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Driussi A, Lamaze FC, Kordahi M, Armero VS, Gaudreault N, Orain M, Enlow W, Abbosh C, Hodgson D, Dasgupta A, Gagné A, Bossé Y, Joubert P. Clinicopathological Predictors of the Presence of Blood Circulating Tumor DNA in Early-Stage Non-Small Cell Lung Cancers. Mod Pathol 2025; 38:100744. [PMID: 40020968 DOI: 10.1016/j.modpat.2025.100744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 02/12/2025] [Accepted: 02/12/2025] [Indexed: 03/03/2025]
Abstract
The implementation of lung cancer screening programs across the world has drawn considerable attention to improving early-stage lung cancer detection and prognostication. Several blood-based assays detecting circulating tumor DNA (ctDNA) recently emerged as noninvasive methods to detect malignancies. However, their limited sensitivity and predictive value remain a hurdle to their clinical use. We aimed to evaluate the association between clinicopathological parameters and presurgical ctDNA detection in clinical stage I non-small cell lung cancer patients to further understand ctDNA shedding biology. The cohort included 180 adenocarcinomas (LUAD) and 80 squamous cell carcinomas (LUSC) stage I patients who underwent lung cancer resection. Patients' clinical and pathological features were collected. A multicancer early-detection test (GRAIL LLC) was used to detect ctDNA using targeted methylation patterns. The association between the cell-free DNA tumor methylated fraction (TMeF) and the clinicopathological predictors was evaluated using univariate and multivariate modeling. LUSC was associated with a higher TMeF than LUAD. Pathological stage, tumor grade, and tumor volume were key determinants of ctDNA detection in both LUSC and LUAD. In LUAD, ctDNA detection also correlated with histologic pattern composition, necrosis, acute inflammation, and, to a lesser degree, spread through alveolar spaces and lymphovascular invasion. Based on our results, we propose classification methods for both LUAD (using histologic pattern composition) and LUSC (using tumor grade and pathological stage) to identify patients likely to have high ctDNA levels. These results confirm previous findings and suggest that previously unidentified factors, including histologic pattern composition and acute inflammation, influence ctDNA levels. These results will help in understanding the ctDNA shedding process and may allow identification of patients eligible for ctDNA detection-based follow-up.
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Affiliation(s)
- Arnaud Driussi
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Fabien C Lamaze
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Manal Kordahi
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Victoria Saavedra Armero
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Nathalie Gaudreault
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Michèle Orain
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - William Enlow
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Chris Abbosh
- Translational Medicine Early Oncology, AstraZeneca, Cambridge, United Kingdom
| | - Darren Hodgson
- Translational Medicine Early Oncology, AstraZeneca, Cambridge, United Kingdom
| | - Abhijit Dasgupta
- Oncology Data Science, Oncology R&D, AstraZeneca, Gaithersburg, Maryland
| | - Andréanne Gagné
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada; Department of Molecular Medicine, Université Laval, Quebec City, Canada
| | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Quebec City, Canada; Department of Molecular Biology, Pathology and Medical Biochemistry, Université Laval, Quebec City, Canada.
