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Liu F, Su Y, Liu X, Zhao L, Wu Z, Liu Y, Zhang L. Cell-free DNA: a metabolic byproduct with diagnostic and prognostic potential in rheumatic disorders. Front Pharmacol 2025; 16:1537934. [PMID: 40008123 PMCID: PMC11850341 DOI: 10.3389/fphar.2025.1537934] [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: 12/02/2024] [Accepted: 01/22/2025] [Indexed: 02/27/2025] Open
Abstract
The release of intracellular DNA into the extracellular area occurs via two pathways: cell death and active secretion by cells. The DNA, which is free in the extracellular space, is commonly known as Cell-Free DNA (cfDNA). In healthy people, the levels of cfDNA in the circulation are notably minimal. Within a healthy organism, cfDNA undergoes swift elimination and filtration upon release, ensuring a persistently low concentration in the bloodstream. Conversely, individuals suffering from diverse illnesses like stroke, trauma, myocardial infarction, and various cancers show markedly higher levels of cfDNA in their blood plasma or serum. Further research has shown that cfDNA is associated with a wide range of human diseases and may have a feedback relationship with inflammation, potentially serving as a non-invasive, accurate, sensitive, and rapid biomarker for clinical applications in disease differential diagnosis, activity monitoring, and prognosis assessment. Studies dating back to the 1970s have indicated elevated cfDNA concentrations in SLE. Currently, increased levels of cfDNA are noted in a range of rheumatic disorders. Inflammatory damage in patients with rheumatic diseases promotes the release of cfDNA, while potential abnormalities in cfDNA metabolism further increase its levels. Elevated concentrations of cfDNA are recognized by DNA receptors, initiating immune-inflammatory reactions which subsequently accelerate the progression of disease. Reducing excess cfDNA may help improve inflammation. Additionally, several trials have demonstrated a correlation between cfDNA concentrations and the activity of rheumatic diseases, indicating the potential of cfDNA, a novel marker for inflammation, in conjunction with C-creative protein (CRP), Erythrocyte Sedimentation Rate (ESR) to monitor disease activity in rheumatic conditions. This paper provides an overview of cfDNA and summarizes current research advancements in cfDNA in rheumatic diseases, aiming to offer new perspectives for researchers.
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Affiliation(s)
- Fancheng Liu
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Shanxi Bethune Hospital, Taiyuan, China
| | - Yazhen Su
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Shanxi Bethune Hospital, Taiyuan, China
| | - Xinling Liu
- Third Clinical College, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Li Zhao
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Shanxi Bethune Hospital, Taiyuan, China
| | - Zewen Wu
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Shanxi Bethune Hospital, Taiyuan, China
| | - Yang Liu
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Shanxi Bethune Hospital, Taiyuan, China
| | - Liyun Zhang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
- Shanxi Province Clinical Research Center for Dermatologic and Immunologic Diseases (Rheumatic Diseases), Shanxi Bethune Hospital, Taiyuan, China
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Taha SI, Samaan SF, Hawash SS, El-Sehsah EM, Shamloul S, Elsheikh DHH, Othman B, Albanghali MA, Aljadani SH, Elmanna A, Ghorab RA. Circulating cell-free DNA as a potential biomarker for prediction of disease activity and prognosis among Egyptian rheumatoid arthritis patients. Int J Immunopathol Pharmacol 2025; 39:3946320251315036. [PMID: 39891356 PMCID: PMC11786270 DOI: 10.1177/03946320251315036] [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: 09/13/2024] [Accepted: 01/07/2025] [Indexed: 02/03/2025] Open
Abstract
Cell-free DNA (cfDNA) has emerged as a potential biomarker for assessing disease activity and prognosis in rheumatoid arthritis (RA). However, the association between cfDNA levels and the established RA markers of inflammation and disease severity remains unclear. The current study aimed to detect plasma levels of cfDNA in patients with RA and to investigate their association with RA activity indicators (erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), disease activity score-28 (DAS28)), prognostic markers (rheumatoid factor (RF), anticitrullinated protein antibodies (ACPA)), and the musculoskeletal ultrasonographic (US7) scores. This controlled cross-sectional study included 108 RA patients and 108 healthy controls. Plasma levels of cfDNA were quantified by real-time PCR using ALU repeats. Levels of ESR, CRP, RF, and ACPA were measured using routine laboratory assays. Synovial inflammation and joint damage evaluation was performed using the US7 scoring system. Plasma levels of cfDNA were higher in RA patients than controls (P < 0.001) and significantly increased with higher DAS28 scores among all RA activity groups. Also, cfDNA levels were significantly positively correlated with ESR, CRP, RF, and ACPA levels (P-values <0.001). Regarding US7, cfDNA was significantly positively correlated with synovitis and erosion scores (P-values <0.05) but did not correlate significantly with tenosynovitis scores (P-values >0.05). In addition, plasma cfDNA was significantly higher in seropositive RA patients than in seronegative patients (P = 0.007). The odds ratio for cfDNA as a risk factor for erosions was 2.254. This study revealed that cfDNA levels are elevated in RA patients and positively associated with disease activity indicators and prognosis markers. Further research is warranted to validate these findings in larger cohorts and explore the clinical implications of cfDNA measurement in RA management.
