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Luo X, Jiang P, Ma J, Li Z, Zhou J, Wei X, A J, Chai J, Lv Y, Cheng P, Cao C, A X. Circulating free DNA as a diagnostic marker for echinococcosis: a systematic review and meta-analysis. Front Microbiol 2024; 15:1413532. [PMID: 39021627 PMCID: PMC11251952 DOI: 10.3389/fmicb.2024.1413532] [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: 04/07/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024] Open
Abstract
Introduction Echinococcosis is a chronic zoonotic disease caused by tapeworms of the genus Echinococcus. The World Health Organization (WHO) has identified encapsulated disease as one of 17 neglected diseases to be controlled or eliminated by 2050. There is no accurate, early, non-invasive molecular diagnostic method to detect echinococcosis. The feasibility of circulating free DNA as a diagnostic method for echinococcosis has yielded inconclusive results in a number of published studies. However, there has been no systematic evaluation to date assessing the overall performance of these assays. We report here the first meta-analysis assessing the diagnostic accuracy of cfDNA in plasma, serum, and urine for echinococcosis. Methods We systematically searched PubMed, Embase, Cochrane Library, China National Knowledge Infrastructure (CNKI), and WeiPu databases up to 17 January 2024, for relevant studies. All analyses were performed using RevMan 5.3, Meta-DiSc 1.4, Stata 17.0, and R 4.3.1 software. The sensitivity, specificity, and other accuracy indicators of circulating free DNA for the diagnosis of echinococcosis were summarized. Subgroup analyses and meta-regression were performed to identify sources of heterogeneity. Results A total of 7 studies included 218 patients with echinococcosis and 214 controls (156 healthy controls, 32 other disease controls (non-hydatid patients), and 26 non-study-targeted echinococcosis controls were included). Summary estimates of the diagnostic accuracy of cfDNA in the diagnosis of echinococcosis were as follows: sensitivity (SEN) of 0.51 (95% CI: 0.45-0.56); specificity (SPE) of 0.99 (95% CI: 0.97-0.99); positive likelihood ratio (PLR) of 11.82 (95% CI: 6.74-20.74); negative likelihood ratio (NLR) of 0.57 (95% CI: 0.41-0.80); diagnostic ratio (DOR) of 36.63 (95% CI: 13.75-97.59); and area under the curve (AUC) value of 0.98 (95% CI: 0.96-1.00). Conclusion Existing evidence indicates that the combined specificity of circulating cfDNA for echinococcosis is high. However, the combined sensitivity performance is unsatisfactory due to significant inter-study heterogeneity. To strengthen the validity and accuracy of our findings, further large-scale prospective studies are required.Systematic review registrationThe systematic review was registered in the International Prospective Register of Systematic Reviews PROSPERO [CRD42023454158]. https://www.crd.york.ac.uk/PROSPERO/.
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Affiliation(s)
- Xiaoqin Luo
- Qinghai University, Xining, China
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
| | | | | | - Zian Li
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
| | - Jianwu Zhou
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
| | | | - Jide A
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
| | - Jinping Chai
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
| | - Yanke Lv
- Qinghai University, Xining, China
| | | | | | - Xiangren A
- Qinghai University, Xining, China
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
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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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Hashimoto T, Yoshida K, Yokoyama Y, Hashimoto N, Kaneshiro K, Yoshikawa T, Tateishi K, Terashima Y, Matsui K, Hashiramoto A. Tocilizumab suppresses NF-kappa B activation via toll-like receptor 9 signaling by reducing cell-free DNA in rheumatoid arthritis. Clin Exp Immunol 2023; 213:209-220. [PMID: 37279559 PMCID: PMC10361738 DOI: 10.1093/cei/uxad064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/10/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023] Open
Abstract
Endogenous DNA is released into the bloodstream as cell-free DNA (cfDNA) following cell death and is associated with various pathological conditions. However, their association with therapeutic drugs against rheumatoid arthritis (RA) remains unknown. Therefore, we investigated the significance of cfDNA in RA treated with tocilizumab and tumour necrosis factor inhibitor (TNF-I). Biological DMARDs (bDMARDs), including tocilizumab and TNF-I, were administered to 77 and 59 RA patients, respectively. Plasma cfDNA levels were measured at weeks 0, 4, and 12 by quantitative polymerase chain reaction. Disease activity was evaluated at the same time point using DAS28ESR. cfDNA levels from RA synovial cells treated with tocilizumab or etanercept for 24 h were measured. Human toll-like receptor 9 (hTLR9)-expressing HEK293 cells, which release secreted embryonic alkaline phosphatase (SEAP) upon NF-κB activation, were stimulated by cfDNA from RA patients, and subsequently, SEAP levels were determined. NF-κB translocation was evaluated by immunofluorescence staining with or without tocilizumab. The DAS28ESR significantly improved in both bDMARD groups at week 12. However, plasma cfDNA levels significantly decreased in the tocilizumab group at week 12 compared to that in week 0. cfDNA levels correlated with DAS28ESR in biological treatment-naïve patients administered tocilizumab. cfDNA levels in synovial cells were significantly suppressed by tocilizumab treatment and unaltered with etanercept. HEK293 cells released SEAP upon cfDNA stimulation, and the observed NF-κB nuclear translocation was suppressed by tocilizumab. Tocilizumab suppressed inflammation via the TLR9 pathway by decreasing cfDNA levels. Regulation of cfDNA may be a therapeutic target for RA.
