: 01/24/2024] Open
Abstract
Cuproptosis is a novel discovered mode of programmed cell death. To identify the molecular regulatory patterns related to cuproptosis, this study was designed for exploring the correlation between cuproptosis-related genes (CRGs) and the prognosis, metabolism, and treatment of hepatocellular carcinoma (HCC). Cancer Genome Atlas (TCGA) database was used to screen 363 HCC samples, which were categorized into 2 clusters based on the expression of CRGs. Survival analysis demonstrated that overall survival (OS) was better in Cluster 1 than Cluster 2 which might to be relevant to differences in metabolic based on functional analysis. With LASSO regression analysis and univariate COX regression, 8 prognosis-related genes were screened, a differently expressed genes (DEGs) were then constructed (HCC patients' DEGs)-based signature. The signature's stability was also validated in the 2 independent cohorts and test cohorts (GSE14520, HCC dataset in PCAWG). The 1-year, 3-year, and 5-year area under the curve (AUC) were 0.756, 0.706, and 0.722, respectively. The signature could also well predict the response to chemotherapy, targeted and transcatheter arterial chemoembolization (TACE) by providing a risk score. Moreover, the correlation was uncovered by the research between the metabolism and risk score. In conclusion, a unique cuproptosis-related signature that be capable of predicting patients' prognosis with HCC, and offered valuable insights into chemotherapy, TACE and targeted therapies for these patients has been developed.
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Affiliation(s)
- Xin Qu
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111, Dade Road, Guangzhou, Guangdong, 510120, China
| | - Ling-cui Meng
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111, Dade Road, Guangzhou, Guangdong, 510120, China
| | - Xi Lu
- Department of Ultrasound, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, 510120, China
| | - Xian Chen
- Guangzhou Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510405, China
| | - Yong Li
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111, Dade Road, Guangzhou, Guangdong, 510120, China
| | - Rui Zhou
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111, Dade Road, Guangzhou, Guangdong, 510120, China
| | - Yan-juan Zhu
- The Second Clinical Medical School of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Yi-chang Luo
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111, Dade Road, Guangzhou, Guangdong, 510120, China
| | - Jin-tao Huang
- Department of Oncology, Guangzhou Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Hospital of Traditional Chinese Medicine Affiliated to Guangzhou Medical University, Guangzhou, 510130, China
| | | | - Hai-Bo Zhang
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111, Dade Road, Guangzhou, Guangdong, 510120, China
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13
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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14
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Gerovska D, Fernández Moreno P, Zabala A, Araúzo-Bravo MJ. Cell-Free Genic Extrachromosomal Circular DNA Profiles of DNase Knockouts Associated with Systemic Lupus Erythematosus and Relation with Common Fragile Sites. Biomedicines 2023; 12:80. [PMID: 38255187 PMCID: PMC10813657 DOI: 10.3390/biomedicines12010080] [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: 11/28/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Cell-free extrachromosomal circular DNA (cf-eccDNA) has been proposed as a promising early biomarker for disease diagnosis, progression and drug response. Its established biomarker features are changes in the number and length distribution of cf-eccDNA. Another novel promising biomarker is a set of eccDNA excised from a panel of genes specific to a condition compared to a control. Deficiencies in two endonucleases that specifically target DNA, Dnase1 and Dnase1l3, are associated with systemic lupus erythematosus (SLE). To study the genic eccDNA profiles in the case of their deficiencies, we mapped sequenced eccDNA data from plasma, liver and buffy coat from Dnase1 and Dnase1l3 knockouts (KOs), and wild type controls in mouse. Next, we performed an eccDNA differential analysis between KO and control groups using our DifCir algorithm. We found a specific genic cf-eccDNA fingerprint of the Dnase1l3 group compared to the wild type controls involving 131 genes; 26% of them were associated with human chromosomal fragile sites (CFSs) and with a statistically significant enrichment of CFS-associated genes. We found six genes in common with the genic cf-eccDNA profile of SLE patients with DNASE1L3 deficiency, namely Rorb, Mvb12b, Osbpl10, Fto, Tnik and Arhgap10; all of them were specific and present in all human plasma samples, and none of them were associated with CFSs. A not so distinctive genic cf-eccDNA difference involving only seven genes was observed in the case of the Dnase1 group compared to the wild type. In tissue-liver and buffy coat-we did not detect the same genic eccDNA difference observed in the plasma samples. These results point to a specific role of a set of genic eccDNA in plasma from DNase KOs, as well as a relation with CFS genes, confirming the promise of the genic cf-eccDNA in studying diseases and the need for further research on the relationship between eccDNA and CFSs.
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Affiliation(s)
- Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Patricia Fernández Moreno
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Aitor Zabala
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Marcos J. Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
- Basque Foundation for Science, IKERBASQUE, Calle María Díaz Harokoa 3, 48013 Bilbao, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
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15
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Zhu D, Wang H, Wu W, Geng S, Zhong G, Li Y, Guo H, Long G, Ren Q, Luan Y, Duan C, Wei B, Ma J, Li S, Zhou J, Mao M. Circulating cell-free DNA fragmentation is a stepwise and conserved process linked to apoptosis. BMC Biol 2023; 21:253. [PMID: 37953260 PMCID: PMC10642009 DOI: 10.1186/s12915-023-01752-6] [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: 11/24/2022] [Accepted: 10/31/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) is a pool of short DNA fragments mainly released from apoptotic hematopoietic cells. Nevertheless, the precise physiological process governing the DNA fragmentation and molecular profile of cfDNA remains obscure. To dissect the DNA fragmentation process, we use a human leukemia cell line HL60 undergoing apoptosis to analyze the size distribution of DNA fragments by shallow whole-genome sequencing (sWGS). Meanwhile, we also scrutinize the size profile of plasma cfDNA in 901 healthy human subjects and 38 dogs, as well as 438 patients with six common cancer types by sWGS. RESULTS Distinct size distribution profiles were observed in the HL60 cell pellet and supernatant, suggesting fragmentation is a stepwise process. Meanwhile, C-end preference was seen in both intracellular and extracellular cfDNA fragments. Moreover, the cfDNA profiles are characteristic and conserved across mammals. Compared with healthy subjects, distinct cfDNA profiles with a higher proportion of short fragments and lower C-end preference were found in cancer patients. CONCLUSIONS Our study provides new insight into fragmentomics of circulating cfDNA processing, which will be useful for early diagnosis of cancer and surveillance during cancer progression.
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Affiliation(s)
- Dandan Zhu
- Clinical Laboratories, Shenyou Bio, Zhengzhou, 450000, China
| | - Haihong Wang
- Shanghai Institute of Hematology, CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wei Wu
- Research & Development, SeekIn Inc, Shenzhen, 518000, China
| | - Shuaipeng Geng
- Clinical Laboratories, Shenyou Bio, Zhengzhou, 450000, China
| | - Guolin Zhong
- Research & Development, SeekIn Inc, Shenzhen, 518000, China
| | - Yunfei Li
- Research & Development, SeekIn Inc, Shenzhen, 518000, China
| | - Han Guo
- Clinical Laboratories, Shenyou Bio, Zhengzhou, 450000, China
| | - Guanghui Long
- Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Qingqi Ren
- Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Yi Luan
- Clinical Laboratories, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510000, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Chaohui Duan
- Clinical Laboratories, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510000, China
| | - Bing Wei
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450003, China
| | - Jie Ma
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, 450003, China
| | - Shiyong Li
- Research & Development, SeekIn Inc, Shenzhen, 518000, China
| | - Jun Zhou
- Shanghai Institute of Hematology, CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Mao Mao
- Research & Development, SeekIn Inc, Shenzhen, 518000, China.
- Yonsei Song-Dang Institute for Cancer Research, Yonsei University, Seoul, 03722, South Korea.
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16
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Swarup N, Cheng J, Choi I, Heo YJ, Kordi M, Aziz M, Arora A, Li F, Chia D, Wei F, Elashoff D, Zhang L, Kim S, Kim Y, Wong DTW. Multi-faceted attributes of salivary cell-free DNA as liquid biopsy biomarkers for gastric cancer detection. Biomark Res 2023; 11:90. [PMID: 37817261 PMCID: PMC10566128 DOI: 10.1186/s40364-023-00524-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Recent advances in circulating cell-free DNA (cfDNA) analysis from biofluids have opened new avenues for liquid biopsy (LB). However, current cfDNA LB assays are limited by the availability of existing information on established genotypes associated with tumor tissues. Certain cancers present with a limited list of established mutated cfDNA biomarkers, and thus, nonmutated cfDNA characteristics along with alternative biofluids are needed to broaden the available cfDNA targets for cancer detection. Saliva is an intriguing and accessible biofluid that has yet to be fully explored for its clinical utility for cancer detection. METHODS In this report, we employed a low-coverage single stranded (ss) library NGS pipeline "Broad-Range cell-free DNA-Seq" (BRcfDNA-Seq) using saliva to comprehensively investigate the characteristics of salivary cfDNA (ScfDNA). The identification of cfDNA features has been made possible by applying novel cfDNA processing techniques that permit the incorporation of ultrashort, ss, and jagged DNA fragments. As a proof of concept using 10 gastric cancer (GC) and 10 noncancer samples, we examined whether ScfDNA characteristics, including fragmentomics, end motif profiles, microbial contribution, and human chromosomal mapping, could differentiate between these two groups. RESULTS Individual and integrative analysis of these ScfDNA features demonstrated significant differences between the two cohorts, suggesting that disease state may affect the ScfDNA population by altering nuclear cleavage or the profile of contributory organism cfDNA to total ScfDNA. We report that principal component analysis integration of several aspects of salivary cell-free DNA fragmentomic profiles, genomic element profiles, end-motif sequence patterns, and distinct oral microbiome populations can differentiate the two populations with a p value of < 0.0001 (PC1). CONCLUSION These novel features of ScfDNA characteristics could be clinically useful for improving saliva-based LB detection and the eventual monitoring of local or systemic diseases.