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Saikia J, Malik PS, Kumar S, Jain D, Madan K, Bharati SJ, Deo S, Kumar S. Can cell-free DNA (cfDNA) in pleural lavage serve as a predictive and prognostic biomarker among surgically treated Stage I-III a nonsmall cell lung cancer (NSCLC)? A pilot study. J Surg Oncol 2024; 129:1224-1234. [PMID: 38436618 DOI: 10.1002/jso.27610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/16/2024] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND AND OBJECTIVES The role of cell-free DNA (cfDNA) in operable nonsmall cell lung cancer (NSCLC) is unclear. This study was aimed to evaluate the feasibility for identification of cfDNA in pleural lavage fluid and its correlation with plasma in resectable NSCLCs. METHODS Consecutively resected NSCLCs were evaluated for cfDNA levels in preoperative plasma (PLS1), intraoperative pleural-lavage (PLV) and postoperative (at 1 month) plasma sample (PLS2). CfDNA was isolated and measured quantitatively by qPCR in a TaqMan probe-detection approach using the human β-actin gene as the amplifying target. RESULTS All (n = 34) except one were negative for malignant cells in PLV cytology. CfDNA could be isolated from all the three samples (PLS1, PLV, and PLS2) successfully in each patient. The median cfDNA levels in PLS1, PLV and PLS2 were 118 ng/mL (IQR 61-158), 167 ng/mL (IQR 59.9-179.9) and 103 ng/mL (IQR 66.5-125.4) respectively. The median follow-up was 34.1 months (IQR 25.2-41.6). A significant overall-survival (OS) and disease-free survival (DFS) were recorded for patients with cfDNA level cut-offs at 125, 170, and 100 ng/mL, respectively for PLS1, PLV, and PLS2. Patients with raised cfDNA in PLS1 (>125 ng/mL) and PLV (>170 ng/mL) had significantly poorer 2-year OS, p = 0.005 and p = 0.012, respectively. The hazards (OS) were also higher for those with raised cfDNA in PLV (HR = 5.779, 95% CI = 1.162-28.745, p = 0.032). PLV (>170 ng/mL) had increased pleural recurrences (p = 0.021) and correlated significantly with poorer DFS at 2-years (p = 0.001) with increased hazards (HR = 9.767, 95% CI = 2.098-45.451, p = 0.004). Multivariable analysis suggested higher cfDNA in PLV as a poor prognostic factor for both OS and DFS. CONCLUSIONS Among patients with operable NSCLC, it is feasible to identify cfDNA in pleural lavage and correlate PLV cfDNA with pleural recurrences and outcomes.
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Affiliation(s)
- Jyoutishman Saikia
- Department of Surgical Oncology, DR.BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Prabhat S Malik
- Department of Medical Oncology, DR.BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Sachin Kumar
- Department of Medical Oncology, DR.BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Karan Madan
- Department of Pulmonary Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sachidanand Jee Bharati
- Department of Oncoanaesthesia, DR.BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Suryanarayana Deo
- Department of Surgical Oncology, DR.BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Sunil Kumar
- Department of Surgical Oncology, DR.BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
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Li J, Su X, Xu X, Zhao C, Liu A, Yang L, Song B, Song H, Li Z, Hao X. Preoperative prediction and risk assessment of microvascular invasion in hepatocellular carcinoma. Crit Rev Oncol Hematol 2023; 190:104107. [PMID: 37633349 DOI: 10.1016/j.critrevonc.2023.104107] [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: 05/24/2023] [Accepted: 08/22/2023] [Indexed: 08/28/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common and highly lethal tumors worldwide. Microvascular invasion (MVI) is a significant risk factor for recurrence and poor prognosis after surgical resection for HCC patients. Accurately predicting the status of MVI preoperatively is critical for clinicians to select treatment modalities and improve overall survival. However, MVI can only be diagnosed by pathological analysis of postoperative specimens. Currently, numerous indicators in serology (including liquid biopsies) and imaging have been identified to effective in predicting the occurrence of MVI, and the multi-indicator model based on deep learning greatly improves accuracy of prediction. Moreover, several genes and proteins have been identified as risk factors that are strictly associated with the occurrence of MVI. Therefore, this review evaluates various predictors and risk factors, and provides guidance for subsequent efforts to explore more accurate predictive methods and to facilitate the conversion of risk factors into reliable predictors.
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Affiliation(s)
- Jian Li
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China; Department of General Surgery, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Xin Su
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China; Department of General Surgery, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Xiao Xu
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China; Department of General Surgery, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Changchun Zhao
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China; Department of General Surgery, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Ang Liu
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China; Department of General Surgery, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Liwen Yang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China
| | - Baoling Song
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China
| | - Hao Song
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China
| | - Zihan Li
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou 730000, China
| | - Xiangyong Hao
- Department of General Surgery, Gansu Provincial Hospital, Lanzhou 730000, China.