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Affiliation(s)
- Teppei Hashimoto
- Department of Diabetes, Endocrinology and Clinical Immunology, School of Medicine, Hyogo Medical University, Nishinomiya, Japan
| | - Kohsuke Yoshida
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Yuichi Yokoyama
- Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Naonori Hashimoto
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Kenta Kaneshiro
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Takahiro Yoshikawa
- Department of Diabetes, Endocrinology and Clinical Immunology, School of Medicine, Hyogo Medical University, Nishinomiya, Japan
| | - Koji Tateishi
- Department of Orthopedics, Konan Kakogawa Hospital, Kakogawa, Japan
| | | | - Kiyoshi Matsui
- Department of Diabetes, Endocrinology and Clinical Immunology, School of Medicine, Hyogo Medical University, Nishinomiya, Japan
| | - Akira Hashiramoto
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan
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Panizzi L, Dittmer KE, Vignes M, Doucet JS, Gedye K, Waterland MR, Rogers CW, Sano H, McIlwraith CW, Riley CB. Plasma and Synovial Fluid Cell-Free DNA Concentrations Following Induction of Osteoarthritis in Horses. Animals (Basel) 2023; 13:ani13061053. [PMID: 36978592 PMCID: PMC10044647 DOI: 10.3390/ani13061053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/03/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Biomarkers for osteoarthritis (OA) in horses have been extensively investigated, but translation into clinical use has been limited due to cost, limited sensitivity, and practicality. Identifying novel biomarkers that overcome these limitations could facilitate early diagnosis and therapy. This study aimed to compare the concentrations of synovial fluid (SF) and plasma cell-free DNA (cfDNA) over time in control horses with those with induced carpal OA. Following an established model, unilateral carpal OA was induced in 9 of 17 healthy Thoroughbred fillies, while the remainder were sham-operated controls. Synovial fluid and plasma samples were obtained before induction of OA (Day 0) and weekly thereafter until Day 63, and cfDNA concentrations were determined using fluorometry. The SF cfDNA concentrations were significantly higher for OA joints than for sham-operated joints on Days 28 (median 1430 μg/L and 631 μg/L, respectively, p = 0.017) and 63 (median 1537 μg/L and 606 μg/L, respectively, p = 0.021). There were no significant differences in plasma cfDNA between the OA and the sham groups after induction of carpal OA. Plasma cfDNA measurement is not sufficiently sensitive for diagnostic purposes in this induced model of OA. Synovial fluid cfDNA measurement may be used as a biomarker to monitor early disease progression in horses with OA.
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Affiliation(s)
- Luca Panizzi
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
- Correspondence:
| | - Keren E. Dittmer
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
| | - Matthieu Vignes
- School of Mathematical and Computational Sciences, College of Science, Massey University, Palmerston North 4442, New Zealand;
| | - Jennie S. Doucet
- Department of Biology, Faculty of Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Kristene Gedye
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
| | - Mark R. Waterland
- School of Natural Sciences, College of Science, Massey University, Palmerston North 4442, New Zealand;
| | - Chris W. Rogers
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
- School of Agriculture and Environment, College of Science, Massey University, Palmerston North 4442, New Zealand
| | - Hiroki Sano
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
| | - C. Wayne McIlwraith
- Orthopaedic Research Center, C. Wayne McIlwraith Translational Medicine Institute, School of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523-1601, USA;
| | - Christopher B. Riley
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
- Department of Clinical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
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Hadipour M, Fasihi Harandi M, Mirhendi H, Yousofi Darani H. Diagnosis of echinococcosis by detecting circulating cell-free DNA and miRNA. Expert Rev Mol Diagn 2023; 23:133-142. [PMID: 36756744 DOI: 10.1080/14737159.2023.2178903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
INTRODUCTION Diagnosis of echinococcosis is difficult and usually performed based on clinical findings, imaging, and serological test. However, all of them have limitations, especially in follow-up approaches. AREAS COVERED Detection of cell-free DNA (cfDNA) and micro-RNA (miRNA) is currently a hot topic for diagnosis of echinococcosis diseases. For detecting cell-free DNA in echinococcosis patient's samples such as sera, some techniques are based on next-generation sequencing (NGS), DNA-deep sequencing, some are based on PCR-based methods, and a few works related to the detection of miRNA for the diagnosis of human echinococcosis. EXPERT OPINION In the detection of cell-free DNA in echinococcosis patient' samples, NGS and DNA-deep sequencing have shown high level of sensitivity, but are not suitable for routine clinical examination as they are expensive and inaccessible in the majority of endemic areas. However, PCR-based methods have shown a sensitivity of about 20-25%. To improve the sensitivity of these tests, improving the DNA extraction method, designing appropriate primers for detecting short-length fragments of circulating DNA, using a higher volume of a serum sample, and application of more sensitive PCR methods are recommended. In the field of miRNA detection, further works are recommended.
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Affiliation(s)
- Mahboubeh Hadipour
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
| | - Majid Fasihi Harandi
- Research center for Hydatid disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hossein Mirhendi
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
| | - Hossein Yousofi Darani
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
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Macáková K, Illésová J, Mlynáriková V, Lesayová A, Konečná B, Vlková B, Celec P, Šteňová E. The dynamics of extracellular DNA associates with treatment response in patients with rheumatoid arthritis. Sci Rep 2022; 12:21099. [PMID: 36473902 PMCID: PMC9726858 DOI: 10.1038/s41598-022-23954-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Rheumatoid arthritis (RA) as a chronic autoimmune inflammatory disease increases extracellular DNA (ecDNA). Our previous study has shown that anti-inflammatory treatment reduces ecDNA, but it is unclear whether there is an association with treatment response. The aim of this study was to analyze the changes of ecDNA induced by biological disease-modifying antirheumatic drugs (bDMARDs) in RA patients with an emphasis on the subcellular origin of ecDNA. Plasma samples from 40 RA patients were collected in three different time-points: before treatment with bDMARDs as well as 3 and 12 months following treatment initiation. Total, nuclear and mitochondrial ecDNA was quantified using fluorometry and real-time PCR. Disease activity score (DAS28) and C-reactive protein (CRP) were used to monitor the clinical status and the response to treatment. Treatment with bDMARDs elicited an overall improvement of the clinical status: DAS28 and CRP showed a significant decrease by 54% and 43%, respectively, after 3 months of treatment. A significant decrease of total ecDNA by 60% and nuclear ecDNA by 58% was detected only in good responders after 3 months of bDMARDs treatment. No significant changes of plasma ecDNA concentration were observed in moderate and non-responders. Deoxyribonuclease activity was not affected by the treatment. None of the analyzed biomarkers differed between the groups at baseline. Plasma ecDNA especially of nuclear origin could potentially be useful to monitor the treatment response in RA. Further studies should shed light on disease-treatment interplay implicated in ecDNA origin potentially linked to neutrophil extracellular traps.
