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Li Y, Ge F, Liu C, Pu W, Lv W, Zeng Z, Yin L, Liu D, Li Y, Tang D, Han P, Dai Y. Genome-wide characterization of extrachromosomal circular DNA in SLE and functional analysis reveal their association with apoptosis. Transl Res 2024; 273:115-126. [PMID: 39173965 DOI: 10.1016/j.trsl.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/31/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024]
Abstract
Extrachromosomal circular DNA (eccDNA) derived from linear chromosomes, are showed typical nucleosomal ladder pattern in agarose gel which as a known feature of apoptosis and demonstrated to be immunogenicity. In systemic lupus erythematosus (SLE) patients, elevated levels of cell-free DNA (cfDNA) can be found in either linear forms or circular forms, while circular ones are much less common and harder to detect. The molecular characteristics and function of circular forms in plasma SLE patients remains elusive. Herein, we characterized the hallmarks of plasma eccDNA in SLE patients, including the lower normalized number and GC content of eccDNA in SLE plasma than in the healthy, and SLE eccDNA number positively correlated with C3 and negatively with anti-dsDNA antibodies. The differential eccGenes (eccDNAs carrying the protein coding gene sequence) of SLE was significantly enriched in apoptosis-related pathways. The artificially synthesized eccDNA with sequences of the PRF1 exon region could promote transcriptional expression of PRF1, IFNA and IFIT3 and inhibit early-stage apoptosis. Plasma eccDNA can serve as a novel autoantigen in the pathogenesis of SLE.
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Affiliation(s)
- Yixi Li
- Center for General Practice Medicine, Department of Rheumatology and Immunology, Zhejiang Provincial People' s Hospital (Affiliated People' s Hospital), Hangzhou Medical College, Hangzhou 310000, China; Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People 's Hospital, the Second Clinical Medical College of Jinan University, Shenzhen 518020, China
| | - Fangfang Ge
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao 266555, China
| | - Chengxun Liu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao 266555, China
| | - Wenjun Pu
- Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People 's Hospital, the Second Clinical Medical College of Jinan University, Shenzhen 518020, China
| | - Wei Lv
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao 266555, China
| | - Zhipeng Zeng
- Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People 's Hospital, the Second Clinical Medical College of Jinan University, Shenzhen 518020, China
| | - Lianghong Yin
- Institute of Nephrology and Blood Purification, the First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Dongzhou Liu
- Department of Rheumatology and Immunology, Shenzhen People's Hospital, the Second Clinical Medical College, Jinan University, Shenzhen 518020, China
| | - Yasong Li
- Center for General Practice Medicine, Department of Rheumatology and Immunology, Zhejiang Provincial People' s Hospital (Affiliated People' s Hospital), Hangzhou Medical College, Hangzhou 310000, China
| | - Donge Tang
- Guangdong Provincial Autoimmune Disease Precision Medicine Engineering Research Center, Shenzhen Autoimmune Disease Engineering Research Center, Shenzhen Geriatrics Clinical Research Center, Shenzhen People 's Hospital, the Second Clinical Medical College of Jinan University, Shenzhen 518020, China
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao 266555, China..
| | - Yong Dai
- The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan 232001, China; Comprehensive Health Industry Research Center, Southern University of Science and Technology Taizhou Research Institute, Taizhou 318000, China.