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Wu G, Song M, Wang K, Cui T, Jiao Z, Ji L, Gao X, Wang J, Liu T, Xia X, Fang H, Guan Y, Yi X. DELFMUT: duplex sequencing-oriented depth estimation model for stable detection of low-frequency mutations. Brief Bioinform 2023; 24:bbad277. [PMID: 37539831 DOI: 10.1093/bib/bbad277] [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: 03/12/2023] [Revised: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 08/05/2023] Open
Abstract
Duplex sequencing technology has been widely used in the detection of low-frequency mutations in circulating tumor deoxyribonucleic acid (DNA), but how to determine the sequencing depth and other experimental parameters to ensure the stable detection of low-frequency mutations is still an urgent problem to be solved. The mutation detection rules of duplex sequencing constrain not only the number of mutated templates but also the number of mutation-supportive reads corresponding to each forward and reverse strand of the mutated templates. To tackle this problem, we proposed a Depth Estimation model for stable detection of Low-Frequency MUTations in duplex sequencing (DELFMUT), which models the identity correspondence and quantitative relationships between templates and reads using the zero-truncated negative binomial distribution without considering the sequences composed of bases. The results of DELFMUT were verified by real duplex sequencing data. In the case of known mutation frequency and mutation detection rule, DELFMUT can recommend the combinations of DNA input and sequencing depth to guarantee the stable detection of mutations, and it has a great application value in guiding the experimental parameter setting of duplex sequencing technology.
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Affiliation(s)
- Guiying Wu
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Mengmeng Song
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Ke Wang
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Tianyu Cui
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Zicong Jiao
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Liyan Ji
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Xuan Gao
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Jiayin Wang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Tao Liu
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Huan Fang
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xin Yi
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
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Viglianisi G, Santonocito S, Polizzi A, Troiano G, Amato M, Zhurakivska K, Pesce P, Isola G. Impact of Circulating Cell-Free DNA (cfDNA) as a Biomarker of the Development and Evolution of Periodontitis. Int J Mol Sci 2023; 24:9981. [PMID: 37373135 DOI: 10.3390/ijms24129981] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
In the last few decades, circulating cell-free DNA (cfDNA) has been shown to have an important role in cell apoptosis or necrosis, including in the development and evolution of several tumors and inflammatory diseases in humans. In this regard, periodontitis, a chronic inflammatory disease that can induce the destruction of supporting components of the teeth, could represent a chronic inflammatory stimulus linked to a various range of systemic inflammatory diseases. Recently, a possible correlation between periodontal disease and cfDNA has been shown, representing new important diagnostic-therapeutic perspectives. During the development of periodontitis, cfDNA is released in biological fluids such as blood, saliva, urine and other body fluids and represents an important index of inflammation. Due to the possibility of withdrawing some of these liquids in a non-invasive way, cfDNA could be used as a possible biomarker for periodontal disease. In addition, discovering a proportional relationship between cfDNA levels and the severity of periodontitis, expressed through the disease extent, could open the prospect of using cfDNA as a possible therapeutic target. The aim of this article is to report what researchers have discovered in recent years about circulating cfDNA in the development, evolution and therapy of periodontitis. The analyzed literature review shows that cfDNA has considerable potential as a diagnostic, therapeutic biomarker and therapeutic target in periodontal disease; however, further studies are needed for cfDNA to be used in clinical practice.
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Affiliation(s)
- Gaia Viglianisi
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Simona Santonocito
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Alessandro Polizzi
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Giuseppe Troiano
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Mariacristina Amato
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
| | - Khrystyna Zhurakivska
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Paolo Pesce
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Ospedale S. Martino, 16148 Genoa, Italy
| | - Gaetano Isola
- Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, 95124 Catania, Italy
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Anzinger I, Nagel D, De Toni EN, Ofner A, Philipp AB, Holdt LM, Teupser D, Kolligs FT, Herbst A. Cell-free circulating ALU repeats in serum have a prognostic value for colorectal cancer patients. Cancer Biomark 2023:CBM210536. [PMID: 37302022 DOI: 10.3233/cbm-210536] [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: 06/12/2023]
Abstract
BACKGROUND Carcinoembryonic antigen (CEA) is the only established serum biomarker for colorectal cancer (CRC). To facilitate therapy decisions and improve the overall survival of CRC patients, prognostic biomarkers are required. OBJECTIVE We studied the prognostic value of five different cell free circulating DNA (fcDNA) fragments. The potential markers were ALU115, ALU247, LINE1-79, LINE1-300 and ND1-mt. METHODS The copy numbers of the DNA fragments were measured in the peripheral blood serum of 268 CRC patients using qPCR, the results were compared to common and previously described markers. RESULTS We found that ALU115 and ALU247 fcDNA levels correlate significantly with several clinicopathological parameters. An increased amount of ALU115 and ALU247 fcDNA fragments coincides with methylation of HPP1 (P< 0.001; P< 0.01), which proved to be a prognostic marker itself in former studies and also with increased CEA level (P< 0.001). ALU115 and ALU247 can define patients with poor survival in UICC stage IV (Alu115: HR = 2.9; 95% Cl 1.8-4.8, P< 0.001; Alu247: HR = 2.2; 95% Cl 1.3-3.6; P= 0.001). Combining ALU115 and HPP1, the prognostic value in UICC stage IV is highly significant (P< 0.001). CONCLUSIONS This study shows that an increased level of ALU fcDNA is an independent prognostic biomarker for advanced colorectal cancer disease.