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Affiliation(s)
- Kristína Macáková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, 81108, Slovakia
| | - Júlia Illésová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, 81108, Slovakia
| | | | - Alexandra Lesayová
- Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Barbora Konečná
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, 81108, Slovakia
| | - Barbora Vlková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, 81108, Slovakia
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, 81108, Slovakia.
- Institute of Pathophysiology, Faculty of Medicine, Comenius University, Bratislava, 81108, Slovakia.
- Institute of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia.
| | - Emöke Šteňová
- 1st Department of Internal Medicine, Faculty of Medicine, University Hospital, Comenius University, Bratislava, 82101, Slovakia
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Li B, Li G, Yang X, Song Z, Wang Y, Zhang Z. NETosis in Psoriatic Arthritis: Serum MPO–DNA Complex Level Correlates With Its Disease Activity. Front Immunol 2022; 13:911347. [PMID: 35774788 PMCID: PMC9238436 DOI: 10.3389/fimmu.2022.911347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundNeutrophil extracellular trap formation (NETosis) has been rarely reported in psoriatic arthritis (PsA). We aimed to explore the involvement of NETosis in the inflammation of PsA.MethodsSerum myeloperoxidase–DNA (MPO-DNA) complex was detected by a modified enzyme-linked immunosorbent assay and compared among 74 patients with PsA, 58 patients with psoriasis (PsO), and 20 healthy controls. The association of MPO–DNA level with disease activity index at baseline and follow-up was analyzed in patients with PsA. Receiver operating characteristic curve was used to evaluate the predictive value of MPO–DNA for treatment response.ResultsMPO–DNA complex level in serum was significantly increased in patients with PsA/PsO compared to healthy controls (p < 0.001). The level of MPO–DNA was positively associated with DAPSA score and its components (including TJC, SJC, PGA, VAS-pain and CRP, r = 0.25–0.409, all p-values < 0.05). Serum MPO–DNA level was downregualted at 12 weeks after treatment compared to baseline (p = 0.022). The decrease of MPO–DNA level was more dramatic in patients with PsA who achieved both ACR50 and PASI50 response than those achieving neither of them at 12 weeks (p = 0.023). ROC analysis revealed that the serum MPO–DNA level predicted both ACR50 and PASI50 achievement at week 12 (p = 0.04; 95% CIs, 0.56–0.94). Moreover, the baseline MPO–DNA level (p = 0.009; 95% CIs, 0.748–1) and change of MPO–DNA at week 12 from baseline (p = 0.004; 95% CIs, 0.802–1) were associated with the achievement of both ACR70 and PASI75 response at week 24.ConclusionsNETosis plays an important role in psoriatic diseases. The level of MPO–DNA complex in serum reflects disease activity. Serum MPO–DNA complex may be a useful biomarker to predict the therapeutic response in PsA.
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Scanu A, Lorenzin M, Luisetto R, Galozzi P, Ortolan A, Oliviero F, Doria A, Ramonda R. Identification in synovial fluid of a new potential pathogenic player in arthropathies. Exp Biol Med (Maywood) 2022; 247:1061-1066. [PMID: 35470716 DOI: 10.1177/15353702221087966] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
STING (stimulator of interferon genes) has been recognized as an important signaling molecule in the innate immune response to cytosolic nucleic acids. Although it has been proposed that STING signaling pathway may play a pathogenic role in developing autoimmune and autoinflammatory diseases, its involvement in rheumatic disease processes remains to be elucidated. Here, we evaluated STING protein levels, expression and relationship with inflammatory parameters in synovial fluid (SF) of patients with psoriatic arthritis (PsA), rheumatoid arthritis (RA), gout, calcium pyrophosphate crystal-induced arthritis (CPP-IA), osteoarthritis (OA), and OA with CPP crystals (OA + CPP). The correlation with its negative regulator, nuclear factor erythroid 2-related factor 2 (Nrf2), was also investigated. SFs from 72 patients were analyzed for white blood cell (WBC) count, polymorphonuclear cell percentage (PMN%), and IL-1β, IL-6, IL-8, extra- and intracellular STING levels. STING and Nrf2 expression was also determined. WBC count and PMN% were greater in SF from inflammatory arthritis, while they were lower in OA groups. RA and gouty SFs have the highest levels of IL-1β, IL-8, and IL-6; while OA and OA + CPP showed the lowest concentrations. Gout and RA had the highest intracellular STING levels, while extracellular STING was greater in CPP-IA and OA SFs. STING was not detectable in PsA. STING mRNA was lower in PsA than other arthritides. Nrf2 mRNA was not detectable in OA. This study determines the presence of STING in SF of different arthritides, except for PsA, and suggests that it may be involved in pathogenesis and progression of arthropathies.