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Affiliation(s)
- Sara I Taha
- Department of Clinical Pathology, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
| | - Sara F Samaan
- Department of Internal Medicine, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
| | - Sally Saber Hawash
- Department of Physical Medicine, Rheumatology and Rehabilitation, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
| | - Eman M El-Sehsah
- Department of Medical Microbiology and Immunology, Mansoura Faculty of Medicine, Mansoura, Egypt
| | - Sara Shamloul
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | - Basim Othman
- Department of Public Health, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Mohammad A Albanghali
- Department of Public Health, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Saeedah H Aljadani
- Department of Basic Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Abdalla Elmanna
- Department of Public Health, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Rasha Ahmed Ghorab
- Department of Clinical Pathology, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
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Lehmann J, Giaglis S, Kyburz D, Daoudlarian D, Walker UA. Plasma mtDNA as a possible contributor to and biomarker of inflammation in rheumatoid arthritis. Arthritis Res Ther 2024; 26:97. [PMID: 38715082 PMCID: PMC11075188 DOI: 10.1186/s13075-024-03329-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
OBJECTIVES Neutrophil extracellular trap formation and cell-free DNA (cfDNA) contribute to the inflammation in rheumatoid arthritis (RA), but it is unknown if mitochondrial DNA (mtDNA) or nuclear DNA (nDNA) is more abundant in the circulation. It is unclear if DNA concentration measurements may assist in clinical decision-making. METHODS This single-center prospective observational study collected plasma from consecutive RA patients and healthy blood donors. Platelets were removed, and mtDNA and nDNA copy numbers were quantified by polymerase chain reaction (PCR). RESULTS One hundred six RA patients and 85 healthy controls (HC) were recruited. Circulating median mtDNA copy numbers were increased 19.4-fold in the plasma of patients with RA (median 1.1 x108 copies/mL) compared to HC (median 5.4 x106 copies/mL, p<0.0001). Receiver operating characteristics (ROC) curve analysis of mtDNA copy numbers identified RA patients with high sensitivity (92.5%) and specificity (89.4%) with an area under the curve (AUC) of 0.97, p <0.0001 and a positive likelihood ratio of 8.7. Demographic, serological (rheumatoid factor (RF) positivity, anti-citrullinated protein antibodies (ACPA) positivity) and treatment factors were not associated with DNA concentrations. mtDNA plasma concentrations, however, correlated significantly with disease activity score-28- erythrocyte sedimentation rate (DAS28-ESR) and increased numerically with increasing DAS28-ESR and clinical disease activity index (CDAI) activity. MtDNA copy numbers also discriminated RA in remission (DAS28 <2.6) from HC (p<0.0001). Also, a correlation was observed between mtDNA and the ESR (p = 0.006, R= 0.29). Similar analyses showed no significance for nDNA. CONCLUSION In contrast to nDNA, mtDNA is significantly elevated in the plasma of RA patients compared with HC. Regardless of RA activity, the abundance of circulating mtDNA is a sensitive discriminator between RA patients and HC. Further validation of the diagnostic value of mtDNA testing is required.