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Affiliation(s)
- Isabel Anzinger
- Department of Urology, St. Elisabeth Hospital, Straubing, Germany
| | - Dorothea Nagel
- Institute of Laboratory Medicine, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | - Enrico N De Toni
- Medical Department 2, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | - Andrea Ofner
- Medical Department 2, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | - Alexander B Philipp
- Medical Department 2, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | - Lesca M Holdt
- Institute of Laboratory Medicine, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
| | | | - Andreas Herbst
- Medical Department 2, Faculty of Medicine, Ludwig Maximilians University, Munich, Germany
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Chen Y, Abbas Z, Hu L, Kang L, Tan X, Xu Q, Wang Y. Extraction and Elevation of Cell-Free DNA under Mastitis and Heat Stress in Dairy Cattle. Animals (Basel) 2023; 13:ani13091487. [PMID: 37174524 PMCID: PMC10177014 DOI: 10.3390/ani13091487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
In this study, four methods (phenol-chloroform protocol, sodium iodide kit, QIAamp DNA Blood Mini Kit, and TIANamp Micro DNA Kit) were used to extract cell-free DNA (cfDNA) from cattle blood, and the yield and purity of cfDNA varied in four different methods from 0.36 to 0.84 ng/mL for yield and 0.67 to 1.80 (A260/A280) for purity. Compared with other methods, the TIANamp Micro DNA kit performed better in both cfDNA amount and purity (p < 0.05); furthermore, blood cfDNA levels were significantly increased in Holstein dairy cows under the influence of heat stress (p < 0.01) and mastitis (p < 0.0001), which showed a potential power to discriminate mastitis (AUC = 0.99, 95% CI = 0.97 to 1.00) or heat stress (AUC = 0.86, 95% CI = 0.73 to 0.98) in cows. In brief, we established a complete experimental system for the extraction of cfDNA from cattle blood based on the high-yielding method of the TIANamp Micro DNA Kit and showed the effect of mastitis and heat stress on cfDNA levels in cattle blood for the first time. Our findings suggested that cfDNA in cattle blood may be a useful marker to measure mastitis and heat stress in dairy cattle.
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Affiliation(s)
- Yumei Chen
- Institute of Life Science and Bioengineering, Beijing Jiaotong University, Haidian, Beijing 100044, China
| | - Zaheer Abbas
- Institute of Life Science and Bioengineering, Beijing Jiaotong University, Haidian, Beijing 100044, China
| | - Lirong Hu
- School of Animal Science and Technology, China Agricultural University, Haidian, Beijing 100193, China
| | - Ling Kang
- Institute of Life Science and Bioengineering, Beijing Jiaotong University, Haidian, Beijing 100044, China
| | - Xiao Tan
- Institute of Life Science and Bioengineering, Beijing Jiaotong University, Haidian, Beijing 100044, China
| | - Qing Xu
- Institute of Life Science and Bioengineering, Beijing Jiaotong University, Haidian, Beijing 100044, China
| | - Yachun Wang
- School of Animal Science and Technology, China Agricultural University, Haidian, Beijing 100193, China
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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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Martínez de Toda I, González-Sánchez M, Díaz-Del Cerro E, Valera G, Carracedo J, Guerra-Pérez N. Sex differences in markers of oxidation and inflammation. Implications for ageing. Mech Ageing Dev 2023; 211:111797. [PMID: 36868323 DOI: 10.1016/j.mad.2023.111797] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023]
Abstract
Sexual dimorphism is a key factor to consider in the ageing process given the impact that it has on life expectancy. The oxidative-inflammatory theory of ageing states that the ageing process is the result of the establishment of oxidative stress which, due to the interplay of the immune system, translates into inflammatory stress, and that both processes are responsible for the damage and loss of function of an organism. We show that there are relevant gender differences in a number of oxidative and inflammatory markers and propose that they may account for the differential lifespan between sexes, given that males display, in general, higher oxidation and basal inflammation. In addition, we explain the significant role of circulating cell-free DNA as a marker of oxidative damage and an inductor of inflammation, connecting both processes and having the potential to become a useful ageing marker. Finally, we discuss how oxidative and inflammatory changes take place differentially with ageing in each sex, which could also have an impact on the sex-differential lifespan. Further research including sex as an essential variable is needed to understand the grounds of sex differences in ageing and to better comprehend ageing itself.
