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Wang F, Liu YJ, Miao HB, Chen Z. Clinical algorithm model based on cfDNA to predict SLE disease activity. Lupus 2024; 33:145-154. [PMID: 38183242 DOI: 10.1177/09612033231226314] [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] [Indexed: 01/07/2024]
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) has been widely used as a new liquid-biopsy marker. Dysregulation of cfDNA has been found in patients with systemic lupus erythematosus (SLE). However, the detailed association between cfDNA and SLE has not been thoroughly studied. METHODS Plasma samples were collected from 88 patients with active SLE and 39 patients with inactive SLE. The cfDNA concentration was determined, and the length and distribution of cfDNA fragments were verified. RESULTS cfDNA concentrations were significantly higher in patients with active SLE than in patients with inactive SLE (0.4 [0.18-0.897] ng/µL vs 0.249 [0.144-0.431] ng/µL; p = .043). cfDNA fragments were enriched in the ranges of 153-198 bp and 300-599 bp. cfDNA concentrations were associated with the reduction of the anti-double-stranded DNA (dsDNA) antibodies titer (r = -0.301, p = .034). The presence of anti-U1 ribonucleoprotein (p = .012), anti-Sjogren syndrome A (p = .024), anti-dsDNA (p = .0208), and anti-nucleosome antibodies (p = .0382) might associate to the variation of cfDNA concentration. Reduced cfDNA concentration was associated with renal damage in active SLE patients (0.31 [0.11-0.73] ng/µL vs 0.65 [0.27-1.53] ng/µL; p = .009). The Active index, a combination model including cfDNA concentration and other clinical indices, had an area of 0.886 under the receiver operating characteristics curve for distinguishing active SLE. The Active index was positively correlated with the SLE disease activity index score (r = 0.6724, p < .0001). CONCLUSIONS Through systematic stratified analysis and clinical algorithm model, this study found that plasma cfDNA concentration is closely related to SLE disease severity, which has guiding significance for the future clinical application of cfDNA in SLE.
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Affiliation(s)
- Fang Wang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- Department of Rheumatology and Immunology, Foresea Life Insurance Guangxi Hospital, Nanning, China
| | - Yi-Jing Liu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Hai-Bing Miao
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Zhen Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
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Peng Y, Wu Y, Chen S, Liu Y, Qian H, He Y, Huang H, Cai M, Liu W, Shi G. Circulating cell-free DNA correlate to disease activity and treatment response of patients with radiographic axial spondyloarthritis. Sci Rep 2024; 14:178. [PMID: 38168507 PMCID: PMC10762258 DOI: 10.1038/s41598-023-50543-0] [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: 08/18/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Microdamage and its related inflammation contribute to the development of radiographic axial spondyloarthritis (r-axSpA). Inflammation and cell death in damaged tissues are associated with cell-free DNA (cfDNA) release. Here we investigated whether circulating cfDNA could be a potential biomarker for evaluating disease activity and treatment response in r-axSpA. Circulating cfDNA was detected in the discovery and validation cohort with 79 and 60 newly diagnosed r-axSpA patients respectively and 42 healthy controls using the Quant-iT PicoGreen dsDNA reagent and kit. As a result, cfDNA levels were significantly higher in r-axSpA patients compared with healthy controls in the discovery and validation cohort. Moreover, cfDNA levels were positively correlated with CRP, ASDAS-CRP and neutrophil counts. Additionally, non-steroid anti-inflammatory drugs (NSAIDs) combined with disease-modifying anti-rheumatic drugs or tumor necrosis factor inhibitors but not NSAIDs alone could reduce cfDNA levels. Moreover, a decrease of cfDNA levels after treatment was associated with an effective therapeutic response. Intriguingly, patients with higher levels of cfDNA at diagnosis responded better to combination therapy rather than NSAIDs. However, patients with lower levels of cfDNA displayed similar responses to combination or mono-NSAID treatment. In conclusion, circulating cfDNA levels showed a significant correlation with disease activity as well as treatment efficacy in patients with r-axSpA. Moreover, cfDNA at diagnosis might predict the response to different therapy. Consequently, cfDNA may serve as a useful biomarker of inflammation in r-axSpA.