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Affiliation(s)
- Julia Lehmann
- Laboratory for Experimental Rheumatology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Rheumatology, University Hospital Basel, Petersgraben 4, CH 4037, Basel, Switzerland
| | - Stavros Giaglis
- Laboratory for Experimental Rheumatology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Diego Kyburz
- Laboratory for Experimental Rheumatology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Rheumatology, University Hospital Basel, Petersgraben 4, CH 4037, Basel, Switzerland
| | - Douglas Daoudlarian
- Laboratory for Experimental Rheumatology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Ulrich A Walker
- Laboratory for Experimental Rheumatology, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Department of Rheumatology, University Hospital Basel, Petersgraben 4, CH 4037, Basel, Switzerland.
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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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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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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: 10] [Impact Index Per Article: 5.0] [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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Bo L, Jin X, Hu Y, Yang R. Role of Liquid Biopsies in Rheumatoid Arthritis. Methods Mol Biol 2023; 2695:237-246. [PMID: 37450123 DOI: 10.1007/978-1-0716-3346-5_16] [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: 07/18/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease caused by genetic and environmental factors. Early diagnosis is crucial for effective therapy and prognosis of RA, while biomarkers play important roles in early diagnosis. Traditional laboratory tests include rheumatoid factor, anti-cyclic citrullinated peptide antibody, which are inadequate in the ability of early diagnosis. Liquid biopsy technology is a technique using biomarkers found in the blood, urine, and other biological samples from patients, including DNA, RNA, exosome, etc. Evidence indicates that these biomarkers are involved in pathological and physiological conditions of RA. We reviewed the effects of liquid biopsy technology in the early diagnosis of RA and may provide new ideas for effective and precise treatment.
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Affiliation(s)
- Lin Bo
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiaojia Jin
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yaqi Hu
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Ru Yang
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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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: 2] [Impact Index Per Article: 0.7] [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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Che H, Jatsenko T, Lannoo L, Stanley K, Dehaspe L, Vancoillie L, Brison N, Parijs I, Van Den Bogaert K, Devriendt K, Severi S, De Langhe E, Vermeire S, Verstockt B, Van Calsteren K, Vermeesch JR. Machine learning-based detection of immune-mediated diseases from genome-wide cell-free DNA sequencing datasets. NPJ Genom Med 2022; 7:55. [PMID: 36100603 PMCID: PMC9470560 DOI: 10.1038/s41525-022-00325-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 07/21/2022] [Indexed: 11/08/2022] Open
Abstract
The early detection of tissue and organ damage associated with autoimmune diseases (AID) has been identified as key to improve long-term survival, but non-invasive biomarkers are lacking. Elevated cell-free DNA (cfDNA) levels have been observed in AID and inflammatory bowel disease (IBD), prompting interest to use cfDNA as a potential non-invasive diagnostic and prognostic biomarker. Despite these known disease-related changes in concentration, it remains impossible to identify AID and IBD patients through cfDNA analysis alone. By using unsupervised clustering on large sets of shallow whole-genome sequencing (sWGS) cfDNA data, we uncover AID- and IBD-specific genome-wide patterns in plasma cfDNA in both the obstetric and general AID and IBD populations. We demonstrate that pregnant women with AID and IBD have higher odds of receiving inconclusive non-invasive prenatal screening (NIPS) results. Supervised learning of the genome-wide patterns allows AID prediction with 50% sensitivity at 95% specificity. Importantly, the method has the potential to identify pregnant women with AID during routine NIPS. Since AID pregnancies have an increased risk of severe complications, early recognition or detection of new-onset AID can redirect pregnancy management and limit potential adverse events. This method opens up new avenues for screening, diagnosis and monitoring of AID and IBD.