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Affiliation(s)
- Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jordan Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Irene Choi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - You Jeong Heo
- The Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06355, Republic of Korea
| | - Misagh Kordi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Mohammad Aziz
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Akanksha Arora
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Indraprastha Institute of Information Technology (IIIT), Delhi, India
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Chia
- Indraprastha Institute of Information Technology (IIIT), Delhi, India
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Elashoff
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Liying Zhang
- Indraprastha Institute of Information Technology (IIIT), Delhi, India
| | - Sung Kim
- Department of Medicine, Biostatistics and Computational Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06355, South Korea
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - David T W Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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17
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Course CW, Lewis PA, Kotecha SJ, Cousins M, Hart K, Watkins WJ, Heesom KJ, Kotecha S. Characterizing the urinary proteome of prematurity-associated lung disease in school-aged children. Respir Res 2023; 24:191. [PMID: 37474963 PMCID: PMC10357627 DOI: 10.1186/s12931-023-02494-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
INTRODUCTION Although different phenotypes of lung disease after preterm birth have recently been described, the underlying mechanisms associated with each phenotype are poorly understood. We, therefore, compared the urinary proteome for different spirometry phenotypes in preterm-born children with preterm- and term-born controls. METHODS Preterm and term-born children aged 7-12 years, from the Respiratory Health Outcomes in Neonates (RHiNO) cohort, underwent spirometry and urine collection. Urine was analysed by Nano-LC Mass-Spectrometry with Tandem-Mass Tag labelling. The preterm-born children were classified into phenotypes of prematurity-associated preserved ratio impaired spirometry (pPRISm, FEV1 < lower limit of normal (LLN), FEV1/FVC ≥ LLN), prematurity-associated obstructive lung disease (POLD, FEV1 < LLN, FEV1/FVC < LLN) and preterm controls (FEV1 ≥ LLN,). Biological relationships between significantly altered protein abundances were analysed using Ingenuity Pathways Analysis software, and receiver operator characteristic curves were calculated. RESULTS Urine was analysed from 160 preterm-born children and 44 term controls. 27 and 21 were classified into the pPRISm and POLD groups, respectively. A total of 785 proteins were detected. Compared to preterm-born controls, sixteen significantly altered proteins in the pPRISm group were linked to six biological processes related to upregulation of inflammation and T-cell biology. In contrast, four significantly altered proteins in the POLD group were linked with neutrophil accumulation. Four proteins (DNASE1, PGLYRP1, B2M, SERPINA3) in combination had an area under the curve of 0.73 for pPRISm and three combined proteins (S100A8, MMP9 and CTSC) had AUC of 0.76 for POLD. CONCLUSIONS In this exploratory study, we demonstrate differential associations of the urinary proteome with pPRISm and POLD. TRIAL REGISTRATION EudraCT: 2015-003712-20.
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Affiliation(s)
- Christopher W Course
- Department of Child Health, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Philip A Lewis
- Proteomics Facility, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Sarah J Kotecha
- Department of Child Health, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Michael Cousins
- Department of Child Health, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
- Department of Paediatrics, Cardiff and Vale University Health Board, Cardiff, UK
| | - Kylie Hart
- Department of Paediatrics, Cardiff and Vale University Health Board, Cardiff, UK
| | - W John Watkins
- Department of Child Health, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Kate J Heesom
- Proteomics Facility, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Sailesh Kotecha
- Department of Child Health, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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18
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Swarup N, Cheng J, Choi I, Heo YJ, Kordi M, Li F, Aziz M, Chia D, Wei F, Elashoff D, Zhang L, Kim S, Kim Y, Wong DT. Multi-Faceted Attributes of Salivary Cell-free DNA as Liquid Biopsy Biomarkers for Gastric Cancer Detection. RESEARCH SQUARE 2023:rs.3.rs-3154388. [PMID: 37503289 PMCID: PMC10371094 DOI: 10.21203/rs.3.rs-3154388/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background Recent advances in circulating cell-free DNA (cfDNA) analysis from biofluids have opened new avenues for liquid biopsy (LB). However, current cfDNA LB assays are limited by the availability of existing information on established genotypes associated with tumor tissues. Certain cancers present with a limited list of established mutated cfDNA biomarkers, and thus, nonmutated cfDNA characteristics along with alternative biofluids are needed to broaden the available cfDNA targets for cancer detection. Saliva is an intriguing and accessible biofluid that has yet to be fully explored for its clinical utility for cancer detection. Methods In this report, we employed a low-coverage single stranded (ss) library NGS pipeline "Broad-Range cell-free DNA-Seq" (BRcfDNA-Seq) using saliva to comprehensively investigate the characteristics of salivary cfDNA (ScfDNA). The identification of cfDNA features has been made possible by applying novel cfDNA processing techniques that permit the incorporation of ultrashort, ss, and jagged DNA fragments. As a proof of concept using 10 gastric cancer (GC) and 10 noncancer samples, we examined whether ScfDNA characteristics, including fragmentomics, end motif profiles, microbial contribution, and human chromosomal mapping, could differentiate between these two groups. Results Individual and integrative analysis of these ScfDNA features demonstrated significant differences between the two cohorts, suggesting that disease state may affect the ScfDNA population by altering nuclear cleavage or the profile of contributory organism cfDNA to total ScfDNA. We report that principal component analysis integration of several aspects of salivary cell-free DNA fragmentomic profiles, genomic element profiles, end-motif sequence patterns, and distinct oral microbiome populations can differentiate the two populations with a p value of < 0.0001 (PC1). Conclusion These novel features of ScfDNA characteristics could be clinically useful for improving saliva-based LB detection and the eventual monitoring of local or systemic diseases.
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Affiliation(s)
- Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jordan Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Irene Choi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - You Jeong Heo
- The Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, Republic of Korea
| | - Misagh Kordi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Mohammad Aziz
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Chia
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Elashoff
- Department of Medicine, Biostatistics and Computational Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Liying Zhang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, South Korea
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David T.W. Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Bhattacharya M, Horswill AR. Breaking bad. J Exp Med 2023; 220:e20230421. [PMID: 37129875 PMCID: PMC10233462 DOI: 10.1084/jem.20230421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
DNASE1 (D1) and DNASE1L3 (D1L3) synergistically reduce the severity of systemic infections caused by Staphylococcus aureus. In this issue of JEM, Lacey et al. (2023. J. Exp. Med.https://doi.org/10.1084/jem.20221086) develop D1-/-, D1L3-/-, and D1-/-D1L3-/- mice to show that exogenous addition of the DNase formulation Dornase alfa can facilitate removal of biofilms.
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Affiliation(s)
- Mohini Bhattacharya
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Alexander R. Horswill
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Veterans Affairs, Eastern Colorado Health Care System, Aurora, CO, USA
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20
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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: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [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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21
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Englert H, Göbel J, Khong D, Omidi M, Wolska N, Konrath S, Frye M, Mailer RK, Beerens M, Gerwers JC, Preston RJS, Odeberg J, Butler LM, Maas C, Stavrou EX, Fuchs TA, Renné T. Targeting NETs using dual-active DNase1 variants. Front Immunol 2023; 14:1181761. [PMID: 37287977 PMCID: PMC10242134 DOI: 10.3389/fimmu.2023.1181761] [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: 03/07/2023] [Accepted: 05/09/2023] [Indexed: 06/09/2023] Open
Abstract
Background Neutrophil Extracellular Traps (NETs) are key mediators of immunothrombotic mechanisms and defective clearance of NETs from the circulation underlies an array of thrombotic, inflammatory, infectious, and autoimmune diseases. Efficient NET degradation depends on the combined activity of two distinct DNases, DNase1 and DNase1-like 3 (DNase1L3) that preferentially digest double-stranded DNA (dsDNA) and chromatin, respectively. Methods Here, we engineered a dual-active DNase with combined DNase1 and DNase1L3 activities and characterized the enzyme for its NET degrading potential in vitro. Furthermore, we produced a mouse model with transgenic expression of the dual-active DNase and analyzed body fluids of these animals for DNase1 and DNase 1L3 activities. We systematically substituted 20 amino acid stretches in DNase1 that were not conserved among DNase1 and DNase1L3 with homologous DNase1L3 sequences. Results We found that the ability of DNase1L3 to degrade chromatin is embedded into three discrete areas of the enzyme's core body, not the C-terminal domain as suggested by the state-of-the-art. Further, combined transfer of the aforementioned areas of DNase1L3 to DNase1 generated a dual-active DNase1 enzyme with additional chromatin degrading activity. The dual-active DNase1 mutant was superior to native DNase1 and DNase1L3 in degrading dsDNA and chromatin, respectively. Transgenic expression of the dual-active DNase1 mutant in hepatocytes of mice lacking endogenous DNases revealed that the engineered enzyme was stable in the circulation, released into serum and filtered to the bile but not into the urine. Conclusion Therefore, the dual-active DNase1 mutant is a promising tool for neutralization of DNA and NETs with potential therapeutic applications for interference with thromboinflammatory disease states.