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Affiliation(s)
- Anna Scanu
- Rheumatology Unit, Department of Medicine (DIMED), University of Padova, Padova 35128, Italy
| | - Mariagrazia Lorenzin
- Rheumatology Unit, Department of Medicine (DIMED), University of Padova, Padova 35128, Italy
| | - Roberto Luisetto
- Department of Surgery, Oncology and Gastroenterology (DISCOG), University of Padova, Padova 35128, Italy
| | - Paola Galozzi
- Rheumatology Unit, Department of Medicine (DIMED), University of Padova, Padova 35128, Italy
| | - Augusta Ortolan
- Rheumatology Unit, Department of Medicine (DIMED), University of Padova, Padova 35128, Italy
| | - Francesca Oliviero
- Rheumatology Unit, Department of Medicine (DIMED), University of Padova, Padova 35128, Italy
| | - Andrea Doria
- Rheumatology Unit, Department of Medicine (DIMED), University of Padova, Padova 35128, Italy
| | - Roberta Ramonda
- Rheumatology Unit, Department of Medicine (DIMED), University of Padova, Padova 35128, Italy
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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: 16] [Impact Index Per Article: 5.3] [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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Circulating Free DNA and Its Emerging Role in Autoimmune Diseases. J Pers Med 2021; 11:jpm11020151. [PMID: 33672659 PMCID: PMC7924199 DOI: 10.3390/jpm11020151] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/06/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Liquid biopsies can be used to analyse tissue-derived information, including cell-free DNA (cfDNA), circulating rare cells, and circulating extracellular vesicles in the blood or other bodily fluids, representing a new way to guide therapeutic decisions in cancer. Among the new challenges of liquid biopsy, we found clinical application in nontumour pathologies, including autoimmune diseases. Since the discovery of the presence of high levels of cfDNA in patients with systemic lupus erythaematosus (SLE) in the 1960s, cfDNA research in autoimmune diseases has mainly focused on the overall quantification of cfDNA and its association with disease activity. However, with technological advancements and the increasing understanding of the role of DNA sensing receptors in inflammation and autoimmunity, interest in cfDNA and autoimmune diseases has not expanded until recently. In this review, we provide an overview of the basic biology of cfDNA in the context of autoimmune diseases as a biomarker of disease activity, progression, and prediction of the treatment response. We discuss and integrate available information about these important aspects.
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Peng B, Liang H, Li Y, Dong C, Shen J, Mao H, Leong KW, Chen Y, Liu L. Tuned Cationic Dendronized Polymer: Molecular Scavenger for Rheumatoid Arthritis Treatment. Angew Chem Int Ed Engl 2019; 58:4254-4258. [DOI: 10.1002/anie.201813362] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/19/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Bo Peng
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
- Department of Biomedical EngineeringColumbia University New York NY 10027 USA
| | - Huiyi Liang
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
| | - Yuyan Li
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
| | - Cong Dong
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
| | - Jun Shen
- Department of RadiologySun Yat-sen Memorial HospitalSun Yat-sen University Guangzhou 510080 China
| | - Hai‐Quan Mao
- Department of Materials Science and EngineeringJohns Hopkins University Baltimore MD 21205 USA
| | - Kam W. Leong
- Department of Biomedical EngineeringColumbia University New York NY 10027 USA
| | - Yongming Chen
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
| | - Lixin Liu
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
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12
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Peng B, Liang H, Li Y, Dong C, Shen J, Mao H, Leong KW, Chen Y, Liu L. Tuned Cationic Dendronized Polymer: Molecular Scavenger for Rheumatoid Arthritis Treatment. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Bo Peng
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
- Department of Biomedical EngineeringColumbia University New York NY 10027 USA
| | - Huiyi Liang
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
| | - Yuyan Li
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
| | - Cong Dong
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
| | - Jun Shen
- Department of RadiologySun Yat-sen Memorial HospitalSun Yat-sen University Guangzhou 510080 China
| | - Hai‐Quan Mao
- Department of Materials Science and EngineeringJohns Hopkins University Baltimore MD 21205 USA
| | - Kam W. Leong
- Department of Biomedical EngineeringColumbia University New York NY 10027 USA
| | - Yongming Chen
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
| | - Lixin Liu
- School of Materials Science and Engineering, and Center of Functional Biomaterials, Key Laboratory of Polymeric Composite Materials and Functional Materials of Ministry of EducationGD Research Center for Functional Biomaterials Engineering and TechnologySun Yat-sen University Guangzhou 510275 China
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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: 148] [Impact Index Per Article: 29.6] [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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Yu D, Tong Y, Guo X, Feng L, Jiang Z, Ying S, Jia J, Fang Y, Yu M, Xia H, Shi L, Lou J. Diagnostic Value of Concentration of Circulating Cell-Free DNA in Breast Cancer: A Meta-Analysis. Front Oncol 2019; 9:95. [PMID: 30881916 PMCID: PMC6405437 DOI: 10.3389/fonc.2019.00095] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/01/2019] [Indexed: 12/30/2022] Open
Abstract
The diagnostic value of the concentration of circulating cell-free DNA (cfDNA) for breast cancer has generated inconsistent results. The aim of this study was to evaluate the first diagnostic value of the concentration of cfDNA for breast cancer by meta-analysis. Studies were retrieved by searching PubMed, Cochrane Library, and Web of Science before June 2018. Sensitivity, specificity, diagnostic odds ratio (DOR), the summary receiver operating characteristic (SROC) curve, and the area under curve (AUC) were used to summarize overall diagnostic performance. The random-effects model was used to calculate the pooled statistics. Subgroup analysis and meta-regression analysis were carried out to detect the source of heterogeneity. A total of 13 studies were identified with 1,087 breast cancer patients and 720 healthy controls. Overall, the pooled sensitivity and specificity of concentration of cfDNA for breast cancer were 87% (95% CI, 73–94%) and 87% (95% CI, 79–93%), respectively. The pooled DOR was 32.93 (95% CI, 13.52–80.19) and the SROC curve revealed an AUC of 0.93 (95% CI, 0.91–0.95). Meta-regression analysis showed that no covariate had a significant correlation with relative DOR (RDOR). Publication bias was not detected in this meta-analysis. This meta-analysis indicates that the concentration of cfDNA has potential first diagnostic value for breast cancer and plasma may be a better source of cfDNA for detection of breast cancer.