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Affiliation(s)
- Irene Martínez de Toda
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Mónica González-Sánchez
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Estefanía Díaz-Del Cerro
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Gemma Valera
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Julia Carracedo
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Natalia Guerra-Pérez
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
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10
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Hao Y, Yang Q, He Q, Hu H, Weng Z, Su Z, Chen S, Peng S, Kuang M, Chen Z, Xu L. Identification of DNA methylation signatures for hepatocellular carcinoma detection and microvascular invasion prediction. Eur J Med Res 2022; 27:276. [PMID: 36464701 PMCID: PMC9720918 DOI: 10.1186/s40001-022-00910-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/22/2022] [Indexed: 12/07/2022] Open
Abstract
BACKGROUND AND AIM Preoperative evaluation of microvascular invasion (MVI) in patients with hepatocellular carcinoma (HCC) is important for surgical strategy determination. We aimed to develop and establish a preoperative predictive model for MVI status based on DNA methylation markers. METHODS A total of 35 HCC tissues and the matched peritumoral normal liver tissues as well as 35 corresponding HCC patients' plasma samples and 24 healthy plasma samples were used for genome-wide methylation sequencing and subsequent methylation haplotype block (MHB) analysis. Predictive models were constructed based on selected MHB markers and 3-cross validation was used. RESULTS We grouped 35 HCC patients into 2 categories, including the MVI- group with 17 tissue and plasma samples, and MVI + group with 18 tissue and plasma samples. We identified a tissue DNA methylation signature with an AUC of 98.0% and a circulating free DNA (cfDNA) methylation signature with an AUC of 96.0% for HCC detection. Furthermore, we established a tissue DNA methylation signature for MVI status prediction, and achieved an AUC of 85.9%. Based on the MVI status predicted by the DNA methylation signature, the recurrence-free survival (RFS) and overall survival (OS) were significantly better in the predicted MVI- group than that in the predicted MVI + group. CONCLUSIONS In this study, we identified a cfDNA methylation signature for HCC detection and a tissue DNA methylation signature for MVI status prediction with high accuracy.
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Affiliation(s)
- Yijie Hao
- grid.412615.50000 0004 1803 6239Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Qingxia Yang
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203 China
| | - Huanjing Hu
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Zongpeng Weng
- grid.12981.330000 0001 2360 039XDepartment of Biology and Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203 China
| | - Shuling Chen
- grid.412615.50000 0004 1803 6239Department of Medical Ultrasonics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Sui Peng
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Clinical Trials Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Ming Kuang
- grid.412615.50000 0004 1803 6239Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Zhihang Chen
- grid.412615.50000 0004 1803 6239Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Lixia Xu
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
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11
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Liu J, Rui K, Peng N, Luo H, Zhu B, Zuo X, Lu L, Chen J, Tian J. The cGAS-STING pathway: Post-translational modifications and functional implications in diseases. Cytokine Growth Factor Rev 2022; 68:69-80. [PMID: 36151014 DOI: 10.1016/j.cytogfr.2022.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 01/30/2023]
Abstract
Recent studies have illustrated the functional significance of DNA recognition in the activation of innate immune responses among a variety of diseases. The cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway has been found to be modulated by post-translational modifications and can regulate the immune response via type I IFNs. Accumulating evidence indicates a pivotal role of cGAS-STING signaling, being protective or pathogenic, in the development of diseases. Thus, a comprehensive understanding of the post-translational modifications of cGAS-STING pathway and their role in disease development will provide insights in predicting individual disease outcomes and developing appropriate therapies. In this review, we will discuss the regulation of the cGAS-STING pathway and its implications in disease pathologies, as well as pharmacologic strategies to target the cGAS-STING pathway for therapeutic intervention.