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2
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Yang F, Su W, Chung OW, Tracy L, Wang L, Ramsden DA, Zhang ZZZ. Retrotransposons hijack alt-EJ for DNA replication and eccDNA biogenesis. Nature 2023; 620:218-225. [PMID: 37438532 PMCID: PMC10691919 DOI: 10.1038/s41586-023-06327-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/14/2023] [Indexed: 07/14/2023]
Abstract
Retrotransposons are highly enriched in the animal genome1-3. The activation of retrotransposons can rewrite host DNA information and fundamentally impact host biology1-3. Although developmental activation of retrotransposons can offer benefits for the host, such as against virus infection, uncontrolled activation promotes disease or potentially drives ageing1-5. After activation, retrotransposons use their mRNA as templates to synthesize double-stranded DNA for making new insertions in the host genome1-3,6. Although the reverse transcriptase that they encode can synthesize the first-strand DNA1-3,6, how the second-strand DNA is generated remains largely unclear. Here we report that retrotransposons hijack the alternative end-joining (alt-EJ) DNA repair process of the host for a circularization step to synthesize their second-strand DNA. We used Nanopore sequencing to examine the fates of replicated retrotransposon DNA, and found that 10% of them achieve new insertions, whereas 90% exist as extrachromosomal circular DNA (eccDNA). Using eccDNA production as a readout, further genetic screens identified factors from alt-EJ as essential for retrotransposon replication. alt-EJ drives the second-strand synthesis of the long terminal repeat retrotransposon DNA through a circularization process and is therefore necessary for eccDNA production and new insertions. Together, our study reveals that alt-EJ is essential in driving the propagation of parasitic genomic retroelements. Our study uncovers a conserved function of this understudied DNA repair process, and provides a new perspective to understand-and potentially control-the retrotransposon life cycle.
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Affiliation(s)
- Fu Yang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Weijia Su
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Oliver W Chung
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Lauren Tracy
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Lu Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Dale A Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Z Z Zhao Zhang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
- Duke Regeneration Center, Duke University School of Medicine, Durham, NC, USA.
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3
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Tsai CY, Li KJ, Shen CY, Lu CH, Lee HT, Wu TH, Ng YY, Tsao YP, Hsieh SC, Yu CL. Decipher the Immunopathological Mechanisms and Set Up Potential Therapeutic Strategies for Patients with Lupus Nephritis. Int J Mol Sci 2023; 24:10066. [PMID: 37373215 DOI: 10.3390/ijms241210066] [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: 05/03/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Lupus nephritis (LN) is one of the most severe complications in patients with systemic lupus erythematosus (SLE). Traditionally, LN is regarded as an immune complex (IC) deposition disease led by dsDNA-anti-dsDNA-complement interactions in the subendothelial and/or subepithelial basement membrane of glomeruli to cause inflammation. The activated complements in the IC act as chemoattractants to chemically attract both innate and adaptive immune cells to the kidney tissues, causing inflammatory reactions. However, recent investigations have unveiled that not only the infiltrating immune-related cells, but resident kidney cells, including glomerular mesangial cells, podocytes, macrophage-like cells, tubular epithelial cells and endothelial cells, may also actively participate in the inflammatory and immunological reactions in the kidney. Furthermore, the adaptive immune cells that are infiltrated are genetically restricted to autoimmune predilection. The autoantibodies commonly found in SLE, including anti-dsDNA, are cross-reacting with not only a broad spectrum of chromatin substances, but also extracellular matrix components, including α-actinin, annexin II, laminin, collagen III and IV, and heparan sulfate proteoglycan. Besides, the glycosylation on the Fab portion of IgG anti-dsDNA antibodies can also affect the pathogenic properties of the autoantibodies in that α-2,6-sialylation alleviates, whereas fucosylation aggravates their nephritogenic activity. Some of the coexisting autoantibodies, including anti-cardiolipin, anti-C1q, anti-ribosomal P autoantibodies, may also enhance the pathogenic role of anti-dsDNA antibodies. In clinical practice, the identification of useful biomarkers for diagnosing, monitoring, and following up on LN is quite important for its treatments. The development of a more specific therapeutic strategy to target the pathogenic factors of LN is also critical. We will discuss these issues in detail in the present article.