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Affiliation(s)
- Dandan Yu
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Yan Tong
- Department of Outpatient Office, Affiliated Hangzhou First People's Hospiital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinnian Guo
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Lingfang Feng
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Zhaoqiang Jiang
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Shibo Ying
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Junlin Jia
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Yuan Fang
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Min Yu
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Hailing Xia
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Li Shi
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Jianlin Lou
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
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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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16
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Spengler J, Lugonja B, Ytterberg AJ, Zubarev RA, Creese AJ, Pearson MJ, Grant MM, Milward M, Lundberg K, Buckley CD, Filer A, Raza K, Cooper PR, Chapple IL, Scheel-Toellner D. Release of Active Peptidyl Arginine Deiminases by Neutrophils Can Explain Production of Extracellular Citrullinated Autoantigens in Rheumatoid Arthritis Synovial Fluid. Arthritis Rheumatol 2016; 67:3135-45. [PMID: 26245941 PMCID: PMC4832324 DOI: 10.1002/art.39313] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 07/30/2015] [Indexed: 01/08/2023]
Abstract
Objective In the majority of patients with rheumatoid arthritis (RA), antibodies specifically recognize citrullinated autoantigens that are generated by peptidylarginine deiminases (PADs). Neutrophils express high levels of PAD and accumulate in the synovial fluid (SF) of RA patients during disease flares. This study was undertaken to test the hypothesis that neutrophil cell death, induced by either NETosis (extrusion of genomic DNA–protein complexes known as neutrophil extracellular traps [NETs]) or necrosis, can contribute to production of autoantigens in the inflamed joint. Methods Extracellular DNA was quantified in the SF of patients with RA, patients with osteoarthritis (OA), and patients with psoriatic arthritis (PsA). Release of PAD from neutrophils was investigated by Western blotting, mass spectrometry, immunofluorescence staining, and PAD activity assays. PAD2 and PAD4 protein expression, as well as PAD enzymatic activity, were assessed in the SF of patients with RA and those with OA. Results Extracellular DNA was detected at significantly higher levels in RA SF than in OA SF (P < 0.001) or PsA SF (P < 0.05), and its expression levels correlated with neutrophil concentrations and PAD activity in RA SF. Necrotic neutrophils released less soluble extracellular DNA compared to NETotic cells in vitro (P < 0.05). Higher PAD activity was detected in RA SF than in OA SF (P < 0.05). The citrullinated proteins PAD2 and PAD4 were found attached to NETs and also freely diffused in the supernatant. PAD enzymatic activity was detected in supernatants of neutrophils undergoing either NETosis or necrosis. Conclusion Release of active PAD isoforms into the SF by neutrophil cell death is a plausible explanation for the generation of extracellular autoantigens in RA.
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Affiliation(s)
- Julia Spengler
- Arthritis Research UK Centre of Excellence for Rheumatoid Arthritis Pathogenesis and University of Birmingham, Birmingham, UK
| | - Božo Lugonja
- Arthritis Research UK Centre of Excellence for Rheumatoid Arthritis Pathogenesis and University of Birmingham, Birmingham, UK
| | - A Jimmy Ytterberg
- Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | | | | | - Mark J Pearson
- Arthritis Research UK Centre of Excellence for Rheumatoid Arthritis Pathogenesis and University of Birmingham, Birmingham, UK
| | | | | | - Karin Lundberg
- Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Christopher D Buckley
- Arthritis Research UK Centre of Excellence for Rheumatoid Arthritis Pathogenesis, University of Birmingham, and Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, UK
| | - Andrew Filer
- Arthritis Research UK Centre of Excellence for Rheumatoid Arthritis Pathogenesis, University of Birmingham, and University Hospitals NHS Foundation Trust, Birmingham, UK
| | - Karim Raza
- Arthritis Research UK Centre of Excellence for Rheumatoid Arthritis Pathogenesis, University of Birmingham, and Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, UK
| | | | | | - Dagmar Scheel-Toellner
- Arthritis Research UK Centre of Excellence for Rheumatoid Arthritis Pathogenesis and University of Birmingham, Birmingham, UK
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17
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Weerakoon KG, McManus DP. Cell-Free DNA as a Diagnostic Tool for Human Parasitic Infections. Trends Parasitol 2016; 32:378-391. [PMID: 26847654 DOI: 10.1016/j.pt.2016.01.006] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/28/2015] [Accepted: 01/11/2016] [Indexed: 12/18/2022]
Abstract
Parasites often cause devastating diseases and represent a significant public health and economic burden. More accurate and convenient diagnostic tools are needed in support of parasite control programmes in endemic regions, and for rapid point-of-care diagnosis in nonendemic areas. The detection of cell-free DNA (cfDNA) is a relatively new concept that is being applied in the current armamentarium of diagnostics. Here, we review the application of cfDNA detection with nucleic acid amplification tests for the diagnosis and evaluation of different human parasitic infections and highlight the significant benefits of the approach using non-invasive clinical samples.
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Affiliation(s)
- Kosala G Weerakoon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; School of Public Health, University of Queensland, Brisbane, QLD, Australia; Department of Parasitology, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka.
| | - Donald P McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
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Ravelli A, Reuben JM, Lanza F, Anfossi S, Cappelletti MR, Zanotti L, Gobbi A, Senti C, Brambilla P, Milani M, Spada D, Pedrazzoli P, Martino M, Bottini A, Generali D. Breast cancer circulating biomarkers: advantages, drawbacks, and new insights. Tumour Biol 2015; 36:6653-65. [PMID: 26307395 DOI: 10.1007/s13277-015-3944-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/17/2015] [Indexed: 12/17/2022] Open
Abstract
As of today, the level of individualization of cancer therapies has reached a level that 20 years ago would be considered visionary. However, most of the diagnostic, prognostic, and therapy-predictive procedures which aim to improve the overall level of personalization are based on the evaluation of tumor tissue samples, therefore requiring surgical operations with consequent low compliance for patients and high costs for the hospital. Hence, the research of a panel of circulating indicators which may serve as source of information about tumor characteristics and which may be obtainable by a simple withdrawal of peripheral blood today represents a growing field of interest. This review aims to objectively summarize the characteristics of the currently available breast cancer circulating biomarkers, also providing an overview about the multitude of novel potential soluble predictors which are still under evaluation. Specifically, the usefulness of a so-called "liquid biopsy" will be discussed in terms of improvements of diagnosis, prognosis, and therapy-prediction, but an overview will be given also on the potentiality of the molecular characterization arising from the isolation of circulating biomarkers and cells. Although this review will focus on the specific case of the breast, in the future liquid biopsies will hopefully be available for virtually any type of neoplasms.