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Affiliation(s)
- Jun Liu
- Institute of Medical Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Laboratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Ke Rui
- Institute of Medical Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Laboratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China.
| | - Na Peng
- Department of Rheumatology, the Second People's Hospital, China Three Gorges University, Yichang, China
| | - Hui Luo
- Department of Rheumatology and immunology, Xiangya Hospital, Central South University, Changsha, China
| | - Bo Zhu
- Department of Laboratory Medicine, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaoxia Zuo
- Department of Rheumatology and immunology, Xiangya Hospital, Central South University, Changsha, China
| | - Liwei Lu
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hong Kong; Chongqing International Institute for Immunology, China
| | - Jixiang Chen
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, China.
| | - Jie Tian
- Institute of Medical Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China; Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China.
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12
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Ullah H, Arbab S, Li K, Khan MIU, Qadeer A, Muhammad N. Schistosomiasis related circulating cell-free DNA: A useful biomarker in diagnostics. Mol Biochem Parasitol 2022; 251:111495. [PMID: 35835258 DOI: 10.1016/j.molbiopara.2022.111495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 12/26/2022]
Abstract
Schistosoma is a genus of trematodes causing schistosomiasis, a major neglected tropical disease infecting more than 240 million people and with 700 million people at the risk of infection in the tropical and subtropical regions of the world, especially low-income countries. For the elimination of the disease, accurate diagnostic tools are needed. Besides allowing early treatment, early detection prevents environmental contamination and in turn ensures safe water sources in the endemic areas. Cell-free DNA (cfDNA) biomarker detection is a relatively new tool, used for the diagnosis of schistosomiasis in the early stages of infection from non-invasive clinical or experimental samples. cfDNA can be detected in Schistosoma infected host body fluids such as urine, serum, saliva and tissues, mainly in blood offering significant benefits for accurate diagnosis. In the current review, we described different characteristics of cfDNA, evidencing and supporting its potential uses in Schistosoma diagnosis and the improvement of treatment effectiveness.
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Affiliation(s)
- Hanif Ullah
- West China School of Nursing, Sichuan University, Chengdu, China.
| | - Safia Arbab
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, China; Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ka Li
- West China School of Nursing, Sichuan University, Chengdu, China.
| | - Muhammad Inayat Ullah Khan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Abdul Qadeer
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology of Ministry of Agriculture and Rural Affairs, Shanghai 200241, China
| | - Nehaz Muhammad
- Department of Zoology, University of Swabi, Swabi 23561, Khyber Pakhtunkhwa, Pakistan
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13
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Feasibility of Cell-Free DNA Measurement from the Earlobe during Physiological Exercise Testing. Diagnostics (Basel) 2022; 12:diagnostics12061379. [PMID: 35741187 PMCID: PMC9222055 DOI: 10.3390/diagnostics12061379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
Circulating, cell-free DNA (cfDNA) has been discussed as an upcoming blood-based biomarker in exercise physiology, reflecting important aspects of exercise load. cfDNA blood sampling has evolved from elaborate venous to efficient capillary sampling from the fingertips. In this study, we aimed to evaluate the principal feasibility of cfDNA blood sampling from the earlobe. Therefore, we obtained cfDNA concentrations from the fingertips, earlobe, and the antecubital vein during physiological exercise testing. Significantly higher concentrations were obtained from the earlobe compared to fingertip samples. All of the measurement methods showed good to excellent repeatability (ICCs of 0.85 to 0.93). In addition, the control experiments revealed that repeated sampling from the earlobe but not from the fingertips increased cfDNA at rest. In summary, cfDNA sampling is feasible for all sampling sources. However, at rest, cfDNA collected from the earlobe tend to increase over time in the absence of physical load, potentially limiting this sampling method.
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14
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Haselmann V, Hedtke M, Neumaier M. Liquid Profiling for Cancer Patient Stratification in Precision Medicine—Current Status and Challenges for Successful Implementation in Standard Care. Diagnostics (Basel) 2022; 12:diagnostics12030748. [PMID: 35328301 PMCID: PMC8947441 DOI: 10.3390/diagnostics12030748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/13/2022] Open
Abstract
Circulating tumor DNA (ctDNA), accurately described by the term liquid profiling (LP), enables real-time assessment of the tumor mutational profile as a minimally invasive test and has therefore rapidly gained traction, particular for the management of cancer patients. By LP, tumor-specific genetic alterations can be determined as part of companion diagnostics to guide selection of appropriate targeted therapeutics. Because LP facilitates longitudinal monitoring of cancer patients, it can be used to detect acquired resistant mechanisms or as a personalized biomarker for earlier detection of disease recurrence, among other applications. However, LP is not yet integrated into routine care to the extent that might be expected. This is due to the lack of harmonization and standardization of preanalytical and analytical workflows, the lack of proper quality controls, limited evidence of its clinical utility, heterogeneous study results, the uncertainty of clinicians regarding the value and appropriate indications for LP and its interpretation, and finally, the lack of reimbursement for most LP tests. In this review, the value proposition of LP for cancer patient management and treatment optimization, the current status of implementation in standard care, and the main challenges that need to be overcome are discussed in detail.