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Affiliation(s)
- Yun Peng
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, Fujian, China
| | - Yuanhui Wu
- Department of Rheumatology and Clinical Immunology, Jiangxi Provincial People's Hospital Affiliated of Nanchang University, Nanchang, Jiangxi, China
| | - Shiju Chen
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, Fujian, China
| | - Yuan Liu
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, Fujian, China
| | - Hongyan Qian
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, Fujian, China
| | - Yan He
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, Fujian, China
| | - Heqing Huang
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, Fujian, China
| | - Meimei Cai
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, Fujian, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, Fujian, China
| | - Wen Liu
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China.
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, Fujian, China.
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, Fujian, China.
| | - Guixiu Shi
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China.
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, Fujian, China.
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen, Fujian, China.
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Novikova TS, Ermakov EA, Kostina EV, Sinyakov AN, Sizikov AE, Nevinsky GA, Buneva VN. Hydrolysis of Oligodeoxyribonucleotides on the Microarray Surface and in Solution by Catalytic Anti-DNA Antibodies in Systemic Lupus Erythematosus. Curr Issues Mol Biol 2023; 45:9887-9903. [PMID: 38132463 PMCID: PMC10742339 DOI: 10.3390/cimb45120617] [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: 11/02/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Anti-DNA antibodies are known to be classical serological hallmarks of systemic lupus erythematosus (SLE). In addition to high-affinity antibodies, the autoantibody pool also contains natural catalytic anti-DNA antibodies that recognize and hydrolyze DNA. However, the specificity of such antibodies is uncertain. In addition, DNA binding to a surface such as the cell membrane, can also affect its recognition by antibodies. Here, we analyzed the hydrolysis of short oligodeoxyribonucleotides (ODNs) immobilized on the microarray surface and in solution by catalytic anti-DNA antibodies from SLE patients. It has been shown that IgG antibodies from SLE patients hydrolyze ODNs more effectively both in solution and on the surface, compared to IgG from healthy individuals. The data obtained indicate a more efficient hydrolysis of ODNs in solution than immobilized ODNs on the surface. In addition, differences in the specificity of recognition and hydrolysis of certain ODNs by anti-DNA antibodies were revealed, indicating the formation of autoantibodies to specific DNA motifs in SLE. The data obtained expand our understanding of the role of anti-DNA antibodies in SLE. Differences in the recognition and hydrolysis of surface-tethered and dissolved ODNs need to be considered in DNA microarray applications.
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Affiliation(s)
- Tatiana S. Novikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Evgeny A. Ermakov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Kostina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexander N. Sinyakov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexey E. Sizikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Institute of Clinical Immunology, Siberian Branch of the Russian Academy of Sciences, 630099 Novosibirsk, Russia
| | - Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Valentina N. Buneva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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Ibrahim MRK, Waly NG, Moness H, Ahmed SS, Ibrahem R. Serum miRNA-21, miRNA-146a and plasma cell free DNA as novel biomarkers for assessing systemic lupus erythematosus activity. Mol Biol Rep 2023; 50:10025-10036. [PMID: 37904010 PMCID: PMC10676317 DOI: 10.1007/s11033-023-08845-z] [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: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND MicroRNA and cell-free DNA have shown significant correlations with several autoimmune disorders including systemic lupus erythematosus (SLE). SLE has been associated with challenges in determining its activity, so that the need for biomarkers contributing to assessing its activity is emerging. The current study investigated miRNA-21, miRNA-146a and plasma cf-DNA in determination of SLE activity, in addition their association with clinical data including complement factor 3 (C3), complement factor(C4), anti-dsDNA, and other disease activity indices. METHODS AND RESULTS Eighty subjects divided into; twenty active patients (with SLE-DAI2K score of 16-18) twenty inactive patients (with SLE-DAI2K score of 1-3), and forty healthy control participants) were included in this study. Serum miR-21, miR-146a, and plasma cf-DNA were quantified by real time PCR and their correlation with clinical data was statistically analyzed. The results demonstrated that active cases have significant upregulation of serum miRNA-21 and plasma cf-DNA. Moreover, miR-21 showed a negative, significant pertaining to C3, C4 and was positively related to Systemic Lupus Erythematosus Disease Activity Index 2 K score (SLE-DAI Index2K score) and Systemic-Lupus-Erythematosus-Disease Activity-Index 2 K activity (SLE-DAI 2 K activity). Also, Active group miRNA-146a was negatively, significantly correlated with C3, as well as a positive significant relationship with SLE-DAI2K score and SLEDAI 2 K activity, in addition to anti DNA Autoantibodies. Furthermore, miR-21 and cf-DNA demonstrated a differential value through Receiver Operating Characteristic (ROC) curve's study. CONCLUSIONS the present study illustrated miR-21, miR-146a, and cf-DNA relationship with SLE clinical data. In addition to their potential value in SLE diagnosis, and activity determination.