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Affiliation(s)
- Hanna Englert
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Josephine Göbel
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Danika Khong
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maryam Omidi
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nina Wolska
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra Konrath
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maike Frye
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Reiner K. Mailer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manu Beerens
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian C. Gerwers
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roger J. S. Preston
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jacob Odeberg
- Department of Clinical Medicine, The Arctic University of Norway, Tromsø, Norway
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lynn M. Butler
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, The Arctic University of Norway, Tromsø, Norway
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Coen Maas
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Evi X. Stavrou
- Medicine Service, Section of Hematology-Oncology, Louis Stokes Veterans Administration Medical Center, Cleveland, OH, United States
- Department of Medicine, Hematology and Oncology Division, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Tobias A. Fuchs
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Neutrolis, Inc., Cambridge, MA, United States
| | - Thomas Renné
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, Mainz, Germany
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22
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Niu N, Ye J, Hu Z, Zhang J, Wang Y. Regulative Roles of Metabolic Plasticity Caused by Mitochondrial Oxidative Phosphorylation and Glycolysis on the Initiation and Progression of Tumorigenesis. Int J Mol Sci 2023; 24:ijms24087076. [PMID: 37108242 PMCID: PMC10139088 DOI: 10.3390/ijms24087076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
One important feature of tumour development is the regulatory role of metabolic plasticity in maintaining the balance of mitochondrial oxidative phosphorylation and glycolysis in cancer cells. In recent years, the transition and/or function of metabolic phenotypes between mitochondrial oxidative phosphorylation and glycolysis in tumour cells have been extensively studied. In this review, we aimed to elucidate the characteristics of metabolic plasticity (emphasizing their effects, such as immune escape, angiogenesis migration, invasiveness, heterogeneity, adhesion, and phenotypic properties of cancers, among others) on tumour progression, including the initiation and progression phases. Thus, this article provides an overall understanding of the influence of abnormal metabolic remodeling on malignant proliferation and pathophysiological changes in carcinoma.
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Affiliation(s)
- Nan Niu
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
- College of Physics and Optoelectronic Engineering, Canghai Campus of Shenzhen University, Shenzhen 518060, China
| | - Jinfeng Ye
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
| | - Zhangli Hu
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
| | - Junbin Zhang
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
| | - Yun Wang
- Shenzhen Engineering Labortaory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Lihu Campus of Shenzhen University, Shenzhen 518055, China
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23
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Gomez-Bañuelos E, Yu Y, Li J, Cashman KS, Paz M, Trejo-Zambrano MI, Bugrovsky R, Wang Y, Chida AS, Sherman-Baust CA, Ferris DP, Goldman DW, Darrah E, Petri M, Sanz I, Andrade F. Affinity maturation generates pathogenic antibodies with dual reactivity to DNase1L3 and dsDNA in systemic lupus erythematosus. Nat Commun 2023; 14:1388. [PMID: 36941260 PMCID: PMC10027674 DOI: 10.1038/s41467-023-37083-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/27/2023] [Indexed: 03/23/2023] Open
Abstract
Anti-dsDNA antibodies are pathogenically heterogeneous, implying distinct origins and antigenic properties. Unexpectedly, during the clinical and molecular characterization of autoantibodies to the endonuclease DNase1L3 in patients with systemic lupus erythematosus (SLE), we identified a subset of neutralizing anti-DNase1L3 antibodies previously catalogued as anti-dsDNA. Based on their variable heavy-chain (VH) gene usage, these antibodies can be divided in two groups. One group is encoded by the inherently autoreactive VH4-34 gene segment, derives from anti-DNase1L3 germline-encoded precursors, and gains cross-reactivity to dsDNA - and some additionally to cardiolipin - following somatic hypermutation. The second group, originally defined as nephritogenic anti-dsDNA antibodies, is encoded by diverse VH gene segments. Although affinity maturation results in dual reactivity to DNase1L3 and dsDNA, their binding efficiencies favor DNase1L3 as the primary antigen. Clinical, transcriptional and monoclonal antibody data support that cross-reactive anti-DNase1L3/dsDNA antibodies are more pathogenic than single reactive anti-dsDNA antibodies. These findings point to DNase1L3 as the primary target of a subset of antibodies classified as anti-dsDNA, shedding light on the origin and pathogenic heterogeneity of antibodies reactive to dsDNA in SLE.
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Affiliation(s)
- Eduardo Gomez-Bañuelos
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Yikai Yu
- Department of Rheumatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Jessica Li
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Kevin S Cashman
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, 30322, USA
| | - Merlin Paz
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | | | - Regina Bugrovsky
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, 30322, USA
| | - Youliang Wang
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, 30322, USA
| | - Asiya Seema Chida
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, 30322, USA
| | - Cheryl A Sherman-Baust
- Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, 21224, USA
| | - Dylan P Ferris
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Daniel W Goldman
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Erika Darrah
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Michelle Petri
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Iñaki Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, 30322, USA
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA.
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24
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Gómez-Bañuelos E, Fava A, Andrade F. An update on autoantibodies in systemic lupus erythematosus. Curr Opin Rheumatol 2023; 35:61-67. [PMID: 36695053 PMCID: PMC9881844 DOI: 10.1097/bor.0000000000000922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
PURPOSE OF REVIEW Autoantibodies are cornerstone biomarkers in systemic lupus erythematosus (SLE), an autoimmune disease characterized by autoantibody-mediated tissue damage. Autoantibodies can inform about disease susceptibility, clinical course, outcomes and the cause of SLE. Identifying pathogenic autoantibodies in SLE, however, remains a significant challenge. This review summarizes recent advances in the field of autoantibodies in SLE. RECENT FINDINGS High-throughput technologies and innovative hypothesis have been applied to identify autoantibodies linked to pathogenic pathways in SLE. This work has led to the discovery of functional autoantibodies targeting key components is SLE pathogenesis (e.g. DNase1L3, cytokines, extracellular immunoregulatory receptors), as well as the identification of endogenous retroelements and interferon-induced proteins as sources of autoantigens in SLE. Others have reinvigorated the study of mitochondria, which has antigenic parallels with bacteria, as a trigger of autoantibodies in SLE, and identified faecal IgA to nuclear antigens as potential biomarkers linking gut permeability and microbial translocation in SLE pathogenesis. Recent studies showed that levels of autoantibodies against dsDNA, C1q, chromatin, Sm and ribosomal P may serve as biomarkers of proliferative lupus nephritis, and identified novel autoantibodies to several unique species of Ro52 overexpressed by SLE neutrophils. SUMMARY Autoantibodies hold promise as biomarkers of pathogenic mechanisms in SLE.
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Affiliation(s)
- Eduardo Gómez-Bañuelos
- Division of Rheumatology, The Johns Hopkins University School of Medicine. Baltimore, MD, 21224. U.S.A
| | - Andrea Fava
- Division of Rheumatology, The Johns Hopkins University School of Medicine. Baltimore, MD, 21224. U.S.A
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine. Baltimore, MD, 21224. U.S.A
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Bai Q, He X, Hu T. Pan‑cancer analysis of the deoxyribonuclease gene family. Mol Clin Oncol 2023; 18:19. [PMID: 36798465 PMCID: PMC9926046 DOI: 10.3892/mco.2023.2615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Deoxyribonuclease (DNase) is an enzyme that catalyzes the cleavage of phosphodiester bonds in the main chain of DNA to degrade DNA. DNase serves a vital role in several immune-related diseases. The present study linked the expression of DNase with overall survival (OS), performed pan-cancer co-expression analysis, and assessed the association between DNase and immune infiltration subtypes, tumor microenvironment and drug sensitivity through pan-cancer studies. Furthermore, gene expression data and clinical data were downloaded from The Cancer Genome Atlas. Next, through a series of bioinformatics analyses, DNase expression and survival, immune subtypes, tumor microenvironment and drug sensitivity in 33 tumor types were systematically studied. The expression of the DNase gene family was shown to have an apparent intratumoral heterogeneity. The expression of DNase 2, lysosomal (DNASE2) was the highest in tumors, whereas that of DNASE2 β was the lowest. DNase 1-like 3 (DNASE1L3) was mainly downregulated in tumors, whereas the rest of the DNases were mainly upregulated in tumors. The expression of DNase family members was also found to be associated with the OS rate of patients. DNase family genes may serve an essential role in the tumor microenvironment. DNase family gene expression was related to the content of cytotoxic cells, Immunescore, Stromalscore, Estimatescore and Tumorpurity. The present study also revealed that the DNase genes may be involved in the drug resistance of cancer cells. Finally, the correlation between DNase, and clinical stage and tumor microenvironment in hepatocellular carcinoma (HCC) was studied. In addition, the difference in DNASE1L3 expression between HCC and adjacent normal tissues, and the relationship between DNASE1L3 expression and clinical stage was verified by analyzing three groups in a Gene Expression Omnibus dataset and by performing immunohistochemistry. In conclusion, the present study assessed DNase gene expression, analyzed its relationship with patient OS, performed pan-cancer co-expression analysis, and assessed the association between DNase and immune infiltration subtypes, tumor microenvironment and drug sensitivity. The present study also confirmed the value of further laboratory research on DNases and their prospects in clinical cancer treatment.