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Affiliation(s)
- Chang-Youh Tsai
- Division of Immunology & Rheumatology, Department of Medicine, Fu Jen Catholic University Hospital & College of Medicine, Fu Jen Catholic University, New Taipei City 24352, Taiwan
| | - Ko-Jen Li
- Division of Rheumatology, Immunology & Allergy, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 106319, Taiwan
| | - Chieh-Yu Shen
- Division of Rheumatology, Immunology & Allergy, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 106319, Taiwan
| | - Cheng-Hsun Lu
- Division of Rheumatology, Immunology & Allergy, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 106319, Taiwan
| | - Hui-Ting Lee
- MacKay Memorial Hospital & MacKay Medical College, New Taipei City 25245, Taiwan
| | - Tsai-Hung Wu
- Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital and Faculty of Medicine, National Yang-Ming Chiao-Tung University, Taipei 112304, Taiwan
| | - Yee-Yung Ng
- Department of Medicine, Fu Jen Catholic University Hospital & College of Medicine, Fu Jen Catholic University, New Taipei City 24352, Taiwan
| | - Yen-Po Tsao
- Division of Holistic and Multidisciplinary Medicine, Department of Medicine, Taipei Veterans General Hospital and Faculty of Medicine, National Yang-Ming Chiao-Tung University, Taipei 112304, Taiwan
| | - Song-Chou Hsieh
- Division of Rheumatology, Immunology & Allergy, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 106319, Taiwan
| | - Chia-Li Yu
- Division of Rheumatology, Immunology & Allergy, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 106319, Taiwan
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4
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Yong J, Mellick AS, Whitelock J, Wang J, Liang K. A Biomolecular Toolbox for Precision Nanomotors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2205746. [PMID: 36055646 DOI: 10.1002/adma.202205746] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/31/2022] [Indexed: 06/15/2023]
Abstract
The application of nanomotors for cancer diagnosis and therapy is a new and exciting area of research, which when combined with precision nanomedicine, promises to solve many of the issues encountered by previous development of passive nanoparticles. The goal of this article is to introduce nanomotor and nanomedicine researchers to the deep pool of knowledge available regarding cancer cell biology and biochemistry, as well as provide a greater appreciation of the complexity of cell membrane compositions, extracellular surfaces, and their functional consequences. A short description of the nanomotor state-of-art for cancer therapy and diagnosis is first provided, as well as recommendations for future directions of the field. Then, a biomolecular targeting toolbox has been collated for researchers looking to apply their nanomaterial of choice to a biological setting, as well as providing a glimpse into currently available clinical therapies and technologies. This toolbox contains an overview of different classes of targeting molecules available for high affinity and specific targeting and cell surface targets to aid researchers in the selection of a clinical disease model and targeting methodology. It is hoped that this review will provide biological context, inspiration, and direction to future nanomotor and nanomedicine research.
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Affiliation(s)
- Joel Yong
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Kensington, New South Wales, 2052, Australia
| | - Albert S Mellick
- Graduate School of Biomedical Engineering, The University of New South Wales, Kensington, New South Wales, 2052, Australia
- Ingham Institute for Applied Medical Research, Liverpool, New South Wales, 2170, Australia
| | - John Whitelock
- Graduate School of Biomedical Engineering, The University of New South Wales, Kensington, New South Wales, 2052, Australia
| | - Joseph Wang
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kang Liang
- School of Chemical Engineering and Australian Centre for NanoMedicine, The University of New South Wales, Kensington, New South Wales, 2052, Australia
- Graduate School of Biomedical Engineering, The University of New South Wales, Kensington, New South Wales, 2052, Australia
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5
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Czarnecka M, Weichelt U, Rödiger S, Hanack K. Novel Anti Double-Stranded Nucleic Acids Full-Length Recombinant Camelid Heavy-Chain Antibody for the Detection of miRNA. Int J Mol Sci 2022; 23:ijms23116275. [PMID: 35682952 PMCID: PMC9181593 DOI: 10.3390/ijms23116275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 11/24/2022] Open
Abstract
The discovery that certain diseases have specific miRNA signatures which correspond to disease progression opens a new biomarker category. The detection of these small non-coding RNAs is performed routinely using body fluids or tissues with real-time PCR, next-generation sequencing, or amplification-based miRNA assays. Antibody-based detection systems allow an easy onset handling compared to PCR or sequencing and can be considered as alternative methods to support miRNA diagnostic in the future. In this study, we describe the generation of a camelid heavy-chain-only antibody specifically recognizing miRNAs to establish an antibody-based detection method. The generation of nucleic acid-specific binders is a challenge. We selected camelid binders via phage display, expressed them as VHH as well as full-length antibodies, and characterized the binding to several miRNAs from a signature specific for dilated cardiomyopathy. The described workflow can be used to create miRNA-specific binders and establish antibody-based detection methods to provide an additional way to analyze disease-specific miRNA signatures.