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Affiliation(s)
- Muhammed R Kh Ibrahim
- Microbiology and Immunology Department, faculty of pharmacy, Minia University, 61511, Minia, Egypt
| | - Nancy Gfm Waly
- Microbiology and Immunology Department, faculty of pharmacy, Minia University, 61511, Minia, Egypt
| | - Hend Moness
- Clinical pathology Department, faculty of Medicine, Minia University, Minia, Egypt
| | - Shimaa S Ahmed
- Rheumatology, Rehabilitation and physical medicine Department, faculty of Medicine, Minia University, Minia, Egypt
| | - Reham Ibrahem
- Microbiology and Immunology Department, faculty of pharmacy, Minia University, 61511, Minia, Egypt.
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Reshetnyak T, Nurbaeva K. The Role of Neutrophil Extracellular Traps (NETs) in the Pathogenesis of Systemic Lupus Erythematosus and Antiphospholipid Syndrome. Int J Mol Sci 2023; 24:13581. [PMID: 37686381 PMCID: PMC10487763 DOI: 10.3390/ijms241713581] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/10/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease of unknown aetiology [...].
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Affiliation(s)
- Tatiana Reshetnyak
- Department of Thromboinflammation, V.A. Nasonova Research Institute of Rheumatology, 115522 Moscow, Russia;
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Callery EL, Morais CLM, Nugent L, Rowbottom AW. Classification of Systemic Lupus Erythematosus Using Raman Spectroscopy of Blood and Automated Computational Detection Methods: A Novel Tool for Future Diagnostic Testing. Diagnostics (Basel) 2022; 12:diagnostics12123158. [PMID: 36553165 PMCID: PMC9777204 DOI: 10.3390/diagnostics12123158] [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: 10/24/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/16/2022] Open
Abstract
The aim of this study was to explore the proof of concept for using Raman spectroscopy as a diagnostic platform in the setting of systemic lupus erythematosus (SLE). We sought to identify unique Raman signatures in serum blood samples to successfully segregate SLE patients from healthy controls (HC). In addition, a retrospective audit was undertaken to assess the clinical utility of current testing platforms used to detect anti-double stranded DNA (dsDNA) antibodies (n = 600). We examined 234 Raman spectra to investigate key variances between SLE patients (n = 8) and HC (n = 4). Multi-variant analysis and classification model construction was achieved using principal component analysis (PCA), PCA-linear discriminant analysis and partial least squares-discriminant analysis (PLS-DA). We achieved the successful segregation of Raman spectra from SLE patients and healthy controls (p-value < 0.0001). Classification models built using PLS-DA demonstrated outstanding performance characteristics with 99% accuracy, 100% sensitivity and 99% specificity. Twelve statistically significant (p-value < 0.001) wavenumbers were identified as potential diagnostic spectral markers. Molecular assignments related to proteins and DNA demonstrated significant Raman intensity changes between SLE and HC groups. These wavenumbers may serve as future biomarkers and offer further insight into the pathogenesis of SLE. Our audit confirmed previously reported inconsistencies between two key methodologies used to detect anti-dsDNA, highlighting the need for improved laboratory testing for SLE. Raman spectroscopy has demonstrated powerful performance characteristics in this proof-of-concept study, setting the foundations for future translation into the clinical setting.
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Affiliation(s)
- Emma L. Callery
- Department of Immunology, Royal Preston Hospital, Preston PR2 9HT, UK
- Correspondence: (E.L.C.); (A.W.R.)
| | - Camilo L. M. Morais
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal 59072-970, Brazil
| | - Lucy Nugent
- Department of Immunology, Whiston Hospital, Prescot L35 5DR, UK
| | - Anthony W. Rowbottom
- Department of Immunology, Royal Preston Hospital, Preston PR2 9HT, UK
- School of Medicine, University of Central Lancashire, Preston PR1 2HE, UK
- Correspondence: (E.L.C.); (A.W.R.)