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Affiliation(s)
- Qingquan Bai
- Department of Hepatology and Gastroenterology, Campus Virchow Clinic and Campus Charité Mitte, Charité University Medicine, D-13353 Berlin, Germany,Cancer Research Center, School of Medicine, Xiamen University, Xiamen, Fujian 361102, P.R. China,Correspondence to: Dr Qingquan Bai, Department of Hepatology and Gastroenterology, Campus Virchow Clinic and Campus Charité Mitte, Charité University Medicine, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Xiao He
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, P.R. China
| | - Tianhui Hu
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, Fujian 361102, P.R. China,Correspondence to: Dr Qingquan Bai, Department of Hepatology and Gastroenterology, Campus Virchow Clinic and Campus Charité Mitte, Charité University Medicine, Augustenburger Platz 1, D-13353 Berlin, Germany
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26
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Korn MA, Steffensen M, Brandl C, Royzman D, Daniel C, Winkler TH, Nitschke L. Epistatic effects of Siglec-G and DNase1 or DNase1l3 deficiencies in the development of systemic lupus erythematosus. Front Immunol 2023; 14:1095830. [PMID: 36969253 PMCID: PMC10030676 DOI: 10.3389/fimmu.2023.1095830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/20/2023] [Indexed: 03/29/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a severe autoimmune disease that displays considerable heterogeneity not only in its symptoms, but also in its environmental and genetic causes. Studies in SLE patients have revealed that many genetic variants contribute to disease development. However, often its etiology remains unknown. Existing efforts to determine this etiology have focused on SLE in mouse models revealing not only that mutations in specific genes lead to SLE development, but also that epistatic effects of several gene mutations significantly amplify disease manifestation. Genome-wide association studies for SLE have identified loci involved in the two biological processes of immune complex clearance and lymphocyte signaling. Deficiency in an inhibitory receptor expressed on B lymphocytes, Siglec-G, has been shown to trigger SLE development in aging mice, as have mutations in DNA degrading DNase1 and DNase1l3, that are involved in clearance of DNA-containing immune complexes. Here, we analyze the development of SLE-like symptoms in mice deficient in either Siglecg and DNase1 or Siglecg and DNase1l3 to evaluate potential epistatic effects of these genes. We found that germinal center B cells and follicular helper T cells were increased in aging Siglecg -/- x Dnase1 -/- mice. In contrast, anti-dsDNA antibodies and anti-nuclear antibodies were strongly increased in aging Siglecg-/- x Dnase1l3-/- mice, when compared to single-deficient mice. Histological analysis of the kidneys revealed glomerulonephritis in both Siglecg -/- x Dnase1 -/- and Siglecg-/- x Dnase1l3-/- mice, but with a stronger glomerular damage in the latter. Collectively, these findings underscore the impact of the epistatic effects of Siglecg with DNase1 and Dnase1l3 on disease manifestation and highlight the potential combinatory effects of other gene mutations in SLE.
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Affiliation(s)
- Marina A. Korn
- Division of Genetics, Department of Biology, University of Erlangen, Erlangen, Germany
| | - Marie Steffensen
- Division of Genetics, Department of Biology, University of Erlangen, Erlangen, Germany
| | - Carolin Brandl
- Division of Genetics, Department of Biology, University of Erlangen, Erlangen, Germany
| | - Dmytro Royzman
- Division of Genetics, Department of Biology, University of Erlangen, Erlangen, Germany
- Department of Immune Modulation, University Hospital of Erlangen, Erlangen, Germany
| | - Christoph Daniel
- Department of Nephropathology, University Hospital of Erlangen, Erlangen, Germany
| | - Thomas H. Winkler
- Division of Genetics, Department of Biology, University of Erlangen, Erlangen, Germany
| | - Lars Nitschke
- Division of Genetics, Department of Biology, University of Erlangen, Erlangen, Germany
- *Correspondence: Lars Nitschke,
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27
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Zhao N, Wu W, Wang Y, Song K, Chen G, Chen Y, Wang R, Xu J, Cui K, Chen H, Tan W, Zhang J, Xiao Z. DNA-modularized construction of bivalent ligands precisely regulates receptor binding and activation. Chem 2023. [DOI: 10.1016/j.chempr.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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28
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Abstract
Cell-free DNA (cfDNA) is nonrandomly fragmented and contains a wealth of molecular information useful for noninvasive prenatal testing and cancer detection. cfDNA fragmentomics contains information beyond genetics, such as gene expression inference. However, the feasibility of using cfDNA fragmentomics for deducing cfDNA methylomics remains unexplored. This study demonstrated the possibility of using cfDNA fragmentation patterns to deduce the methylation patterns of cfDNA molecules, breaking free from the limitation of bisulfite sequencing. By using cfDNA cleavage profiles surrounding a cytosine-phosphate-guanine (CpG) site, we determined the methylation status ranging from a particular region down to a single CpG assisted by a deep learning algorithm. Both genetic and epigenetic information of cfDNA can therefore be obtained in a single nondestructive assay. Cell-free DNA (cfDNA) fragmentation patterns contain important molecular information linked to tissues of origin. We explored the possibility of using fragmentation patterns to predict cytosine-phosphate-guanine (CpG) methylation of cfDNA, obviating the use of bisulfite treatment and associated risks of DNA degradation. This study investigated the cfDNA cleavage profile surrounding a CpG (i.e., within an 11-nucleotide [nt] window) to analyze cfDNA methylation. The cfDNA cleavage proportion across positions within the window appeared nonrandom and exhibited correlation with methylation status. The mean cleavage proportion was ∼twofold higher at the cytosine of methylated CpGs than unmethylated ones in healthy controls. In contrast, the mean cleavage proportion rapidly decreased at the 1-nt position immediately preceding methylated CpGs. Such differential cleavages resulted in a characteristic change in relative presentations of CGN and NCG motifs at 5′ ends, where N represented any nucleotide. CGN/NCG motif ratios were correlated with methylation levels at tissue-specific methylated CpGs (e.g., placenta or liver) (Pearson’s absolute r > 0.86). cfDNA cleavage profiles were thus informative for cfDNA methylation and tissue-of-origin analyses. Using CG-containing end motifs, we achieved an area under a receiver operating characteristic curve (AUC) of 0.98 in differentiating patients with and without hepatocellular carcinoma and enhanced the positive predictive value of nasopharyngeal carcinoma screening (from 19.6 to 26.8%). Furthermore, we elucidated the feasibility of using cfDNA cleavage patterns to deduce CpG methylation at single CpG resolution using a deep learning algorithm and achieved an AUC of 0.93. FRAGmentomics-based Methylation Analysis (FRAGMA) presents many possibilities for noninvasive prenatal, cancer, and organ transplantation assessment.
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29
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Dhawan UK, Margraf A, Lech M, Subramanian M. Hypercholesterolemia promotes autoantibody production and a lupus-like pathology via decreased DNase-mediated clearance of DNA. J Cell Mol Med 2022; 26:5267-5276. [PMID: 36098213 PMCID: PMC9575094 DOI: 10.1111/jcmm.17556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/28/2022] Open
Abstract
Hypercholesterolemia exacerbates autoimmune response and accelerates the progression of several autoimmune disorders, but the mechanistic basis is not well understood. We recently demonstrated that hypercholesterolemia is associated with increased serum extracellular DNA levels secondary to a defect in DNase-mediated clearance of DNA. In this study, we tested whether the impaired DNase response plays a causal role in enhancing anti-nuclear antibody levels and renal immune complex deposition in an Apoe-/- mouse model of hypercholesterolemia. We demonstrate that hypercholesterolemic mice have enhanced anti-ds-DNA and anti-nucleosome antibody levels which is associated with increased immune complex deposition in the renal glomerulus. Importantly, treatment with DNase1 led to a decrease in both the autoantibody levels as well as renal pathology. Additionally, we show that humans with hypercholesterolemia have decreased systemic DNase activity and increased anti-nuclear antibodies. In this context, our data suggest that recombinant DNase1 may be an attractive therapeutic strategy to lower autoimmune response and disease progression in patients with autoimmune disorders associated with concomitant hypercholesterolemia.
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Affiliation(s)
- Umesh Kumar Dhawan
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Andreas Margraf
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Maciej Lech
- LMU Hospital Department of Medicine, Munich, Germany
| | - Manikandan Subramanian
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
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30
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McCord JJ, Engavale M, Masoumzadeh E, Villarreal J, Mapp B, Latham MP, Keyel PA, Sutton RB. Structural features of Dnase1L3 responsible for serum antigen clearance. Commun Biol 2022; 5:825. [PMID: 35974043 PMCID: PMC9381713 DOI: 10.1038/s42003-022-03755-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
Autoimmunity develops when extracellular DNA released from dying cells is not cleared from serum. While serum DNA is primarily digested by Dnase1 and Dnase1L3, Dnase1 cannot rescue autoimmunity arising from Dnase1L3 deficiencies. Dnase1L3 uniquely degrades antigenic forms of cell-free DNA, including DNA complexed with lipids and proteins. The distinct activity of Dnase1L3 relies on its unique C-terminal Domain (CTD), but the mechanism is unknown. We used multiple biophysical techniques and functional assays to study the interplay between the core catalytic domain and the CTD. While the core domain resembles Dnase1, there are key structural differences between the two enzymes. First, Dnase1L3 is not inhibited by actin due to multiple differences in the actin recognition site. Second, the CTD augments the ability of the core to bind DNA, thereby facilitating the degradation of complexed DNA. Together, these structural insights will inform the development of Dnase1L3-based therapies for autoimmunity.
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Affiliation(s)
- Jon J McCord
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA
| | - Minal Engavale
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - Elahe Masoumzadeh
- Texas Tech University, Dept. of Chemistry & Biochemistry, Lubbock, TX, USA
| | - Johanna Villarreal
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA
| | - Britney Mapp
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - Michael P Latham
- Texas Tech University, Dept. of Chemistry & Biochemistry, Lubbock, TX, USA
| | - Peter A Keyel
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - R Bryan Sutton
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA.
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31
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Li B, Ge YZ, Yan WW, Gong B, Cao K, Zhao R, Li C, Zhang YW, Jiang YH, Zuo S. DNASE1L3 inhibits proliferation, invasion and metastasis of hepatocellular carcinoma by interacting with β-catenin to promote its ubiquitin degradation pathway. Cell Prolif 2022; 55:e13273. [PMID: 35748106 PMCID: PMC9436914 DOI: 10.1111/cpr.13273] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/02/2022] [Accepted: 05/11/2022] [Indexed: 01/27/2023] Open
Abstract
As a member of the deoxyribonuclease 1 family, DNASE1L3 plays a significant role both inside and outside the cell. However, the role of DNASE1L3 in hepatocellular carcinoma (HCC) and its molecular basis remains to be further investigated. In this study, we report that DNASE1L3 is downregulated in clinical HCC samples and evaluate the relationship between its expression and HCC clinical features. In vivo and in vitro experiments showed that DNASE1L3 negatively regulates the proliferation, invasion and metastasis of HCC cells. Mechanistic studies showed that DNASE1L3 recruits components of the cytoplasmic β‐catenin destruction complex (GSK‐3β and Axin), promotes the ubiquitination degradation of β‐catenin, and inhibits its nuclear transfer, thus, decreasing c‐Myc, P21 and P27 level. Ultimately, cell cycle and EMT signals are restrained. In general, this study provides new insight into the mechanism for HCC and suggests that DNASE1L3 can become a considerable target for HCC.