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Affiliation(s)
- Malgorzata Czarnecka
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; (M.C.); (U.W.)
| | - Ulrike Weichelt
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; (M.C.); (U.W.)
| | - Stefan Rödiger
- Faculty of Health Sciences Brandenburg, Brandenburg University of Technology, Cottbus-Senftenberg, Universitätsplatz 1, 01968 Senftenberg, Germany;
| | - Katja Hanack
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; (M.C.); (U.W.)
- Correspondence: ; Tel.: +49-3319-775-348
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6
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Bou-Nader C, Bothra A, Garboczi DN, Leppla SH, Zhang J. Structural basis of R-loop recognition by the S9.6 monoclonal antibody. Nat Commun 2022; 13:1641. [PMID: 35347133 PMCID: PMC8960830 DOI: 10.1038/s41467-022-29187-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/02/2022] [Indexed: 12/31/2022] Open
Abstract
R-loops are ubiquitous, dynamic nucleic-acid structures that play fundamental roles in DNA replication and repair, chromatin and transcription regulation, as well as telomere maintenance. The DNA-RNA hybrid–specific S9.6 monoclonal antibody is widely used to map R-loops. Here, we report crystal structures of a S9.6 antigen-binding fragment (Fab) free and bound to a 13-bp hybrid duplex. We demonstrate that S9.6 exhibits robust selectivity in binding hybrids over double-stranded (ds) RNA and in categorically rejecting dsDNA. S9.6 asymmetrically recognizes a compact epitope of two consecutive RNA nucleotides via their 2′-hydroxyl groups and six consecutive DNA nucleotides via their backbone phosphate and deoxyribose groups. Recognition is mediated principally by aromatic and basic residues of the S9.6 heavy chain, which closely track the curvature of the hybrid minor groove. These findings reveal the molecular basis for S9.6 recognition of R-loops, detail its binding specificity, identify a new hybrid-recognition strategy, and provide a framework for S9.6 protein engineering. The S9.6 monoclonal antibody is widely used to map R-loops genome wide. Here, Bou-Nader et al., define the nucleic acid-binding specificity of S9.6 and report its crystal structures free and bound to a hybrid, which reveal the asymmetric recognition of the RNA and DNA strands and its A-form conformation.
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
| | - Ankur Bothra
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - David N Garboczi
- Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - Stephen H Leppla
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA.
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA.