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Wang F, Miao HB, Pei ZH, Chen Z. Serological, fragmentomic, and epigenetic characteristics of cell-free DNA in patients with lupus nephritis. Front Immunol 2022; 13:1001690. [PMID: 36578480 PMCID: PMC9791112 DOI: 10.3389/fimmu.2022.1001690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
Objectives The biological characteristics of plasma circulating cell-free DNA (cfDNA) are related to the pathogenesis of lupus nephritis (LN). The aim of this study was to explore the biological characteristics of cfDNA in patients with LN in terms of serology, fragment omics, and epigenetics, and to discuss the possibility of liquid biopsy for cfDNA as an alternative to conventional tissue biopsy. Methods cfDNA was extracted from plasma samples of 127 patients with systemic lupus erythematosus (64 with LN, 63 without LN). The cfDNA concentration was determined using the Qubit method. Next-generation sequencing cfDNA methylation profiling was performed for three LN patients and six non-LN patients. The methylation panel was designed based on data from The Cancer Genome Atlas cohort. The fragmentation index, motif score, and DELFI score were calculated to explore the fragmentation profile of cfDNA in patients with LN. Statistical and machine learning methods were used to select features to calculate the methylation scores of the samples. Results Patients with LN had significantly lower cfDNA concentrations (P = 0.0347) than those without LN. This may be associated with the presence of anti-double-stranded DNA antibodies (r = -0.4189; P = 0.0296). The mean DELFI score (proportion of short fragments of cfDNA) in patients with LN was significantly higher than that in patients without LN (P = 0.0238). Based on the pan-cancer data, 73, 66, 8, and 10 features were selected and used to calculate the methylation scores. The mean methylation scores of these features in patients with LN differed significantly from those in patients without LN (P = 0.0238). Conclusions The specificity of cfDNA in patients with LN was identified using serological, fragmentomic, and epigenetic analyses. The findings may have implications for the development of new molecular markers of LN.
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Affiliation(s)
- Fang Wang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China,Department of Immunology, Foresea Life Insurance Guangxi Hospital, Nanning, Guangxi, China
| | - Hai-bing Miao
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Zhi-hua Pei
- Hubei Provincial Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhen Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China,*Correspondence: Zhen Chen,
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Lou H, Ling GS, Cao X. Autoantibodies in systemic lupus erythematosus: From immunopathology to therapeutic target. J Autoimmun 2022; 132:102861. [PMID: 35872103 DOI: 10.1016/j.jaut.2022.102861] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 11/26/2022]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by multiple organ inflammatory damage and wide spectrum of autoantibodies. The autoantibodies, especially anti-dsDNA and anti-Sm autoantibodies are highly specific to SLE, and participate in the immune complex formation and inflammatory damage on multiple end-organs such as kidney, skin, and central nervous system (CNS). However, the underlying mechanisms of autoantibody-induced tissue damage and systemic inflammation are still not fully understood. Single cell analysis of autoreactive B cells and monoclonal antibody screening from patients with active SLE has improved our understanding on the origin of autoreactive B cells and the antigen targets of the pathogenic autoantibodies. B cell depletion therapies have been widely studied in the clinics, but the development of more specific therapies against the pathogenic B cell subset and autoantibodies with improved efficacy and safety still remain a big challenge. A more comprehensive autoantibody profiling combined with functional characterization of autoantibodies in diseases development will shed new insights on the etiology and pathogenesis of SLE and guide a specific treatment to individual SLE patients.
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Affiliation(s)
- Hantao Lou
- Ludwig Institute of Cancer Research, University of Oxford, Oxford, OX3 7DR, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
| | - Guang Sheng Ling
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xuetao Cao
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK; Nankai-Oxford International Advanced Institute, College of Life Sciences, Nankai University, Tianjin, 300071, China.