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Affiliation(s)
- Bo Li
- Department of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, China.,Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Yu-Zhen Ge
- Department of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Wei-Wei Yan
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Bin Gong
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Kun Cao
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Rui Zhao
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Chao Li
- Department of General Surgery, The First People's Hospital of Fuquan, Fuquan, Guizhou, China
| | - Ye-Wei Zhang
- Department of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yi-Heng Jiang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Shi Zuo
- Department of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou, China.,Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
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Mori G, Delfino D, Pibiri P, Rivetti C, Percudani R. Origin and significance of the human DNase repertoire. Sci Rep 2022; 12:10364. [PMID: 35725583 PMCID: PMC9208542 DOI: 10.1038/s41598-022-14133-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/01/2022] [Indexed: 11/23/2022] Open
Abstract
The human genome contains four DNase1 and two DNase2 genes. The origin and functional specialization of this repertoire are not fully understood. Here we use genomics and transcriptomics data to infer the evolutionary history of DNases and investigate their biological significance. Both DNase1 and DNase2 families have expanded in vertebrates since ~ 650 million years ago before the divergence of jawless and jawed vertebrates. DNase1, DNase1L1, and DNase1L3 co-existed in jawless fish, whereas DNase1L2 originated in amniotes by tandem duplication of DNase1. Among the non-human DNases, DNase1L4 and newly identified DNase1L5 derived from early duplications that were lost in terrestrial vertebrates. The ancestral gene of the DNase2 family, DNase2b, has been conserved in synteny with the Uox gene across 700 million years of animal evolution,while DNase2 originated in jawless fish. DNase1L1 acquired a GPI-anchor for plasma membrane attachment in bony fishes, and DNase1L3 acquired a C-terminal basic peptide for the degradation of microparticle DNA in jawed vertebrates. The appearance of DNase1L2, with a distinct low pH optimum and skin localization, is among the amniote adaptations to life on land. The expansion of the DNase repertoire in vertebrates meets the diversified demand for DNA debris removal in complex multicellular organisms.
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Affiliation(s)
- Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy.
| | - Danila Delfino
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Paola Pibiri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy.
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Protease and DNase Activities of a Very Stable High-Molecular-Mass Multiprotein Complex from Sea Cucumber Eupentacta fraudatrix. Int J Mol Sci 2022; 23:ijms23126677. [PMID: 35743119 PMCID: PMC9224385 DOI: 10.3390/ijms23126677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 12/04/2022] Open
Abstract
Only some human organs, including the liver, are capable of very weak self-regeneration. Some marine echinoderms are very useful for studying the self-regeneration processes of organs and tissues. For example, sea cucumbers Eupentacta fraudatrix (holothurians) demonstrate complete restoration of all organs and the body within several weeks after their division into two parts. Therefore, these cucumbers are a prospective model for studying the general mechanisms of self-regeneration. However, there is no data available yet concerning biomolecules of holothurians, which can stimulate the processes of organ and whole-body regeneration. Investigation of these restoration mechanisms is very important for modern medicine and biology because it can help to understand which hormones, nucleic acids, proteins, enzymes, or complexes play an essential role in self-regeneration. It is possible that stable, polyfunctional, high-molecular-weight protein complexes play an essential role in these processes. It has recently been shown that sea cucumbers Eupentacta fraudatrix contain a very stable multiprotein complex of about 2000 kDa. The first analysis of possible enzymatic activities of a stable protein complex was carried out in this work, revealing that the complex possesses several protease and DNase activities. The complex metalloprotease is activated by several metal ions (Zn2+ > Mn2+ > Mg2+). The relative contribution of metalloproteases (~63.4%), serine-like protease (~30.5%), and thiol protease (~6.1%) to the total protease activity of the complex was estimated. Metal-independent proteases of the complex hydrolyze proteins at trypsin-specific sites (after Lys and Arg). The complex contains both metal-dependent and metal-independent DNases. Mg2+, Mn2+, and Co2+ ions were found to strongly increase the DNase activity of the complex.
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Mamtimin M, Pinarci A, Han C, Braun A, Anders HJ, Gudermann T, Mammadova-Bach E. Extracellular DNA Traps: Origin, Function and Implications for Anti-Cancer Therapies. Front Oncol 2022; 12:869706. [PMID: 35574410 PMCID: PMC9092261 DOI: 10.3389/fonc.2022.869706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/07/2022] [Indexed: 12/16/2022] Open
Abstract
Extracellular DNA may serve as marker in liquid biopsies to determine individual diagnosis and prognosis in cancer patients. Cell death or active release from various cell types, including immune cells can result in the release of DNA into the extracellular milieu. Neutrophils are important components of the innate immune system, controlling pathogens through phagocytosis and/or the release of neutrophil extracellular traps (NETs). NETs also promote tumor progression and metastasis, by modulating angiogenesis, anti-tumor immunity, blood clotting and inflammation and providing a supportive niche for metastasizing cancer cells. Besides neutrophils, other immune cells such as eosinophils, dendritic cells, monocytes/macrophages, mast cells, basophils and lymphocytes can also form extracellular traps (ETs) during cancer progression, indicating possible multiple origins of extracellular DNA in cancer. In this review, we summarize the pathomechanisms of ET formation generated by different cell types, and analyze these processes in the context of cancer. We also critically discuss potential ET-inhibiting agents, which may open new therapeutic strategies for cancer prevention and treatment.
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Affiliation(s)
- Medina Mamtimin
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Akif Pinarci
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany
| | - Chao Han
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Attila Braun
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany
| | - Hans-Joachim Anders
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Thomas Gudermann
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,German Center for Lung Research, Munich, Germany
| | - Elmina Mammadova-Bach
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
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35
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Hashimoto T, Ueki S, Kamide Y, Miyabe Y, Fukuchi M, Yokoyama Y, Furukawa T, Azuma N, Oka N, Takeuchi H, Kanno K, Ishida-Yamamoto A, Taniguchi M, Hashiramoto A, Matsui K. Increased Circulating Cell-Free DNA in Eosinophilic Granulomatosis With Polyangiitis: Implications for Eosinophil Extracellular Traps and Immunothrombosis. Front Immunol 2022; 12:801897. [PMID: 35095884 PMCID: PMC8790570 DOI: 10.3389/fimmu.2021.801897] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/20/2021] [Indexed: 12/21/2022] Open
Abstract
Background Endogenous DNA derived from nuclei or mitochondria is released into the blood circulation as cell-free DNA (cfDNA) following cell damage or death. cfDNA is associated with various pathological conditions; however, its clinical significance in antineutrophil cytoplasmic antibody-associated vasculitis (AAV) remains unclear. This study aimed to evaluate the clinical significance of cfDNA in AAV. Methods We enrolled 35 patients with AAV, including 10 with eosinophilic granulomatosis with polyangiitis (EGPA), 13 with microscopic polyangiitis, and 12 with granulomatosis with polyangiitis. Serum cf-nuclear DNA (cf-nDNA) and cf-mitochondrial DNA (cf-mtDNA) levels were measured by quantitative polymerase chain reaction before and after the initiation of immunosuppressive therapy. Tissue samples from EGPA patients were examined by immunofluorescence and transmission electron microscopy. The structure of eosinophil extracellular traps (EETs) and neutrophil extracellular traps (NETs) and stability against DNase were assessed in vitro. Platelet adhesion of EETs were also assessed. Results Serum cf-nDNA and cf-mtDNA levels were significantly higher in AAV than in healthy controls, with the highest levels in EGPA; however, serum DNase activities were comparable among all groups. cf-nDNA and cf-mtDNA decreased after treatment and were associated with disease activity only in EGPA. Blood eosinophil count and plasma D-dimer levels were significantly correlated with cf-nDNA in EGPA and cf-mtDNA. EGPA tissue samples showed lytic eosinophils and EETs in small-vessel thrombi. The structure of EETs showed bolder net-like chromatin threads in vitro and EETs showed greater stability against DNase than NETs. EETs provided a scaffold for platelet adhesion. Conclusion cfDNA was increased in EGPA, associated with disease activity. The presence of DNase-resistant EETs in small-vessel thrombi might contribute to higher concentration of cfDNA and the occurrence of immunothrombosis in EGPA.