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7
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Gallardo-Carreño I, Moreno-Paz M, Aguirre J, Blanco Y, Alonso-Pintado E, Raymond-Bouchard I, Maggiori C, Rivas LA, Engelbrektson A, Whyte L, Parro V. A Multiplex Immunosensor for Detecting Perchlorate-Reducing Bacteria for Environmental Monitoring and Planetary Exploration. Front Microbiol 2021; 11:590736. [PMID: 33391207 PMCID: PMC7772991 DOI: 10.3389/fmicb.2020.590736] [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: 08/02/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
Perchlorate anions are produced by chemical industries and are important contaminants in certain natural ecosystems. Perchlorate also occurs in some natural and uncontaminated environments such as the Atacama Desert, the high Arctic or the Antarctic Dry Valleys, and is especially abundant on the surface of Mars. As some bacterial strains are capable of using perchlorate as an electron acceptor under anaerobic conditions, their detection is relevant for environmental monitoring on Earth as well as for the search for life on Mars. We have developed an antibody microarray with 20 polyclonal antibodies to detect perchlorate-reducing bacteria (PRB) strains and two crucial and highly conserved enzymes involved in perchlorate respiration: perchlorate reductase and chlorite dismutase. We determined the cross-reactivity, the working concentration, and the limit of detection of each antibody individually and in a multiplex format by Fluorescent Sandwich Microarray Immunoassay. Although most of them exhibited relatively high sensitivity and specificity, we applied a deconvolution method based on graph theory to discriminate between specific signals and cross-reactions from related microorganisms. We validated the system by analyzing multiple bacterial isolates, crude extracts from contaminated reactors and salt-rich natural samples from the high Arctic. The PRB detecting chip (PRBCHIP) allowed us to detect and classify environmental isolates as well as to detect similar strains by using crude extracts obtained from 0.5 g even from soils with low organic-matter levels (<103 cells/g of soil). Our results demonstrated that PRBCHIP is a valuable tool for sensitive and reliable detection of perchlorate-reducing bacteria for research purposes, environmental monitoring and planetary exploration.
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Affiliation(s)
| | - Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | - Jacobo Aguirre
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain.,Centro Nacional de Biotecnología, CSIC, Madrid, Spain.,Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | | | | | - Catherine Maggiori
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Luis A Rivas
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain.,Inmunología y Genética Aplicada, S.A. (INGENASA), Madrid, Spain
| | - Anna Engelbrektson
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Víctor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
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8
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Gao Y, Tian J, Zhang X, Qiao B, Cao Y, Wang X, Wu Q. A fluorescence assay for microRNA let-7a by a double-stranded DNA modified gold nanoparticle nanoprobe combined with graphene oxide. Analyst 2020; 145:1190-1194. [DOI: 10.1039/c9an02274k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A fluorescence switching platform was developed to monitor target microRNA let-7a by coupling dsDNA–AuNPs with the GO nanosheet.
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Affiliation(s)
- Yuanyuan Gao
- State Key Laboratory of Marine Resource Utilization in South China Sea
- College of Material science and Engineering
- Hainan University
- Haikou 570228
- China
| | - Jingjing Tian
- State Key Laboratory of Marine Resource Utilization in South China Sea
- College of Material science and Engineering
- Hainan University
- Haikou 570228
- China
| | - Xing Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea
- College of Material science and Engineering
- Hainan University
- Haikou 570228
- China
| | - Bin Qiao
- Key Laboratory of Emergency and Trauma of Ministry of Education & Research Unit of Island Emergency Medicine of Chinese Academy of Medical Sciences
- Hainan Medical University
- Haikou 571199
- China
- School of Tropical Medicine and Laboratory Medicine
| | - Yang Cao
- Qiongtai Normal University
- Haikou 571127
- China
| | - Xiaohong Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea
- College of Material science and Engineering
- Hainan University
- Haikou 570228
- China
| | - Qiang Wu
- Key Laboratory of Emergency and Trauma of Ministry of Education & Research Unit of Island Emergency Medicine of Chinese Academy of Medical Sciences
- Hainan Medical University
- Haikou 571199
- China
- School of Tropical Medicine and Laboratory Medicine
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9
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Wang X, Xia Y. Anti-double Stranded DNA Antibodies: Origin, Pathogenicity, and Targeted Therapies. Front Immunol 2019; 10:1667. [PMID: 31379858 PMCID: PMC6650533 DOI: 10.3389/fimmu.2019.01667] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 07/03/2019] [Indexed: 01/02/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is characterized by high-titer serological autoantibodies, including antibodies that bind to double-stranded DNA (dsDNA). The origin, specificity, and pathogenicity of anti-dsDNA antibodies have been studied from a wider perspective. These autoantibodies have been suggested to contribute to multiple end-organ injuries, especially to lupus nephritis, in patients with SLE. Moreover, serum levels of anti-DNA antibodies fluctuate with disease activity in patients with SLE. By directly binding to self-antigens or indirectly forming immune complexes, anti-dsDNA antibodies can accumulate in the glomerular and tubular basement membrane. These autoantibodies can also trigger the complement cascade, penetrate into living cells, modulate gene expression, and even induce profibrotic phenotypes of renal cells. In addition, the expression of suppressor of cytokine signaling 1 is reduced by anti-DNA antibodies simultaneously with upregulation of profibrotic genes. Anti-dsDNA antibodies may even participate in the pathogenesis of SLE by catalyzing hydrolysis of certain DNA molecules or peptides in cells. Recently, anti-dsDNA antibodies have been explored in greater depth as a therapeutic target in the management of SLE. A substantial amount of data indicates that blockade of pathogenic anti-dsDNA antibodies can prevent or even reverse organ damage in murine models of SLE. This review focuses on the recent research advances regarding the origin, specificity, classification, and pathogenicity of anti-dsDNA antibodies and highlights the emerging therapies associated with them.