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Affiliation(s)
- Huiwen Che
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Tatjana Jatsenko
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Lore Lannoo
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Kate Stanley
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Luc Dehaspe
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Nathalie Brison
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Ilse Parijs
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Sabien Severi
- Department of Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Ellen De Langhe
- Department of Rheumatology, University Hospitals Leuven, Leuven, Belgium
- Department of Development and Regeneration, Laboratory of Tissue Homeostasis and Disease, KU Leuven, Leuven, Belgium
| | - Severine Vermeire
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, TARGID-IBD, KU Leuven, Leuven, Belgium
| | - Bram Verstockt
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, TARGID-IBD, KU Leuven, Leuven, Belgium
| | - Kristel Van Calsteren
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Joris Robert Vermeesch
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium.
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium.
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SHIROUCHI Y, MISHIMA Y, TAKAYAMA T, MINOWA S, ISHIHARA Y, TAMBA M, HIRANO M, ONDA N, TAKEUCHI K, MARUYAMA D. Serum cell-free DNA concentration as a possible prognostic marker in newly diagnosed diffuse large B-cell lymphoma. Biomed Res 2022; 43:99-106. [DOI: 10.2220/biomedres.43.99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yuko SHIROUCHI
- Department of Hematology Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research
| | - Yuko MISHIMA
- Department of Hematology Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research
| | - Tomoko TAKAYAMA
- Division of Clinical Research, The Cancer Chemotherapy Center, Japanese Foundation for Cancer Research
| | - Sayuri MINOWA
- Division of Clinical Research, The Cancer Chemotherapy Center, Japanese Foundation for Cancer Research
| | - Yuko ISHIHARA
- Department of Hematology Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research
| | - Mikako TAMBA
- Department of Hematology Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research
| | - Mitsuhito HIRANO
- Department of Hematology Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research
| | - Naoki ONDA
- Department of Hematology Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research
| | - Kengo TAKEUCHI
- Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research
| | - Dai MARUYAMA
- Department of Hematology Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research
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Stawski R, Nowak D, Perdas E. Cell-Free DNA: Potential Application in COVID-19 Diagnostics and Management. Viruses 2022; 14:321. [PMID: 35215914 PMCID: PMC8880801 DOI: 10.3390/v14020321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 12/04/2022] Open
Abstract
WHO has declared COVID-19 as a worldwide, public health emergency. The elderly, pregnant women, and people with associated co-morbidities, including pulmonary disease, heart failure, diabetes, and cancer are the most predisposed population groups to infection. Cell-free DNA is a very commonly applied marker, which is elevated in various pathological conditions. However, it has a much higher sensitivity than standard biochemical markers. cfDNA appears to be an effective marker of COVID-19 complications, and also serves as a marker of certain underlying health conditions and risk factors of severe illness during COVID-19 infection. We aimed to present the possible mechanisms and sources of cfDNA released during moderate and severe infections. Moreover, we attempt to verify how efficiently cfDNA increase could be applied in COVID-19 risk assessment and how it corresponds with epidemiological data.
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Affiliation(s)
- Robert Stawski
- Department of Clinical Physiology, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Dariusz Nowak
- Department of Clinical Physiology, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Ewelina Perdas
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
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Alonso A, Yuwono NL, Houshdaran S, Abbott J, Rodgers R, Ford CE, Warton K. Comparison of total and endometrial circulating cell-free DNA in women with and without endometriosis. Reprod Biomed Online 2021; 44:495-503. [PMID: 35031240 DOI: 10.1016/j.rbmo.2021.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 10/25/2021] [Accepted: 11/08/2021] [Indexed: 11/26/2022]
Abstract
RESEARCH QUESTION Do women with laparoscopically confirmed endometriosis have higher plasma concentrations of circulating cell-free DNA (cirDNA) than those without endometriosis? DESIGN Prospective study of women aged 18-45 years undergoing benign gynaecological laparoscopy at two tertiary hospitals. Venous blood was collected immediately before surgery, and women were allocated to the endometriosis or control groups based on surgical findings. Total plasma cirDNA and cirDNA integrity were measured by quantitative polymerase chain reaction (qPCR) targeting short (115 bases) and long (247 bases) ALU segments. Endometrial-derived cirDNA was measured by qPCR of bisulfite-treated cirDNA using primers selective for a FAM101A sequence uniquely unmethylated in endometrial tissue. Five cirDNA parameters were compared between the control and endometriosis cohorts: total cirDNA concentration, long-stranded cirDNA concentration, integrity ratio, endometrial cirDNA concentration and endometrial cirDNA proportion. RESULTS Twenty-eight endometriosis and 15 control samples were included. Women with and without endometriosis had cirDNA concentrations of 2.24 ± 0.89 ng/ml and 2.56 ± 0.92 ng/ml, respectively. Analysis by phenotype of endometriosis revealed a significantly higher endometrial cirDNA concentration in women with superficial disease (n = 10) compared with deep endometriosis (n = 18) (mean difference 0.14 ng/ml; 95% CI 0.15 to 0.26; P = 0.025), but not with controls. CONCLUSIONS No significant differences were found in any of the cirDNA parameters between women with and without endometriosis. The low statistical power and heterogenous pelvic pathology in the control group render it difficult to determine whether the negative results reflect a true lack of increase in cirDNA in endometriosis.