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Affiliation(s)
- Teppei Hashimoto
- Division of Diabetes, Endocrinology and Clinical Immunology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya, Japan
| | - Shigeharu Ueki
- Department of General Internal Medicine and Clinical Laboratory Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Yosuke Kamide
- National Hospital Organization Sagamihara National Hospital, Clinical Research Center, Sagamihara, Japan
| | - Yui Miyabe
- Department of General Internal Medicine and Clinical Laboratory Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Mineyo Fukuchi
- Department of General Internal Medicine and Clinical Laboratory Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Yuichi Yokoyama
- Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Tetsuya Furukawa
- Division of Diabetes, Endocrinology and Clinical Immunology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya, Japan
| | - Naoto Azuma
- Division of Diabetes, Endocrinology and Clinical Immunology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya, Japan
| | - Nobuyuki Oka
- Department of Neurology, Kyoto Konoe Rehabilitation Hospital, Kyoto, Japan
| | - Hiroki Takeuchi
- Department of Neurology, National Hospital Organization Minami Kyoto Hospital, Kyoto, Japan
| | - Kyoko Kanno
- Department of Dermatology, Asahikawa Medical University, Asahikawa, Japan
| | | | - Masami Taniguchi
- National Hospital Organization Sagamihara National Hospital, Clinical Research Center, Sagamihara, Japan
| | - Akira Hashiramoto
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Kiyoshi Matsui
- Division of Diabetes, Endocrinology and Clinical Immunology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya, Japan
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Hudecova I, Smith CG, Hänsel-Hertsch R, Chilamakuri CS, Morris JA, Vijayaraghavan A, Heider K, Chandrananda D, Cooper WN, Gale D, Garcia-Corbacho J, Pacey S, Baird RD, Rosenfeld N, Mouliere F. Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA. Genome Res 2022; 32:215-227. [PMID: 34930798 PMCID: PMC8805718 DOI: 10.1101/gr.275691.121] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 12/16/2021] [Indexed: 11/24/2022]
Abstract
Current evidence suggests that plasma cell-free DNA (cfDNA) is fragmented around a mode of 166 bp. Data supporting this view has been mainly acquired through the analysis of double-stranded cfDNA. The characteristics and diagnostic potential of single-stranded and damaged double-stranded cfDNA in healthy individuals and cancer patients remain unclear. Here, through a combination of high-affinity magnetic bead-based DNA extraction and single-stranded DNA sequencing library preparation (MB-ssDNA), we report the discovery of a large proportion of cfDNA fragments centered at ∼50 bp. We show that these "ultrashort" cfDNA fragments have a greater relative abundance in plasma of healthy individuals (median = 19.1% of all sequenced cfDNA fragments, n = 28) than in plasma of patients with cancer (median = 14.2%, n = 21, P < 0.0001). The ultrashort cfDNA fragments map to accessible chromatin regions of blood cells, particularly in promoter regions with the potential to adopt G-quadruplex (G4) DNA secondary structures. G4-positive promoter chromatin accessibility is significantly enriched in ultrashort plasma cfDNA fragments from healthy individuals relative to patients with cancers (P < 0.0001), in whom G4-cfDNA enrichment is inversely associated with copy number aberration-inferred tumor fractions. Our findings redraw the landscape of cfDNA fragmentation by identifying and characterizing a novel population of ultrashort plasma cfDNA fragments. Sequencing of MB-ssDNA libraries could facilitate the characterization of gene regulatory regions and DNA secondary structures via liquid biopsy. Our data underline the diagnostic potential of ultrashort cfDNA through classification for cancer patients.
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Affiliation(s)
- Irena Hudecova
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Christopher G Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Robert Hänsel-Hertsch
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Center for Molecular Medicine Cologne CMMC, University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital Cologne, 50931 Cologne, Germany
- Institute of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
| | - Chandra S Chilamakuri
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - James A Morris
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Aadhitthya Vijayaraghavan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Katrin Heider
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Wendy N Cooper
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Davina Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Javier Garcia-Corbacho
- Clinical Trials Unit, Clinic Institute of Hematological and Oncological Diseases, Hospital Clinic, 170 08036 Barcelona, Spain
| | - Simon Pacey
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Richard D Baird
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
| | - Florent Mouliere
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Centre Amsterdam, 1081 HV Amsterdam, The Netherlands
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cfDNA and DNases: New Biomarkers of Sepsis in Preterm Neonates-A Pilot Study. Cells 2022; 11:cells11020192. [PMID: 35053308 PMCID: PMC8774011 DOI: 10.3390/cells11020192] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/10/2022] Open
Abstract
INTRODUCTION An early and accurate diagnosis of early onset neonatal sepsis (EONS) and late onset neonatal sepsis (LONS) is essential to improve the outcome of this devastating conditions. Especially, preterm infants are at risk. Reliable biomarkers are rare, clinical decision-making depends on clinical appearance and multiple laboratory findings. Markers of NET formation and NET turnover might improve diagnostic precision. Aim of this study was to evaluate the diagnostic value of NETs in sepsis diagnosis in neonatal preterm infants. METHODS Plasma samples of neonatal preterm infants with suspected sepsis were collected. Blood samples were assayed for markers of NET formation and NET turnover: cfDNA, DNase1, nucleosome, NE, and H3Cit. All clinical findings, values of laboratory markers, and epidemiological characteristics were collected retrospectively. Two subpopulations were created to divide EONS from LONS. EMA sepsis criteria for neonatal sepsis were used to generate a sepsis group (EMA positive) and a control group (EMA negative). RESULTS A total of 31 preterm neonates with suspected sepsis were included. Out of these, nine patients met the criteria for sepsis according to EMA. Regarding early onset neonatal sepsis (3 EONS vs. 10 controls), cfDNA, DNase I, nucleosome, and CRP were elevated significantly. H3Cit and NE did not show any significant elevations. In the late onset sepsis collective (6 LONS vs. 12 controls), cfDNA, DNase I, and CRP differed significantly compared to control group.
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Xiao Y, Yang K, Liu P, Ma D, Lei P, Liu Q. Deoxyribonuclease 1-like 3 Inhibits Hepatocellular Carcinoma Progression by Inducing Apoptosis and Reprogramming Glucose Metabolism. Int J Biol Sci 2022; 18:82-95. [PMID: 34975319 PMCID: PMC8692146 DOI: 10.7150/ijbs.57919] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/20/2021] [Indexed: 12/21/2022] Open
Abstract
HCC has remained one of the challenging cancers to treat, owing to the paucity of drugs targeting the critical survival pathways. Considering the cancer cells are deficient in DNase activity, the increase of an autonomous apoptisis endonuclease should be a reasonable choice for cancer treatment. In this study, we investigated whether DNASE1L3, an endonuclease implicated in apoptosis, could inhibit the progress of HCC. We found DNASE1L3 was down-regulated in HCC tissues, whereas its high expression was positively associated with the favorable prognosis of patients with HCC. Besides, serum DNASE1L3 levels were lower in HCC patients than in healthy individuals. Functionally, we found that DNASE1L3 inhibited the proliferation of tumor cells by inducing G0/G1 cell cycle arrest and cell apoptosis in vitro. Additionally, DNASE1L3 overexpression suppressed tumor growth in vivo. Furthermore, we found that DNASE1L3 overexpression weakened glycolysis in HCC cells and tissues via inactivating the rate-limiting enzymes involved in PTPN2-HK2 and CEBPβ-p53-PFK1 pathways. Finally, we identified the HBx to inhibit DNASE1L3 expression by up-regulating the expression of ZNF384. Collectively, our findings demonstrated that DNASE1L3 could inhibit the HCC progression through inducing cell apoptosis and weakening glycolysis. We believe DNASE1L3 could be considered as a promising prognostic biomarker and therapeutic target for HCC.
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Affiliation(s)
- Yusha Xiao
- Department of Cardiovascular Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, P.R. China.,Department of Hepatobiliary Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, P.R. China
| | - Kang Yang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Pengpeng Liu
- Department of Hepatobiliary Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, P.R. China
| | - Dong Ma
- Department of Hepatobiliary Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, P.R. China
| | - Ping Lei
- Department of Geriatrics, Tianjin Medical University General Hospital Hospital, Tianjin, 300052, P.R. China
| | - Quanyan Liu
- Department of Hepatobiliary Surgery, Tianjin Medical University General Hospital , Tianjin, 300052, P.R. China
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Li T, Yum S, Li M, Chen X, Zuo X, Chen ZJ. TBK1 recruitment to STING mediates autoinflammatory arthritis caused by defective DNA clearance. J Exp Med 2022; 219:e20211539. [PMID: 34901991 PMCID: PMC8672646 DOI: 10.1084/jem.20211539] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/28/2021] [Accepted: 11/17/2021] [Indexed: 01/02/2023] Open
Abstract
Defective DNA clearance in DNase II-/- mice leads to lethal inflammatory diseases that can be rescued by deleting cGAS or STING, but the role of distinct signaling pathways downstream of STING in the disease manifestation is not known. We found that the STING S365A mutation, which abrogates IRF3 binding and type I interferon induction, rescued the embryonic lethality of DNase II-/- mice. However, the STING S365A mutant retains the ability to recruit TBK1 and activate NF-κB, and DNase II-/-STING-S365A mice exhibited severe polyarthritis, which was alleviated by neutralizing antibodies against TNF-α or IL-6 receptor. In contrast, the STING L373A mutation or C-terminal tail truncation, which disrupts TBK1 binding and therefore prevents activation of both IRF3 and NF-κB, completely rescued the phenotypes of DNase II-/- mice. These results demonstrate that TBK1 recruitment to STING mediates autoinflammatory arthritis independently of type I interferons. Inhibiting TBK1 binding to STING may be a therapeutic strategy for certain autoinflammatory diseases instigated by self-DNA.