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Affiliation(s)
- Andrea Ravelli
- U.O. Ematologia e CTMO, AZ. Istituti Ospitalieri di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - James M Reuben
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francesco Lanza
- U.O. Ematologia e CTMO, AZ. Istituti Ospitalieri di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Simone Anfossi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Rosa Cappelletti
- U.O. Multidisciplinare di Patologia Mammaria, U.S. Terapia Molecolare e Farmacogenomica, AZ. Istituti Ospitalieri di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Laura Zanotti
- U.O. Multidisciplinare di Patologia Mammaria, U.S. Terapia Molecolare e Farmacogenomica, AZ. Istituti Ospitalieri di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Angela Gobbi
- U.O. Multidisciplinare di Patologia Mammaria, U.S. Terapia Molecolare e Farmacogenomica, AZ. Istituti Ospitalieri di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Chiara Senti
- U.O. Multidisciplinare di Patologia Mammaria, U.S. Terapia Molecolare e Farmacogenomica, AZ. Istituti Ospitalieri di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Paola Brambilla
- U.O. Ematologia e CTMO, AZ. Istituti Ospitalieri di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Manuela Milani
- U.O. Multidisciplinare di Patologia Mammaria, U.S. Terapia Molecolare e Farmacogenomica, AZ. Istituti Ospitalieri di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Daniele Spada
- U.O. Multidisciplinare di Patologia Mammaria, U.S. Terapia Molecolare e Farmacogenomica, AZ. Istituti Ospitalieri di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Paolo Pedrazzoli
- S.C Oncologia, Dipartimento di Onco-Ematologia, Policlinico IRCCS San Matteo, Pavia, Italy
| | - Massimo Martino
- U.O. Ematologia con Trapianto di Midollo Osseo e Terapia Intensiva, Dipartimento di Oncologia, AZ. Ospedaliera Bianchi-Melacrino-Morelli, 89100, Reggio Calabria, Italy
| | - Alberto Bottini
- U.O. Multidisciplinare di Patologia Mammaria, U.S. Terapia Molecolare e Farmacogenomica, AZ. Istituti Ospitalieri di Cremona, Viale Concordia 1, 26100, Cremona, Italy
| | - Daniele Generali
- U.O. Multidisciplinare di Patologia Mammaria, U.S. Terapia Molecolare e Farmacogenomica, AZ. Istituti Ospitalieri di Cremona, Viale Concordia 1, 26100, Cremona, Italy.
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Chandrananda D, Thorne NP, Bahlo M. High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA. BMC Med Genomics 2015; 8:29. [PMID: 26081108 PMCID: PMC4469119 DOI: 10.1186/s12920-015-0107-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/04/2015] [Indexed: 12/13/2022] Open
Abstract
Background High-throughput sequencing of cell-free DNA fragments found in human plasma has been used to non-invasively detect fetal aneuploidy, monitor organ transplants and investigate tumor DNA. However, many biological properties of this extracellular genetic material remain unknown. Research that further characterizes circulating DNA could substantially increase its diagnostic value by allowing the application of more sophisticated bioinformatics tools that lead to an improved signal to noise ratio in the sequencing data. Methods In this study, we investigate various features of cell-free DNA in plasma using deep-sequencing data from two pregnant women (>70X, >50X) and compare them with matched cellular DNA. We utilize a descriptive approach to examine how the biological cleavage of cell-free DNA affects different sequence signatures such as fragment lengths, sequence motifs at fragment ends and the distribution of cleavage sites along the genome. Results We show that the size distributions of these cell-free DNA molecules are dependent on their autosomal and mitochondrial origin as well as the genomic location within chromosomes. DNA mapping to particular microsatellites and alpha repeat elements display unique size signatures. We show how cell-free fragments occur in clusters along the genome, localizing to nucleosomal arrays and are preferentially cleaved at linker regions by correlating the mapping locations of these fragments with ENCODE annotation of chromatin organization. Our work further demonstrates that cell-free autosomal DNA cleavage is sequence dependent. The region spanning up to 10 positions on either side of the DNA cleavage site show a consistent pattern of preference for specific nucleotides. This sequence motif is present in cleavage sites localized to nucleosomal cores and linker regions but is absent in nucleosome-free mitochondrial DNA. Conclusions These background signals in cell-free DNA sequencing data stem from the non-random biological cleavage of these fragments. This sequence structure can be harnessed to improve bioinformatics algorithms, in particular for CNV and structural variant detection. Descriptive measures for cell-free DNA features developed here could also be used in biomarker analysis to monitor the changes that occur during different pathological conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0107-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dineika Chandrananda
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Natalie P Thorne
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Melanie Bahlo
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3010, Australia.
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20
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Abstract
The existence of cell free DNA in the human circulatory system has been known since the 1950s, however, intensive research in this area has been conducted for the last ten years. This review paper brings a short overview of the existing literature concerning the cell free DNA research in various clinical fields and pathological states and considers the application possibilities of this new analyte in clinical laboratory diagnostics. At the moment, cell free DNA is most widely used for the purpose of non-invasive prenatal diagnosis of fetal sex or fetal RhD status. The recent discovery of epigenetic changes in placental/fetal DNA and the detection of fetal/placental-specific RNAs have made it possible to use this technology in all pregnancies irrespective of the gender of the fetus. With the application of new techniques such as next generation sequencing, digital PCR and mass spectrometry, it is now possible to detect very small amounts of specific DNA in the presence of excess of other nonspecific nucleic acids. Second most probable application is in oncology, where detection and monitoring of tumors is now possible by the detection of tumor-derived nucleic acids. Third promising field for near future implementation of this analyte is transplantation medicine, where free DNA level could serve as a marker of transplant rejection. Before any further utilization of this new biomarker, pre-analytical and analytical aspects of free DNA analysis remain to be standardized. In the field of noninvasive prenatal diagnosis, important ethical, legal and social questions remain to be discussed.