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Affiliation(s)
- Xiaoyu Wang
- Department of Dermatology, The Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Yumin Xia
- Department of Dermatology, The Second Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Xi'an, China
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10
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El Hage A, Webb S, Kerr A, Tollervey D. Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria. PLoS Genet 2014; 10:e1004716. [PMID: 25357144 PMCID: PMC4214602 DOI: 10.1371/journal.pgen.1004716] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 08/27/2014] [Indexed: 01/08/2023] Open
Abstract
During transcription, the nascent RNA can invade the DNA template, forming extended RNA-DNA duplexes (R-loops). Here we employ ChIP-seq in strains expressing or lacking RNase H to map targets of RNase H activity throughout the budding yeast genome. In wild-type strains, R-loops were readily detected over the 35S rDNA region, transcribed by Pol I, and over the 5S rDNA, transcribed by Pol III. In strains lacking RNase H activity, R-loops were elevated over other Pol III genes, notably tRNAs, SCR1 and U6 snRNA, and were also associated with the cDNAs of endogenous TY1 retrotransposons, which showed increased rates of mobility to the 5′-flanking regions of tRNA genes. Unexpectedly, R-loops were also associated with mitochondrial genes in the absence of RNase H1, but not of RNase H2. Finally, R-loops were detected on actively transcribed protein-coding genes in the wild-type, particularly over the second exon of spliced ribosomal protein genes. R-loops (RNA-DNA hybrids) are potentially deleterious for gene expression and genome stability, but can be beneficial, for example, during immunoglobulin gene class-switch recombination. Here we made use of antibody S9.6, with specificity for RNA-DNA duplexes independently of their sequence. The genome-wide distribution of R-loops in wild-type yeast showed association with the highly transcribed ribosomal DNA, and protein-coding genes, particularly the second exon of spliced genes. On RNA polymerase III loci such as the highly transcribed transfer RNA genes (tRNAs), R-loop accumulation was strongly detected in the absence of both ribonucleases H1 and H2 (RNase H1 and H2), indicating that R-loops are inherently formed but rapidly cleared by RNase H. Importantly, stable R-loops lead to reduced synthesis of tRNA precursors in mutants lacking RNase H and DNA topoisomerase activities. RNA-DNA hybrids associated with TY1 cDNA retrotransposition intermediates were elevated in the absence of RNase H, and this was accompanied by increased retrotransposition, in particular to 5′-flanking regions of tRNAs. Our findings show that RNase H participates in silencing of TY1 life cycle. Surprisingly, R-loops associated with mitochondrial transcription units were suppressed specifically by RNase H1. These findings have potentially important implications for understanding human diseases caused by mutations in RNase H.
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Affiliation(s)
- Aziz El Hage
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (AEH); (DT)
| | - Shaun Webb
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alastair Kerr
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (AEH); (DT)
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