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Affiliation(s)
- Anais Alonso
- Gynaecological Research and Clinical Evaluation (GRACE) Unit, Royal Hospital for Women, Sydney NSW, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney NSW, Australia
| | - Nicole Laurencia Yuwono
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney NSW, Australia
| | - Sahar Houshdaran
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, USA
| | - Jason Abbott
- Gynaecological Research and Clinical Evaluation (GRACE) Unit, Royal Hospital for Women, Sydney NSW, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney NSW, Australia
| | - Rachael Rodgers
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, USA; Department of Gynaecology and Reproductive Medicine, Royal Hospital for Women, Sydney NSW, Australia
| | - Caroline Elizabeth Ford
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney NSW, Australia
| | - Kristina Warton
- Gynaecological Cancer Research Group, Adult Cancer Program, School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Sydney NSW, Australia.
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Daraghmeh DN, King C, Wiese MD. A review of liquid biopsy as a tool to assess epigenetic, cfDNA and miRNA variability as methotrexate response predictors in patients with rheumatoid arthritis. Pharmacol Res 2021; 173:105887. [PMID: 34536550 DOI: 10.1016/j.phrs.2021.105887] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/27/2021] [Accepted: 09/12/2021] [Indexed: 11/28/2022]
Abstract
Rheumatoid arthritis (RA) is a common autoimmune inflammatory disease affecting 0.5-1% of adults worldwide. Achieving long term remission or low disease activity is possible through early diagnosis, rapid initiation of disease modifying anti-rheumatic drugs (DMARDs) and implementation of a treat to target approach. Initial DMARD therapy usually involves methotrexate (MTX), either alone or in combination with other agents, however 40% of RA patients do not respond adequately, putting them at risk of disease progression and unnecessary exposure to MTX related adverse effects. Early predictors of MTX response would therefore enable a more personalized treatment strategy, ensuring timely access to MTX for those likely to respond and importantly, early initiation of alternative treatment for those in which MTX is unlikely to be efficacious. Predicting response to treatment will most likely require consideration of the clinical characteristics of the patient and interrogation of a number of factors including genetic, epigenetic, cell free DNA (cfDNA) and microRNA (miRNA), all of which can be investigated through blood derived liquid biopsies. This review will summarize the existing literature examining the use of epigenetic factors, cfDNA and miRNA as response predictors among RA patients treated with MTX.
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Affiliation(s)
- Dala N Daraghmeh
- Health and Biomedical Innovation, UniSA: Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia.
| | - Catherine King
- Health and Biomedical Innovation, UniSA: Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Michael D Wiese
- Health and Biomedical Innovation, UniSA: Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
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Hashimoto T, Yoshida K, Hashiramoto A, Matsui K. Cell-Free DNA in Rheumatoid Arthritis. Int J Mol Sci 2021; 22:8941. [PMID: 34445645 PMCID: PMC8396202 DOI: 10.3390/ijms22168941] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 02/07/2023] Open
Abstract
Endogenous DNA derived from the nuclei or mitochondria is released into the bloodstream following cell damage or death. Extracellular DNA, called cell-free DNA (cfDNA), is associated with various pathological conditions. Recently, multiple aspects of cfDNA have been assessed, including cfDNA levels, integrity, methylation, and mutations. Rheumatoid arthritis (RA) is the most common form of autoimmune arthritis, and treatment of RA has highly varied outcomes. cfDNA in patients with RA is elevated in peripheral blood and synovial fluid and is associated with disease activity. Profiling of cfDNA in patients with RA may then be utilized in various aspects of clinical practice, such as the prediction of prognosis and treatment responses; monitoring disease state; and as a diagnostic marker. In this review, we discuss cfDNA in patients with RA, particularly the sources of cfDNA and the correlation of cfDNA with RA pathogenesis. We also highlight the potential of analyzing cfDNA profiles to guide individualized treatment approaches for RA.