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Affiliation(s)
- Tong Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Seoyun Yum
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX
| | - Minghao Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xiang Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhijian J. Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX
- Center for Inflammation Research, University of Texas Southwestern Medical Center, Dallas, TX
- Howard Hughes Medical Institute, Chevy Chase, MD
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Ding SC, Chan RWY, Peng W, Huang L, Zhou Z, Hu X, Volpi S, Hiraki LT, Vaglio A, Fenaroli P, Bocca P, Tam LS, Wong PCH, Tam LHP, Jiang P, Chiu RWK, Allen Chan KC, Dennis Lo YM. OUP accepted manuscript. Clin Chem 2022; 68:917-926. [PMID: 35587043 DOI: 10.1093/clinchem/hvac050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/15/2022] [Indexed: 11/14/2022]
Affiliation(s)
- Spencer C Ding
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rebecca W Y Chan
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wenlei Peng
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Liangbo Huang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Ze Zhou
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Xi Hu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Stefano Volpi
- Clinica Pediatrica e Reumatologia, Centro per le malattie Autoinfiammatorie e Immunodeficienze, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genova, Italy
- Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-Infantili (DINOGMI), Università degli Studi di Genova, Genova, Italy
| | - Linda T Hiraki
- Division of Rheumatology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Augusto Vaglio
- Department of Biomedical, Experimental and Clinical Sciences Mario Serio, University of Florence, Florence, Italy
- Medical Genetics Unit, Meyer Children's Hospital, Florence, Italy
- Nephrology and Dialysis Unit, Meyer Children's Hospital, Florence, Italy
| | | | - Paola Bocca
- Clinica Pediatrica e Reumatologia, Centro per le malattie Autoinfiammatorie e Immunodeficienze, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, Genova, Italy
| | - Lai Shan Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Priscilla C H Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Lydia H P Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - K C Allen Chan
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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Balian A, Hernandez FJ. Nucleases as molecular targets for cancer diagnosis. Biomark Res 2021; 9:86. [PMID: 34809722 PMCID: PMC8607607 DOI: 10.1186/s40364-021-00342-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
Early cancer diagnosis is a crucial element to improved treatment options and survival. Great research efforts have been made in the search for better performing cancer diagnostic biomarkers. However, the quest continues as novel biomarkers with high accuracy for an early diagnosis remain an unmet clinical need. Nucleases, which are enzymes capable of cleaving nucleic acids, have been long considered as potential cancer biomarkers. The implications of nucleases are key for biological functions, their presence in different cellular counterparts and catalytic activity led the enthusiasm towards investigating the role of nucleases as promising cancer biomarkers. However, the most essential feature of these proteins, which is their enzymatic activity, has not been fully exploited. This review discusses nucleases interrogated as cancer biomarkers, providing a glimpse of their physiological roles. Moreover, it highlights the potential of harnessing the enzymatic activity of cancer-associated nucleases as a novel diagnostic biomarker using nucleic acid probes as substrates.
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Affiliation(s)
- Alien Balian
- Department of Physics, Chemistry and Biology, Linköping University, 58185, Linköping, Sweden
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Frank J Hernandez
- Department of Physics, Chemistry and Biology, Linköping University, 58185, Linköping, Sweden.
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden.
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Gossypol Treatment Restores Insufficient Apoptotic Function of DFF40/CAD in Human Glioblastoma Cells. Cancers (Basel) 2021; 13:cancers13215579. [PMID: 34771741 PMCID: PMC8583586 DOI: 10.3390/cancers13215579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/30/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Glioblastoma (GBM) is a highly aggressive brain tumor and almost all patients die because of relapses. GBM-derived cells undergo cell death without nuclear fragmentation upon treatment with different apoptotic agents. Nuclear dismantling determines the point-of-no-return in the apoptotic process. DFF40/CAD is the main endonuclease implicated in apoptotic nuclear disassembly. To be properly activated, DFF40/CAD should reside in the cytosol. However, the endonuclease is poorly expressed in the cytosol and remains cumulated in the nucleus of GBM cells. Here, by employing commercial and non-commercial patient-derived GBM cells, we demonstrate that the natural terpenoid aldehyde gossypol prompts DFF40/CAD-dependent nuclear fragmentation. A comparative analysis between gossypol- and staurosporine-treated cells evidenced that levels of neither caspase activation nor DNA damage were correlated with the ability of each compound to induce nuclear fragmentation. Deconvoluted confocal images revealed that DFF40/CAD was almost completely excluded from the nucleus early after the staurosporine challenge. However, gossypol-treated cells maintained DFF40/CAD in the nucleus for longer times, shaping a ribbon-like structure piercing the nuclear fragments and building a network of bridged masses of compacted chromatin. Therefore, GBM cells can fragment their nuclei if treated with the adequate insult, making the cell death process irreversible.
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43
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Dhawan UK, Bhattacharya P, Narayanan S, Manickam V, Aggarwal A, Subramanian M. Hypercholesterolemia Impairs Clearance of Neutrophil Extracellular Traps and Promotes Inflammation and Atherosclerotic Plaque Progression. Arterioscler Thromb Vasc Biol 2021; 41:2598-2615. [PMID: 34348488 PMCID: PMC8454501 DOI: 10.1161/atvbaha.120.316389] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/26/2021] [Indexed: 01/02/2023]
Abstract
Objective: Hypercholesterolemia-induced NETosis and accumulation of neutrophil extracellular traps (NETs) in the atherosclerotic lesion exacerbates inflammation and is causally implicated in plaque progression. We investigated whether hypercholesterolemia additionally impairs the clearance of NETs mediated by endonucleases such as DNase1 and DNase1L3 and its implication in advanced atherosclerotic plaque progression. Approach and Results: Using a mouse model, we demonstrate that an experimental increase in the systemic level of NETs leads to a rapid increase in serum DNase activity, which is critical for the prompt clearance of NETs and achieving inflammation resolution. Importantly, hypercholesterolemic mice demonstrate an impairment in this critical NET-induced DNase response with consequent delay in the clearance of NETs and defective inflammation resolution. Administration of tauroursodeoxycholic acid, a chemical chaperone that relieves endoplasmic reticulum stress, rescued the hypercholesterolemia-induced impairment in the NET-induced DNase response suggesting a causal role for endoplasmic reticulum stress in this phenomenon. Correction of the defective DNase response with exogenous supplementation of DNase1 in Apoe-/- mice with advanced atherosclerosis resulted in a decrease in plaque NET content and significant plaque remodeling with decreased area of plaque necrosis and increased collagen content. From a translational standpoint, we demonstrate that humans with hypercholesterolemia have elevated systemic extracellular DNA levels and decreased plasma DNase activity. Conclusions: These data suggest that hypercholesterolemia impairs the NET-induced DNase response resulting in defective clearance and accumulation of NETs in the atherosclerotic plaque. Therefore, strategies aimed at rescuing this defect could be of potential therapeutic benefit in promoting inflammation resolution and atherosclerotic plaque stabilization.
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Affiliation(s)
- Umesh Kumar Dhawan
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (U.K.D., M.S.)
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
| | - Purbasha Bhattacharya
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
- Academy of Scientific and Innovative Research, Ghaziabad, India (P.B., A.A.)
| | - Sriram Narayanan
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
| | - Vijayprakash Manickam
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
| | - Ayush Aggarwal
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
- Academy of Scientific and Innovative Research, Ghaziabad, India (P.B., A.A.)
| | - Manikandan Subramanian
- Centre for Biochemical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (U.K.D., M.S.)
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India (U.K.D., P.B., S.N., V.M., A.A., M.S.)
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Zanini G, De Gaetano A, Selleri V, Savino G, Cossarizza A, Pinti M, Mattioli AV, Nasi M. Mitochondrial DNA and Exercise: Implications for Health and Injuries in Sports. Cells 2021; 10:cells10102575. [PMID: 34685555 PMCID: PMC8533813 DOI: 10.3390/cells10102575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 12/31/2022] Open
Abstract
Recently, several studies have highlighted the tight connection between mitochondria and physical activity. Mitochondrial functions are important in high-demanding metabolic activities, such as endurance sports. Moreover, regular training positively affects metabolic health by increasing mitochondrial oxidative capacity and regulating glucose metabolism. Exercise could have multiple effects, also on the mitochondrial DNA (mtDNA) and vice versa; some studies have investigated how mtDNA polymorphisms can affect the performance of general athletes and mtDNA haplogroups seem to be related to the performance of elite endurance athletes. Along with several stimuli, including pathogens, stress, trauma, and reactive oxygen species, acute and intense exercise also seem to be responsible for mtDNA release into the cytoplasm and extracellular space, leading to the activation of the innate immune response. In addition, several sports are characterized by a higher frequency of injuries, including cranial trauma, associated with neurological consequences. However, with regular exercise, circulating cell-free mtDNA levels are kept low, perhaps promoting cf-mtDNA removal, acting as a protective factor against inflammation.
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Affiliation(s)
- Giada Zanini
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (G.Z.); (A.D.G.); (V.S.); (M.P.)
| | - Anna De Gaetano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (G.Z.); (A.D.G.); (V.S.); (M.P.)
- National Institute for Cardiovascular Research-INRC, 40126 Bologna, Italy; (A.C.); (A.V.M.)
| | - Valentina Selleri
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (G.Z.); (A.D.G.); (V.S.); (M.P.)
| | - Gustavo Savino
- Department of Public Healthcare, Sports Medicine Service, Azienda USL of Modena, 41121 Modena, Italy;
| | - Andrea Cossarizza
- National Institute for Cardiovascular Research-INRC, 40126 Bologna, Italy; (A.C.); (A.V.M.)
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Marcello Pinti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (G.Z.); (A.D.G.); (V.S.); (M.P.)
| | - Anna Vittoria Mattioli
- National Institute for Cardiovascular Research-INRC, 40126 Bologna, Italy; (A.C.); (A.V.M.)
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Milena Nasi
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Correspondence: ; Tel.: +39-059-205-5422
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DNase activity in human seminal plasma and follicular fluid and its inhibition by follicular fluid chelating agents. Reprod Biomed Online 2021; 43:1079-1086. [PMID: 34753679 DOI: 10.1016/j.rbmo.2021.09.015] [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: 05/17/2021] [Revised: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 11/23/2022]
Abstract
RESEARCH QUESTION What is the mechanism by which human follicular fluid inhibits seminal plasma DNase activity? DESIGN Human genomic DNA was incubated with human follicular fluid and seminal plasma (reaction mixture) under different experimental conditions; increasing volumes of human follicular fluid; proteinase K digested or heat inactivated human follicular fluid; and the addition of Ca2+ or Mg2+ to the reaction mixture. RESULTS Increasing volume of human follicular fluid resulted in a dose-dependent inhibition of seminal plasma DNase activity. Inhibition was not caused by proteins in the human follicular fluid as digestion with proteinase K or heat inactivation of human follicular fluid failed to abolish its inhibitory effect. Addition of divalent cations resulted in a reversion of the inhibitory effect, providing evidence that human follicular fluid inhibition of seminal plasma DNase activity seems to be mediated by a compound with chelating activity. Furthermore, incubation of genomic DNA with human follicular fluid in the presence of divalent cations served to elicit the existence of DNase activity. CONCLUSIONS Human follicular fluid seems to contain a molecule or molecules with chelating capacity that inhibits DNase activity of both follicular fluid and seminal plasma. Our findings provide new insight to understanding sperm preservation and the physiology of fertilization biology.