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de Souza Barbosa Ê, Santos Ibiapina HN, Rocha da Silva S, Costa AG, Val FF, Mendonça-da-Silva I, Carlos de Lima Ferreira L, Sartim MA, Monteiro WM, Cardoso de Melo G, de Almeida Gonçalves Sachett J. Association of cfDNA levels and bothrops envenomation. Toxicon 2021; 192:66-73. [PMID: 33497746 DOI: 10.1016/j.toxicon.2021.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/21/2020] [Accepted: 01/20/2021] [Indexed: 01/05/2023]
Abstract
In the Amazon, around 90% of snakebites are caused by the Bothrops genus. Complications arising from Bothrops envenomations result from the inflammatory and coagulotoxic activities of the venom. The aim of this study was to investigate the potential of cell-free DNA (cfDNA) as a biomarker of severity in Bothrops snakebites. Patients were treated at the Fundação de Medicina Tropical Dr. Heitor Vieira Dourado (FMT-HVD), Manaus, in the Brazilian Amazon. cfDNA plasma levels were measured by amplifying the human telomerase reverse transcriptase (hTERT) sequence using quantitative RT-PCR. Median levels of cfDNA were compared between envenomed and healthy volunteers and among patients presenting different complications, such as renal failure, bleeding and infection. Of the 76 patients included, 82.9% were male, with a mean age of 32.8 years, and envenomations were mainly classified as severe (39.5%). ROC curve analysis showed a good accuracy of cfDNA levels (AUROC of 0.745) in envenomation diagnosis. A correlation analysis using laboratory variables showed positive correlation with lactate dehydrogenase (p = 0.033) and platelet count (p = 0.003). When cfDNA levels were compared with clinical complications, significant statistical differences were only found among individuals with mild and severe pain (p < 0.05). In summary, our results demonstrated that cfDNA levels are sufficiently accurate for discriminating between envenomed and non-envenomed patients, but are not able to distinguish different complications and the level of severity among envenomed patients. Thus, the role of cfDNA in the pathogenesis of the snakebite envenomations needs to be further investigated.
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Affiliation(s)
- Êndila de Souza Barbosa
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Brazil; Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
| | - Hiochelson Najibe Santos Ibiapina
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Brazil; Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
| | | | - Allyson Guimarães Costa
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Brazil; Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil; Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil; Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Brazil
| | - Fernando Fonseca Val
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Brazil; Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
| | - Iran Mendonça-da-Silva
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Brazil; Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
| | - Luiz Carlos de Lima Ferreira
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Brazil; Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil; Faculdade de Medicina, Universidade Federal do Amazonas, Manaus, Brazil
| | - Marco Aurélio Sartim
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil; Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Brazil
| | - Wuelton Marcelo Monteiro
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Brazil; Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
| | - Gisely Cardoso de Melo
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Brazil; Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
| | - Jacqueline de Almeida Gonçalves Sachett
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Brazil; Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil; Diretoria de Ensino e Pesquisa, Fundação Alfredo da Matta, Manaus, Brazil.
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Nandi K, Verma R, Dawar R, Goswami B. Cell free DNA: revolution in molecular diagnostics - the journey so far. Horm Mol Biol Clin Investig 2020; 41:/j/hmbci.ahead-of-print/hmbci-2019-0012/hmbci-2019-0012.xml. [PMID: 32083442 DOI: 10.1515/hmbci-2019-0012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022]
Abstract
Cell free DNA (cf-DNA) refers to all non -ncapsulated DNA present in the blood stream which may originate from apoptotic cells as a part of the physiological cell turnover, or from cancer cells or fetal cells. Recent studies have highlighted the utility of cfDNA analysis for genetic profiling of cancer, non-invasive prenatal testing besides many other clinical applications. In our review we discuss the sources of cfDNA in the body, the techniques most commonly being used for its isolation and analysis, the applications of cfDNA testing and the associated pros-cons. We conclude that for prenatal testing, cfDNA analysis provides an effective, non-invasive and safer alternative to traditional amniocentesis and chorionic villus sampling tests. Also, in cancer patients, cfDNA analysis is useful for genetic profiling and follow-up during treatment. However, standardization of methods of isolation and analysis has become crucial for the success of widespread use of cfDNA analysis.