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Affiliation(s)
- Jasenka Wagner
- Cytogenetics laboratory, Department of Medical Biology, Faculty of Medicine, University J. J. Strossmayer, Osijek, Croatia.
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21
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Page K, Hava N, Ward B, Brown J, Guttery DS, Ruangpratheep C, Blighe K, Sharma A, Walker RA, Coombes RC, Shaw JA. Detection of HER2 amplification in circulating free DNA in patients with breast cancer. Br J Cancer 2011; 104:1342-8. [PMID: 21427727 PMCID: PMC3078598 DOI: 10.1038/bjc.2011.89] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Human epidermal growth factor receptor 2 (HER2) is amplified and overexpressed in 20-25% of breast cancers. This study investigated circulating free DNA (cfDNA) for detection of HER2 gene amplification in patients with breast cancer. METHODS Circulating free DNA was extracted from plasma of unselected patients with primary breast cancer (22 before surgery and 68 following treatment), 30 metastatic patients and 98 female controls using the QIAamp Blood DNA Mini Kit (Qiagen). The ratio of HER2 to an unamplified reference gene (contactin-associated protein 1 (CNTNAP1)) was measured in cfDNA samples by quantitative PCR (qPCR) using SK-BR-3 cell line DNA as a positive control. RESULTS We validated the qPCR assay with DNA extracted from 23 HER2 3+ and 40 HER2-negative tumour tissue samples; the results agreed for 60 of 63 (95.2%) tumours. Amplification was detected in cfDNA for 8 of 68 patients following primary breast cancer treatment and 5 of 30 metastatic patients, but was undetected in 22 patients with primary breast cancer and 98 healthy female controls. Of the patients with amplification in cfDNA, 10 had HER2 3+ tumour status by immunohistochemistry. CONCLUSIONS The results demonstrate for the first time the existence of amplified HER2 in cfDNA in the follow-up of breast cancer patients who are otherwise disease free. This approach could potentially provide a marker in patients with HER2-positive breast cancer.
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Affiliation(s)
- K Page
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Robert Kilpatrick Building, PO Box 65, Leicester Royal Infirmary, Leicester LE2 7LX, UK
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Casciano I, Vinci AD, Banelli B, Brigati C, Forlani A, Allemanni G, Romani M. Circulating Tumor Nucleic Acids: Perspective in Breast Cancer. Breast Care (Basel) 2010; 5:75-80. [PMID: 20847818 PMCID: PMC2931039 DOI: 10.1159/000310113] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In 1940, it was demonstrated that free DNA could be identified in the bloodstream. It was later shown that circulating nucleic acids (CNA), both DNA and RNA, are present in several neoplastic and non-neoplastic diseases, and that in cancer they originate mostly from the tumor. In this review, we discuss the potential application of CNA as a breast cancer biomarker for early diagnosis and patient evaluation. Most of the initial studies on CNA compared the levels of CNA in cancer patients and healthy individuals. To increase sensitivity and specificity, cancer-specific molecular alterations were then utilized. In this respect, epigenetic alterations and microRNA offer considerable advantages over mutations because of their easiness of detection. Epigenetic signatures, being early events of carcinogenesis, may also be valuable markers for screening purposes. Monitoring the follow-up of the patients is one of the most interesting applications of CNA-based assays, and it is reasonable to hypothesize that CNA may become a surrogate marker for circulating cancer cells in the prediction of patient outcome. Transferring these findings to the clinical practice is the next effort, and this will be possible when a 'common language' is defined to allow proper validation of these new markers.
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Affiliation(s)
| | | | | | | | | | | | - Massimo Romani
- Laboratory of Tumor Genetics, Istituto Nazionale per la Ricerca sul Cancro – IST Genova, Italy
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García JM, García V, Peña C, Domínguez G, Silva J, Diaz R, Espinosa P, Citores MJ, Collado M, Bonilla F. Extracellular plasma RNA from colon cancer patients is confined in a vesicle-like structure and is mRNA-enriched. RNA 2008; 14:1424-32. [PMID: 18456845 PMCID: PMC2441977 DOI: 10.1261/rna.755908] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Little is yet known about the origin and protective mechanism of free nucleic acids in plasma. We investigated the possibility of these free nucleic acids being particle associated. Plasma samples from colon cancer patients and cell culture media were subjected to various antibody incubations, ultracentrifugation, and RNA extraction protocols for total RNA, epithelial RNA, and mRNA. Flow cytometry using a Ber-EP4 antibody and confocal laser microscopy after staining with propidium iodide were also performed. mRNA levels of the LISCH7 and SDHA genes were determined in cells and in culture media. Ber-EP4 antibody and polystyrene beads coated with oligo dT sequences were employed. We observed that, after incubation, total RNA and mRNA were always detected after membrane digestion, and that epithelial RNA was detected before this procedure. In ultracentrifugation, mRNA was caught in the supernatant only if a former lysis mediated or in the pellet if there was no previous digestion. Flow cytometry determinations showed that antibody-coated microbeads keep acellular structures bearing epithelial antigens apart. Confocal laser microscopy made 1- to 2-microm-diameter particles perceptible in the vicinity of magnetic polystyrene beads. Relevant differences were observed between mRNA of cells and culture media, as there was a considerable difference in LISCH7 mRNA levels between HT29 and IMR90 cell co-cultures and their culture media. Our results support the view that extracellular RNA found in plasma from cancer patients circulates in association with or is protected in a multiparticle complex, and that an active release mechanism by tumor cells may be a possible origin.