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46
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Verhülsdonk L, Mannherz HG, Napirei M. Comparison of the secretory murine DNase1 family members expressed in Pichia pastoris. PLoS One 2021; 16:e0253476. [PMID: 34329318 PMCID: PMC8323900 DOI: 10.1371/journal.pone.0253476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
Soluble nucleases of the deoxyribonuclease 1 (DNase1) family facilitate DNA and chromatin disposal (chromatinolysis) during certain forms of cell differentiation and death and participate in the suppression of anti-nuclear autoimmunity as well as thrombotic microangiopathies caused by aggregated neutrophil extracellular traps. Since a systematic and direct comparison of the specific activities and properties of the secretory DNase1 family members is still missing, we expressed and purified recombinant murine DNase1 (rmDNase1), DNase1-like 2 (rmDNase1L2) and DNase1-like 3 (rmDNase1L3) using Pichia pastoris. Employing different strategies for optimizing culture and purification conditions, we achieved yields of pure protein between ~3 mg/l (rmDNase1L2 and rmDNase1L3) and ~9 mg/l (rmDNase1) expression medium. Furthermore, we established a procedure for post-expressional maturation of pre-mature DNase still bound to an unprocessed tri-N-glycosylated pro-peptide of the yeast α-mating factor. We analyzed glycosylation profiles and determined specific DNase activities by the hyperchromicity assay. Additionally, we evaluated substrate specificities under various conditions at equimolar DNase isoform concentrations by lambda DNA and chromatin digestion assays in the presence and absence of heparin and monomeric skeletal muscle α-actin. Our results suggest that due to its biochemical properties mDNase1L2 can be regarded as an evolutionary intermediate isoform of mDNase1 and mDNase1L3. Consequently, our data show that the secretory DNase1 family members complement each other to achieve optimal DNA degradation and chromatinolysis under a broad spectrum of biological conditions.
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Affiliation(s)
- Lukas Verhülsdonk
- Department of Anatomy and Molecular Embryology, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
| | - Hans Georg Mannherz
- Department of Anatomy and Molecular Embryology, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Molecular and Experimental Cardiology, St. Josef-Hospital, Clinics of the Ruhr University Bochum, Bochum, Germany
| | - Markus Napirei
- Department of Anatomy and Molecular Embryology, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
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47
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Yang H, Peng Y, Xu M, Xu S, Zhou Y. Development of DNA Biosensors Based on DNAzymes and Nucleases. Crit Rev Anal Chem 2021; 53:161-176. [PMID: 34225516 DOI: 10.1080/10408347.2021.1944046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA biosensors play important roles in environmental, medical, industrial and agricultural analysis. Many DNA biosensors have been designed based on the enzyme catalytic reaction. Because of the importance of enzymes in biosensors, we present a review on this topic. In this review, the enzymes were divided into DNAzymes and nucleases according to their chemical nature. Firstly, we introduced the DNAzymes with different function inducing cleavage, metalation, peroxidase, ligation and allosterism. In this section, the G-quadruplex DNAzyme, as a hot topic in recent years, was described in detail. Then, the nucleases-assisted signal amplification method was also reviewed in three categories including exonucleases, endonucleases and other nucleases according to the digestion sites in DNA substrates. In exonucleases section, the Exo I and Exo III were selected as examples. Then, the DNase I, BamH I, nicking endonuclease, S1 nuclease, the duplex specific nuclease (DSN) and RNases were chosen to illustrate the application of endonucleases. In other nucleases section, DNA polymerases and DNA ligases were detailed. Last, the challenges and future perspectives in the field were discussed.
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Affiliation(s)
- Hualin Yang
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil &Water Pollution, Chengdu University of Technology, Chengdu, Sichuan, China
| | - Yu Peng
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Mingming Xu
- College of Life Science, Yangtze University, Jingzhou, Hubei, China
| | - Shuxia Xu
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil &Water Pollution, Chengdu University of Technology, Chengdu, Sichuan, China.,College of Ecology and Environment, Chengdu University of Technology, Chengdu, Sichuan, China
| | - Yu Zhou
- College of Life Science, Yangtze University, Jingzhou, Hubei, China.,College of Animal Science, Yangtze University, Jingzhou, Hubei, China
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Trumpff C, Michelson J, Lagranha CJ, Taleon V, Karan KR, Sturm G, Lindqvist D, Fernström J, Moser D, Kaufman BA, Picard M. Stress and circulating cell-free mitochondrial DNA: A systematic review of human studies, physiological considerations, and technical recommendations. Mitochondrion 2021; 59:225-245. [PMID: 33839318 PMCID: PMC8418815 DOI: 10.1016/j.mito.2021.04.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/23/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]
Abstract
Cell-free mitochondrial DNA (cf-mtDNA) is a marker of inflammatory disease and a predictor of mortality, but little is known about cf-mtDNA in relation to psychobiology. A systematic review of the literature reveals that blood cf-mtDNA varies in response to common real-world stressors including psychopathology, acute psychological stress, and exercise. Moreover, cf-mtDNA is inducible within minutes and exhibits high intra-individual day-to-day variation, highlighting the dynamic regulation of cf-mtDNA levels. We discuss current knowledge on the mechanisms of cf-mtDNA release, its forms of transport ("cell-free" does not mean "membrane-free"), potential physiological functions, putative cellular and neuroendocrine triggers, and factors that may contribute to cf-mtDNA removal from the circulation. A review of in vitro, pre-clinical, and clinical studies shows conflicting results around the dogma that physiological forms of cf-mtDNA are pro-inflammatory, opening the possibility of other physiological functions, including the cell-to-cell transfer of whole mitochondria. Finally, to enhance the reproducibility and biological interpretation of human cf-mtDNA research, we propose guidelines for blood collection, cf-mtDNA isolation, quantification, and reporting standards, which can promote concerted advances by the community. Defining the mechanistic basis for cf-mtDNA signaling is an opportunity to elucidate the role of mitochondria in brain-body interactions and psychopathology.
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Affiliation(s)
- Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Jeremy Michelson
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Claudia J Lagranha
- University of Pittsburgh, School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, Pittsburgh, PA, United States
| | - Veronica Taleon
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Kalpita R Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Daniel Lindqvist
- Faculty of Medicine, Department of Clinical Sciences, Psychiatry, Lund University, Lund, Sweden; Office of Psychiatry and Habilitation, Region Skåne, Sweden
| | - Johan Fernström
- Faculty of Medicine, Department of Clinical Sciences, Psychiatry, Lund University, Lund, Sweden
| | - Dirk Moser
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - Brett A Kaufman
- University of Pittsburgh, School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, Pittsburgh, PA, United States
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Medical Center, New York, USA; New York State Psychiatric Institute, NY, USA.
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49
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Basnakian AG, Moore CL. Apoptotic DNase network: Mutual induction and cooperation among apoptotic endonucleases. J Cell Mol Med 2021; 25:6496-6499. [PMID: 34085765 PMCID: PMC8278086 DOI: 10.1111/jcmm.16665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
DNA fragmentation produced by apoptotic DNases (endonucleases) leads to irreversible cell death. Although apoptotic DNases are simultaneously induced following toxic/oxidative cell injury and/or failed DNA repair, the study of DNases in apoptosis has generally been reductionist in approach, focusing on individual DNases rather than their possible cooperativity. Coordinated induction of DNases would require a mechanism of communication; however, mutual DNase induction or activation of DNases by enzymatic or non‐enzymatic mechanisms is not currently recognized. The evidence presented in this review suggests apoptotic DNases operate in a network in which members induce each other through the DNA breaks they produce. With DNA breaks being a common communicator among DNases, it would be logical to propose that DNA breaks from other sources such as oxidative DNA damage or actions of DNA repair endonucleases and DNA topoisomerases may also serve as triggers for a cooperative DNase feedback loop leading to elevated DNA fragmentation and subsequent cell death. Therefore, mutual induction of apoptotic DNases has serious implications for studies focused on activation or inhibition of specific DNases as a strategy for therapeutic intervention aimed at modulation of cell death.
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Affiliation(s)
- Alexei G Basnakian
- University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Central Arkansas Veterans Healthcare System, Little Rock, AR, USA
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Dead cell and debris clearance in the atherosclerotic plaque: Mechanisms and therapeutic opportunities to promote inflammation resolution. Pharmacol Res 2021; 170:105699. [PMID: 34087352 DOI: 10.1016/j.phrs.2021.105699] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/05/2021] [Accepted: 05/28/2021] [Indexed: 01/08/2023]
Abstract
Phagocytic clearance of dead cells and debris is critical for inflammation resolution and maintenance of tissue homeostasis. Consequently, defective clearance of dead cells and debris is associated with initiation and exacerbation of several autoimmune disorders and chronic inflammatory diseases such as atherosclerosis. The progressive loss of dead cell clearance capacity within the atherosclerotic plaque leads to accumulation of necrotic cells, chronic non-resolving inflammation, and expansion of the necrotic core, which triggers atherosclerotic plaque rupture and clinical manifestation of acute thrombotic cardiovascular adverse events. In this review, we describe the fundamental molecular and cellular mechanisms of dead cell clearance and how it goes awry in atherosclerosis. Finally, we highlight novel therapeutic strategies that enhance dead cell and debris clearance within the atherosclerotic plaque to promote inflammation resolution and atherosclerotic plaque stabilization.
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