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Affiliation(s)
- Kajal Nandi
- Department of Biochemistry, HIMSR, Mehrauli, New Delhi, India
| | - Rashmi Verma
- Department of Biochemistry, Maulana Azad Medical College, New Delhi 110002, India
| | - Rajni Dawar
- Department of Biochemistry, Vardhaman Mahavir Medical College, New Delhi 110029, India
| | - Binita Goswami
- Department of Biochemistry, Maulana Azad Medical College, New Delhi 110002, India
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Arneth B. Systemic Lupus Erythematosus and DNA Degradation and Elimination Defects. Front Immunol 2019; 10:1697. [PMID: 31440232 PMCID: PMC6692764 DOI: 10.3389/fimmu.2019.01697] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/08/2019] [Indexed: 12/25/2022] Open
Abstract
Introduction: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that is characterized by the production of autoantibodies specific for components of the cell nucleus and that causes damage to body tissues and organs. The pathogenesis of SLE remains unclear, with numerous studies pointing to a combination of genetic and environmental factors. A critical stage in SLE development is cell necrosis, in which undegraded chromatin and nucleoproteins are released into the blood, resulting in circulating cell-free DNA and serum nucleoproteins that trigger anti-dsDNA autoantibody production. This systematic literature review aimed to examine whether SLE stems from a DNA degradation and elimination defect. Materials and Methods: An advanced literature search was conducted in PubMed using the following keywords: [(“SLE” OR “Systemic Lupus Erythematosus” OR “Lupus”)] AND [(“DNA” OR “DNA Degradation”)] AND [(“Defect Elimination”)]. More articles were obtained from the references of the identified articles and basic Google searches. Twenty-five peer-reviewed articles published within the past 10 years (2007–2018) were included for review. Results: The findings of each study are summarized in Tables 1, 2. Discussion and Conclusion: The etiopathogenesis of SLE remains controversial, which limits therapeutic inventions for this disease. However, SLE is a DNA degradation and elimination disorder caused by uncleared histones and nuclear material that leak into the extracellular space and form cell-free DNA, triggering an immune response that destroys tissues and organs. Under normal conditions, apoptosis allows DNA and other nuclear material to be efficiently cleared through degradation and additional complex mechanisms such that this material does not trigger the immune system to produce nuclear autoantibodies.
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Affiliation(s)
- Borros Arneth
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, University Hospital of Giessen and Marburg, Justus Liebig University Giessen, Giessen, Germany
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Duvvuri B, Lood C. Cell-Free DNA as a Biomarker in Autoimmune Rheumatic Diseases. Front Immunol 2019; 10:502. [PMID: 30941136 PMCID: PMC6433826 DOI: 10.3389/fimmu.2019.00502] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/25/2019] [Indexed: 12/11/2022] Open
Abstract
Endogenous DNA is primarily found intracellularly in nuclei and mitochondria. However, extracellular, cell-free (cf) DNA, has been observed in several pathological conditions, including autoimmune diseases, prompting the interest of developing cfDNA as a potential biomarker. There is an upsurge in studies considering cfDNA to stratify patients, monitor the treatment response and predict disease progression, thus evaluating the prognostic potential of cfDNA for autoimmune diseases. Since the discovery of elevated cfDNA levels in lupus patients in the 1960s, cfDNA research in autoimmune diseases has mainly focused on the overall quantification of cfDNA and the association with disease activity. However, with recent technological advancements, including genomic and methylomic sequencing, qualitative changes in cfDNA are being explored in autoimmune diseases, similar to the ones used in molecular profiling of cfDNA in cancer patients. Further, the intracellular origin, e.g., if derived from mitochondrial or nuclear source, as well as the complexing with carrier molecules, including LL-37 and HMGB1, has emerged as important factors to consider when analyzing the quality and inflammatory potential of cfDNA. The clinical relevance of cfDNA in autoimmune rheumatic diseases is strengthened by mechanistic insights into the biological processes that result in an enhanced release of DNA into the circulation during autoimmune and inflammatory conditions. Prior work have established an important role of accelerated apoptosis and impaired clearance in leakage of nucleic acids into the extracellular environment. Findings from more recent studies, including our own investigations, have demonstrated that NETosis, a neutrophil cell death process, can result in a selective extrusion of inflammatory mitochondrial DNA; a process which is enhanced in patients with lupus and rheumatoid arthritis. In this review, we will summarize the evolution of cfDNA, both nuclear and mitochondrial DNA, as biomarkers for autoimmune rheumatic diseases and discuss limitations, challenges and implications to establish cfDNA as a biomarker for clinical use. This review will also highlight recent advancements in mechanistic studies demonstrating mitochondrial DNA as a central component of cfDNA in autoimmune rheumatic diseases.