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15
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Colmenares R, Álvarez N, Barrio S, Martínez-López J, Ayala R. The Minimal Residual Disease Using Liquid Biopsies in Hematological Malignancies. Cancers (Basel) 2022; 14:1310. [PMID: 35267616 PMCID: PMC8909350 DOI: 10.3390/cancers14051310] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 12/02/2022] Open
Abstract
The study of cell-free DNA (cfDNA) and other peripheral blood components (known as "liquid biopsies") is promising, and has been investigated especially in solid tumors. Nevertheless, it is increasingly showing a greater utility in the diagnosis, prognosis, and response to treatment of hematological malignancies; in the future, it could prevent invasive techniques, such as bone marrow (BM) biopsies. Most of the studies about this topic have focused on B-cell lymphoid malignancies; some of them have shown that cfDNA can be used as a novel way for the diagnosis and minimal residual monitoring of B-cell lymphomas, using techniques such as next-generation sequencing (NGS). In myelodysplastic syndromes, multiple myeloma, or chronic lymphocytic leukemia, liquid biopsies may allow for an interesting genomic representation of the tumor clones affecting different lesions (spatial heterogeneity). In acute leukemias, it can be helpful in the monitoring of the early treatment response and the prediction of treatment failure. In chronic lymphocytic leukemia, the evaluation of cfDNA permits the definition of clonal evolution and drug resistance in real time. However, there are limitations, such as the difficulty in obtaining sufficient circulating tumor DNA for achieving a high sensitivity to assess the minimal residual disease, or the lack of standardization of the method, and clinical studies, to confirm its prognostic impact. This review focuses on the clinical applications of cfDNA on the minimal residual disease in hematological malignancies.
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Affiliation(s)
- Rafael Colmenares
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
| | - Noemí Álvarez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - Santiago Barrio
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - Joaquín Martínez-López
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Department of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Department of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain
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16
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Terasawa H, Kinugasa H, Nouso K, Yamamoto S, Hirai M, Tanaka T, Takaki A, Okada H. Circulating tumor DNA dynamics analysis in a xenograft mouse model with esophageal squamous cell carcinoma. World J Gastroenterol 2021; 27:7134-7143. [PMID: 34887633 PMCID: PMC8613646 DOI: 10.3748/wjg.v27.i41.7134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/21/2021] [Accepted: 08/30/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND It remains unclear which factors, such as tumor volume and tumor invasion, influence circulating tumor DNA (ctDNA), and the origin of ctDNA in liquid biopsy is always problematic. To use liquid biopsies clinically, it will be very important to address these questions. AIM To assess the origin of ctDNA, clarify the dynamics of ctDNA levels, assess ctDNA levels by using a xenograft mouse after treatment, and to determine whether tumor volume and invasion are related to ctDNA levels. METHODS Tumor xenotransplants were established by inoculating BALB/c-nu/nu mice with the TE11 cell line. Groups of mice were injected with xenografts at two or four sites and sacrificed at the appropriate time point after xenotransplantation for ctDNA analysis. Analysis of ctDNA was performed by droplet digital PCR, using the human telomerase reverse transcriptase (hTERT) gene. RESULTS Mice given two-site xenografts were sacrificed for ctDNA at week 4 and week 8. No hTERT was detected at week 4, but it was detected at week 8. However, in four-site xenograft mice, hTERT was detected both at week 4 and week 6. These experiments revealed that both tumor invasion and tumor volume were associated with the detection of ctDNA. In resection experiments, hTERT was detected at resection, but had decreased by 6 h, and was no longer detected 1 and 3 d after resection. CONCLUSION We clarified the origin and dynamics of ctDNA, showing that tumor volume is an important factor. We also found that when the tumor was completely resected, ctDNA was absent after one or more days.