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Affiliation(s)
- Teppei Hashimoto
- Division of Diabetes, Endocrinology and Clinical Immunology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya 6638501, Japan;
| | - Kohsuke Yoshida
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe 6540142, Japan; (K.Y.); (A.H.)
| | - Akira Hashiramoto
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe 6540142, Japan; (K.Y.); (A.H.)
| | - Kiyoshi Matsui
- Division of Diabetes, Endocrinology and Clinical Immunology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya 6638501, Japan;
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Martins VF, Dobson CR, Begur M, Parekh J, Ball ST, Gonzalez F, Hughes-Austin JM, Schenk S. Surgical site peptidylarginine deaminase 4 (PAD4), a biomarker of NETosis, correlates with insulin resistance in total joint arthroplasty patients: A preliminary report. PLoS One 2021; 16:e0245594. [PMID: 33481860 PMCID: PMC7822240 DOI: 10.1371/journal.pone.0245594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 01/04/2021] [Indexed: 01/12/2023] Open
Abstract
While obesity and insulin resistance are known risk factors for wound complications after total joint arthroplasty (TJA), the biologic causes remain to be elucidated. Recently, neutrophil extracellular trap formation (NETosis) was identified as a mediator of delayed wound healing in insulin resistant states. Herein, we explored the relationship between obesity, insulin resistance and biomarkers of NET formation in TJA subjects. We enrolled 14 obese (body mass index [BMI]≥30 kg/m2), and 15 lean (BMI<30 kg/m2) subjects undergoing primary knee or hip TJA. On the day of surgery, skeletal muscle proximal to the operated joint and plasma were collected. Protein abundance of NETosis biomarkers, peptidylarginine deaminase 4 (PAD4) and neutrophil elastase (NE) were assessed in skeletal muscle by immunoblotting and metabolic parameters (glucose, insulin, triglycerides, free fatty acids) and cell-free double-stranded DNA (cf-dsDNA) were assessed in plasma and were correlated with obesity and insulin resistance (as measured by the homeostatic model assessment for insulin resistance). When comparing lean and obese subjects, there were no significant differences in plasma cf-dsDNA or skeletal muscle NE or PAD4 abundance. In contrast, skeletal muscle PAD4 abundance, but not NE or plasma cf-dsDNA, was positively correlated with insulin resistance. Compared to insulin sensitive subjects, insulin resistant TJA subjects have higher expression of PAD4 at the surgical site and therefore may have higher rates of NET formation, which may lead to delayed surgical site wound healing.
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Affiliation(s)
- Vitor F. Martins
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States of America
| | - Christopher R. Dobson
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Maedha Begur
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Jesal Parekh
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Scott T. Ball
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Francis Gonzalez
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Jan M. Hughes-Austin
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
| | - Simon Schenk
- Department of Orthopaedic Surgery, University of California San Diego, La Jolla, CA, United States of America
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States of America
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16
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Han J, Li X, Luo X, He J, Huang X, Zhou Q, Han Y, Jie H, Zhuang J, Li Y, Yang F, Zhai Z, Wu S, He Y, Yang B, Sun E. The mechanisms of hydroxychloroquine in rheumatoid arthritis treatment: Inhibition of dendritic cell functions via Toll like receptor 9 signaling. Biomed Pharmacother 2020; 132:110848. [PMID: 33049581 PMCID: PMC7547638 DOI: 10.1016/j.biopha.2020.110848] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 02/07/2023] Open
Abstract
HCQ efficiently inhibited DC phenotypic and functional maturation stimulated by serum from RA patients. HCQ prevented progression of arthritis by inhibiting DC maturation and migration from peripheral blood to LNs. HCQ inhibited CpG ODN 1826-activated BMDC maturation and migration. The effect of HCQ on DCs was related to the block in TLR9 signaling. The development of arthritis was impaired in TLR9−/− mice.