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Affiliation(s)
- Bhargavi Duvvuri
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Christian Lood
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
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Khanna S, Padhan P, Das S, Jaiswal KS, Tripathy A, Smita S, Tripathy SK, Raghav SK, Gupta B. A Simple Colorimetric Method for Naked-Eye Detection of Circulating Cell-Free DNA Using Unlabelled Gold Nanoparticles. ChemistrySelect 2018. [DOI: 10.1002/slct.201802671] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Shweta Khanna
- Disease Biology Laboratory; School of Biotechnology; Kalinga Institute of Industrial Technology (KIIT); Deemed to be University, Bhubaneswar, Odisha; 751024 India
| | - Prasanta Padhan
- Department of Rheumatology; Kalinga Institute of Medical Sciences, Bhubaneswar, Odisha; India
| | - Sourav Das
- Chemical and Bioprocess Engineering Lab; School of Chemical Technology; Kalinga Institute of Industrial Technology (KIIT); Deemed to be University, Bhubaneswar, Odisha; 751024 India
| | - Kumar Sagar Jaiswal
- Disease Biology Laboratory; School of Biotechnology; Kalinga Institute of Industrial Technology (KIIT); Deemed to be University, Bhubaneswar, Odisha; 751024 India
| | - Archana Tripathy
- Disease Biology Laboratory; School of Biotechnology; Kalinga Institute of Industrial Technology (KIIT); Deemed to be University, Bhubaneswar, Odisha; 751024 India
| | - Shuchi Smita
- Laboratory of Immuno-Genomics and Systems Biology; Institute of Life Sciences, Bhubaneswar, Odisha; India
| | - Suraj K. Tripathy
- Chemical and Bioprocess Engineering Lab; School of Chemical Technology; Kalinga Institute of Industrial Technology (KIIT); Deemed to be University, Bhubaneswar, Odisha; 751024 India
| | - Sunil Kumar Raghav
- Laboratory of Immuno-Genomics and Systems Biology; Institute of Life Sciences, Bhubaneswar, Odisha; India
| | - Bhawna Gupta
- Disease Biology Laboratory; School of Biotechnology; Kalinga Institute of Industrial Technology (KIIT); Deemed to be University, Bhubaneswar, Odisha; 751024 India
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Xu Y, Song Y, Chang J, Zhou X, Qi Q, Tian X, Li M, Zeng X, Xu M, Zhang W, Cram DS, Liu J. High levels of circulating cell-free DNA are a biomarker of active SLE. Eur J Clin Invest 2018; 48:e13015. [PMID: 30079480 DOI: 10.1111/eci.13015] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 08/02/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND High levels of circulating cell-free DNA (cfDNA) have been reported in patients with inflammatory conditions. The aim of the study was to investigate the levels of cfDNA in patients with systemic lupus erythematosus (SLE). MATERIALS AND METHODS Comparative groups comprised 22 nonpregnant and 36 pregnant women with SLE (test groups) and 60 nonpregnant and 199 pregnant women with no history of SLE (control groups). The levels of cfDNA in plasma were quantitated by a fluorometric dsDNA assay. RESULTS Compared to controls, the median levels of cfDNA were significantly higher in nonpregnant SLE patients (7.38 ng/mL vs 4.6 ng/mL, P = 0.033) and in pregnant SLE patients (7.65 ng/mL vs 5.25 ng/mL, P = 0.003). Based on SLE disease activity index (SLEDAI) scores, the median cfDNA levels were significantly higher in patients with active disease (4 < SLEDAI < 15) compared with patients with inactive disease (SLEDAI < 4) (13.58 ng/mL vs 6.72 ng/mL, P = 0.01). While there was a trend of increased cfDNA levels with higher SLEDAI scores (R2 = 0.3, P < 0.001), we found no association of increased cfDNA levels with nephritis, skin manifestations, multiorgan inflammations or with other inflammatory markers such as decreased C3 and C4 levels or increased anti-ds DNA antibodies. CONCLUSIONS Our results suggest that in addition to classical SLE serological markers, measurement of circulating plasma cfDNA levels has potential as a useful biomarker for assessing SLE disease activity in patients and monitoring treatment.
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Affiliation(s)
- Yalan Xu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China.,Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Yijun Song
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - Jiazhen Chang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - Xiya Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - Qingwei Qi
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
| | - Xinping Tian
- Department of Rheumatology and Immunology, Peking Union Medical College Hospital, Beijing, China
| | - Mengtao Li
- Department of Rheumatology and Immunology, Peking Union Medical College Hospital, Beijing, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Immunology, Peking Union Medical College Hospital, Beijing, China
| | - Mengnan Xu
- Berry Genomics Corporation, Beijing, China
| | | | | | - Juntao Liu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, China
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Abdelal IT, Zakaria MA, Sharaf DM, Elakad GM. Levels of plasma cell-free DNA and its correlation with disease activity in rheumatoid arthritis and systemic lupus erythematosus patients. EGYPTIAN RHEUMATOLOGIST 2016. [DOI: 10.1016/j.ejr.2016.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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