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Affiliation(s)
- José Miguel García
- Department of Medical Oncology, Hospital Universitario Puerta de Hierro, E-28035 Madrid, Spain
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Board RE, Knight L, Greystoke A, Blackhall FH, Hughes A, Dive C, Ranson M. DNA Methylation in Circulating Tumour DNA as a Biomarker for Cancer. Biomark Insights 2008. [DOI: 10.1177/117727190700200003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Free circulating DNA, which is thought to be derived from the primary tumour, can be detected in the blood of patients with cancer. Detection of genetic and epigenetic alteration in this tumour DNA offers a potential source of development of prognostic and predictive biomarkers for cancer. One such change is DNA methylation of the promotor region of tumour suppressor genes. This causes down regulation of tumour suppressor gene expression, a frequent event in carcinogenesis. Hypermethylation of the promotor region of a number of genes has been detected in many tumour types and more recently these changes have been detected in circulating tumour DNA. This review will summarise the literature detailing DNA methylation in circulating tumour DNA and discuss some of the current controversies and technical challenges facing its use as a potential biomarker for cancer.
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Affiliation(s)
- Ruth E Board
- Clinical and Experimental Pharmacology, Paterson Institute of Cancer Research, Wilmslow Road, Manchester M20 4BX
| | - Lucy Knight
- Discovery Medicine, AstraZeneca Pharmaceuticals, Alderley Park, Macclesfield, Cheshire. SK10 4TG
| | - Alastair Greystoke
- Clinical and Experimental Pharmacology, Paterson Institute of Cancer Research, Wilmslow Road, Manchester M20 4BX
| | - Fiona H Blackhall
- CRUK Department of Medical Oncology, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX
| | - Andrew Hughes
- Discovery Medicine, AstraZeneca Pharmaceuticals, Alderley Park, Macclesfield, Cheshire. SK10 4TG
| | - Caroline Dive
- Clinical and Experimental Pharmacology, Paterson Institute of Cancer Research, Wilmslow Road, Manchester M20 4BX
| | - Malcolm Ranson
- CRUK Department of Medical Oncology, Christie Hospital NHS Trust, Wilmslow Road, Manchester M20 4BX
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25
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Abstract
Previous studies showed that patients with neoplasms of various types and origins have abnormally high concentration of DNA in their serum. The current work compares circulating DNA levels in patients with benign or malignant disease of the gastrointestinal tract and determines the diagnostic value of such measurements. DNA was quantitated by radioimmunoassay capable of detecting 25 ng/ml, and as a simple and noninvasive test, it could be a useful addition to other diagnostic procedures. The GI tract was chosen because it affords a comparison of benign, precancerous, and malignant lesions of the same organ. Of the 386 patients studied prospectively, 48% had benign disease and mean DNA levels (+/- SE) of 118 +/- 14 ng/ml, whereas 52% had malignant disease and 412 +/- 63 ng DNA/ml. The difference was statistically significant (P less than 0.001). The DNA assay showed the highest sensitivity for pancreas carcinoma: 90% of the patients had DNA levels above 100 ng/ml, chosen as the upper normal limit. Simultaneous measurements of both DNA and carcinoembryonic antigen (CEA) resulted in increased sensitivity and specificity, even when either marker alone had low sensitivity (gastric carcinoma). The results indicate that serum DNA concentration is markedly elevated in malignancy, and moderately elevated in benign disease, as compared with normal controls. These findings may have diagnostic and prognostic value.
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26
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Shapiro B, Chakrabarty M, Cohn EM, Leon SA. Determination of circulating DNA levels in patients with benign or malignant gastrointestinal disease. Cancer 1983; 51:2116-20. [PMID: 6188527 DOI: 10.1002/1097-0142(19830601)51:11<2116::aid-cncr2820511127>3.0.co;2-s] [Citation(s) in RCA: 263] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Previous studies showed that patients with neoplasms of various types and origins have abnormally high concentration of DNA in their serum. The current work compares circulating DNA levels in patients with benign or malignant disease of the gastrointestinal tract and determines the diagnostic value of such measurements. DNA was quantitated by radioimmunoassay capable of detecting 25 ng/ml, and as a simple and noninvasive test, it could be a useful addition to other diagnostic procedures. The GI tract was chosen because it affords a comparison of benign, precancerous, and malignant lesions of the same organ. Of the 386 patients studied prospectively, 48% had benign disease and mean DNA levels (+/- SE) of 118 +/- 14 ng/ml, whereas 52% had malignant disease and 412 +/- 63 ng DNA/ml. The difference was statistically significant (P less than 0.001). The DNA assay showed the highest sensitivity for pancreas carcinoma: 90% of the patients had DNA levels above 100 ng/ml, chosen as the upper normal limit. Simultaneous measurements of both DNA and carcinoembryonic antigen (CEA) resulted in increased sensitivity and specificity, even when either marker alone had low sensitivity (gastric carcinoma). The results indicate that serum DNA concentration is markedly elevated in malignancy, and moderately elevated in benign disease, as compared with normal controls. These findings may have diagnostic and prognostic value.
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27
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Dorsch CA, Killmayer J. The effect of native and single stranded DNA on the platelet release reaction. Enhancement of aggregated IgG-induced serotonin release. ARTHRITIS AND RHEUMATISM 1983; 26:179-85. [PMID: 6824515 DOI: 10.1002/art.1780260209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Native (n) but not single stranded (ss) DNA was found to induce release of 3H-serotonin (5-HT) from platelets of the majority of normal individuals. However, ssDNA markedly enhanced 5-HT release induced by heat-aggregated IgG (aggIgG), while less enhancement was seen using nDNA. Similar enhancement was produced by polyinosinic acid but not by polyinosinic:polycytidylic acid. The ability of ssDNA to potentiate aggIgG-induced 5-HT release seemed specific for aggIgG, since no effect on ADP or epinephrine-induced release was observed and thrombin-induced release was inhibited. In contrast, nDNA in high concentrations (100 micrograms/ml) potentiated ADP, epinephrine, and thrombin-induced 5-HT release. These results suggest that ss-and nDNA may interact with platelets by different mechanisms and provide a means by which DNA, released at sites of tissue injury, could modulate the role of platelets in the inflammatory response. The ability of DNA to enhance the aggIgG-induced platelet release reaction may be important in immune complex diseases such as systemic lupus erythematosus.
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