Hydroxychloroquine (HCQ) is one of the most commonly prescribed immune-suppressants in treating rheumatoid arthritis (RA). Our previous research showed that HCQ suppressed RA development by inhibiting T follicular helper (Tfh) cells directly. Dendritic cells (DCs) serve as the link between innate and acquired immunity. Whether HCQ suppressed Tfh cell through DCs was not clear. In current study, we found that HCQ efficiently inhibited CD86, chemokine (C-X-C motif) receptor 4 (CXCR4) expression and interferon-α (IFN-α) secretion of healthy donor derived purified DCs stimulated by RA patient serum. To mimic RA, collagen-induced arthritis (CIA) mouse model was used and treated with HCQ daily for fifty-four days prior to sacrifice. We found HCQ inhibited DC maturation and migration to lymph nodes (LNs), manifested as down-regulated expression of CD40, CD80, CD86, MHCII (I-Aq) on LN DCs. In addition, HCQ reduced the level of chemokine receptor 7 (CCR7) and L-selectin on peripheral blood DCs and diminished percentage of LN DCs. Of note, HCQ only inhibited CpG ODN 1826-induced IL-12 secretion by bone marrow DCs (BMDCs) stimulated by various toll like receptor (TLR) agonists. Mechanistically, HCQ down-regulated the expression of TLR9 not only in healthy donor PBMC-derived DCs stimulated by RA patient serum, but also in LN DCs of CIA mice and CpG-activated BMDCs. Furthermore, arthritis scores in TLR9−/− mice were much lower than that in wild type mice with impaired maturity and migration capability of DCs. Collectively, activation of DCs contributes to the pathogenesis of RA and HCQ shows protective effects on RA by inhibition of DC activation via blocking TLR9.
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Affiliation(s)
- Jiaochan Han
- Department of Rheumatology and Immunology, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong, China; Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xing Li
- Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoqing Luo
- Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Juan He
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Xuechan Huang
- Department of Rheumatology and Immunology, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Qingyou Zhou
- Department of Neurology, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Yanping Han
- Clinical Lab, Hospital of South China Normal University, Guangzhou, China
| | - Hongyu Jie
- Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jian Zhuang
- Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yehao Li
- Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Fangyuan Yang
- Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zeqing Zhai
- Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Shufan Wu
- Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yi He
- Department of Rheumatology and Immunology, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong, China; Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Bin Yang
- Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Erwei Sun
- Department of Rheumatology and Immunology, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong, China; Department of Rheumatology and Immunology, The Third Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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Hameed AK, El-Said TO, Askar HY, ElKady BA. Performance of serum adenosine deaminase in measuring disease activity in rheumatoid arthritis patients. EGYPTIAN RHEUMATOLOGIST 2019. [DOI: 10.1016/j.ejr.2018.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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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: 163] [Impact Index Per Article: 27.2] [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: 0.9] [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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Gheita TA, Abaza NM, Hammam N, Mohamed AAA, El-Gazzar II, Eissa AH. Anti-dsDNA titre in female systemic lupus erythematosus patients: relation to disease manifestations, damage and antiphospholipid antibodies. Lupus 2018; 27:1081-1087. [PMID: 29460701 DOI: 10.1177/0961203318760209] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Attempts are ongoing to unveil unresolved queries about anti-double-stranded deoxyribonucleic acid (anti-dsDNA), their precise pathogenic effects and to what extent blocking them would be a useful therapeutic goal. Objectives The aim of the present study was to determine the anti-dsDNA antibodies titre in systemic lupus erythematosus (SLE) patients and investigate their relation to the disease characteristics, activity, damage and antiphospholipid autoantibodies (aPL). Methods Seventy female SLE patients and 35 age- and sex-matched controls were included. The anti-dsDNA level and aPL were measured. Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) and Systemic Lupus International Collaborative Clinics/American College of Rheumatology Damage Index (SLICC/ACR-DI) were assessed. Results The mean age of the patients was 27.5 ± 5.1 years, disease duration 7.7 ± 5.4 years, and SLEDAI and SLICC/ACR-DI scores were 6.8 ± 8.04 and 1.2 ± 1.3, respectively. Anti-dsDNA was positive in 61.4% of the patients and the titre (133.2 ± 100.5 IU/ml) was significantly higher compared to controls (22.03 ± 17.2 IU/ml) ( p < 0.0001). The anti-dsDNA level was significantly increased in those with musculoskeletal manifestations ( p = 0.007) and positive anti-β2 glycoprotein (anti-β2GP) ( p = 0.037) and decreased in those with neuropsychiatric manifestations ( p = 0.004) and those receiving cyclophosphamide (CYC) ( p = 0.013). The anti-dsDNA level tended to be higher in active patients. The anti-dsDNA titre significantly correlated with the erythrocyte sedimentation rate ( p = 0.001), anticardiolipin IgG and IgA antibodies ( p = 0.008) and anti-β2GP IgG ( p = 0.03) and IgA ( p = 0.002) and inversely with the total leucocytic count ( p < 0.0001) and SLICC/ACR-DI ( p = 0.001). Conclusion Anti-dsDNA is remarkably increased in SLE patients especially those with musculoskeletal manifestations and aPL. A protective role seems likely in those with neuropsychiatric manifestations and those receiving CYC and may form a shield against disease tissue damage.
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Affiliation(s)
- T A Gheita
- 1 Rheumatology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - N M Abaza
- 2 Physical Medicine, Rheumatology and Rehabilitation Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - N Hammam
- 3 Rheumatology and Rehabilitation Department, Faculty of Medicine, Assuit University, Assiut, Egypt.,4 Faculty of Rehabilitation, University of Alberta, Edmonton, Alberta, Canada
| | - A A A Mohamed
- 3 Rheumatology and Rehabilitation Department, Faculty of Medicine, Assuit University, Assiut, Egypt
| | - I I El-Gazzar
- 1 Rheumatology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - A H Eissa
- 5 Clinical Pathology (Immunology) Department, Faculty of Medicine, Cairo University, Cairo, Egypt
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Abstract
INTRODUCTION Osteoarthritis (OA), a chronic, debilitating and degenerative disease of the joints, is the most common form of arthritis. The seriousness of this prevalent and chronic disease is often overlooked. Disease modifying OA drug development is hindered by the lack of soluble biomarkers to detect OA early. The objective of OA biomarker research is to identify early OA prior to the appearance of radiographic signs and the development of pain. Areas covered: This review has focused on extracellular genomic material that could serve as biomarkers of OA. Recent studies have examined the expression of extracellular genomic material such as miRNA, lncRNA, snoRNA, mRNA and cell-free DNA, which are aberrantly expressed in the body fluids of OA patients. Changes in genomic content of peripheral blood mononuclear cells in OA could also function as biomarkers of OA. Expert commentary: There is an unmet need for soluble biomarkers for detecting and then monitoring OA disease progression. Extracellular genomic material research may also reveal more about the underlying pathophysiology of OA. Minimally-invasive liquid biopsies such as synovial fluid and blood sampling of genomic material may be more sensitive over radiography in the detection, diagnosis and monitoring of OA in the future.
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Affiliation(s)
- Emma Budd
- a The D-BOARD European Consortium for Biomarker Discovery, School of Veterinary Medicine , University of Surrey , Guildford , UK.,b Department of Veterinary Pre-Clinical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences , University of Surrey , Guildford , UK
| | - Giovanna Nalesso
- b Department of Veterinary Pre-Clinical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences , University of Surrey , Guildford , UK
| | - Ali Mobasheri
- a The D-BOARD European Consortium for Biomarker Discovery, School of Veterinary Medicine , University of Surrey , Guildford , UK.,b Department of Veterinary Pre-Clinical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences , University of Surrey , Guildford , UK.,c Arthritis Research UK Centre for Sport, Exercise and Osteoarthritis , Queen's Medical Centre , Nottingham , UK
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