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Affiliation(s)
- Hiroyuki Terasawa
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 7008558, Japan
| | - Hideaki Kinugasa
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 7008558, Japan
| | - Kazuhiro Nouso
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 7008558, Japan
| | - Shumpei Yamamoto
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 7008558, Japan
| | - Mami Hirai
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 7008558, Japan
| | - Takehiro Tanaka
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 7008558, Japan
| | - Akinobu Takaki
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 7008558, Japan
| | - Hiroyuki Okada
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 7008558, Japan
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17
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Truszewska A, Wirkowska A, Gala K, Truszewski P, Krzemień-Ojak Ł, Mucha K, Pączek L, Foroncewicz B. EBV load is associated with cfDNA fragmentation and renal damage in SLE patients. Lupus 2021; 30:1214-1225. [PMID: 33866897 DOI: 10.1177/09612033211010339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND For long Epstein-Barr virus (EBV) has been suspected to be involved in the pathogenesis of systemic lupus erythematosus (SLE). The aim of this study was to verify the association between EBV, cell-free DNA (cfDNA) and kidney disease in SLE. METHODS Blood samples were obtained from 43 SLE patients and 50 healthy individuals. EBV load was measured via real-time PCR assay. Sizing and quantification of plasma cfDNA was performed on Bioanalyzer. We proposed that the uniformity of cfDNA fragmentation can be described using cfDNA fragmentation index. RESULTS SLE patients with chronic kidney disease (CKD +) had higher EBV load compared to CKD(-) patients (P = 0.042). Patients with high cfDNA level had higher EBV load (P = 0.041) and higher cfDNA fragmentation index (P < 0.001) compared to patients with low cfDNA level. Among patients with high cfDNA level, EBV load was higher in CKD(+) group compared to CKD(-) group (P = 0.035). EBV load was positively correlated with the fragmentation index in all SLE patients (P = 0.028, R2 = 0.13), and the correlation was even more pronounced in CKD (+) patients (P < 0.001, R2 = 0.20). CONCLUSIONS We showed that EBV load was associated with non-uniform cfDNA fragmentation, higher cfDNA levels, and kidney disease in SLE patients. Although the causality of this relationship could not be determined with the current study, it brings rationale for further investigations on the role of EBV and cfDNA interplay in SLE pathogenesis.
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Affiliation(s)
- Anna Truszewska
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Wirkowska
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Gala
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Truszewski
- Department of Orthopedics and Traumatology of Musculoskeletal System, Baby Jesus Clinical Hospital, Warsaw, Poland
| | - Łucja Krzemień-Ojak
- Laboratory of the Molecular Biology of Cancer, Centre of New Technologies, Warsaw, Poland
| | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszaw, Poland
| | - Leszek Pączek
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszaw, Poland
| | - Bartosz Foroncewicz
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
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18
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Leers MPG. Circulating tumor DNA and their added value in molecular oncology. Clin Chem Lab Med 2021; 58:152-161. [PMID: 31490771 DOI: 10.1515/cclm-2019-0436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022]
Abstract
New methods for molecular diagnosis are now available in oncology thanks to the discovery of circulating tumor DNA molecules in the plasma of cancer patients. By utilizing blood samples, rather than traditional tissue sampling, clinical practice is on the verge of new discoveries from the analysis of cell-free DNA (cfDNA). The method, known as a "liquid biopsy", consists of analyzing therapeutic targets and drug-resistant conferring gene mutations in circulating tumor cells (CTC) and cell-free circulating tumor DNA (ctDNA). These are subsequently released from primary tumors and metastatic deposits into the peripheral blood. The advantages of the method can be observed in the diagnosis, but also in the choice of treatment for solid tumors (e.g. non-small cell lung carcinomas [NSCLC]). In order to interpret the results, an understanding of the biological characteristics of circulating tumor DNA is required. Currently there is no consensus as to how a liquid biopsy should be conducted. In this review, we will assess the pros of ctDNA as analytes in peripheral blood samples and its impact on clinical applications in solid tumors and hematological malignancies. We will also address practical issues facing clinical implementation, such as pre-analytical factors. Moreover, we will emphasize the open questions that remain when considering the current state of personalized medicine and targeted therapy.
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Affiliation(s)
- Math P G Leers
- Department of Clinical Chemistry and Hematology, Zuyderland Medical Center Sittard-Geleen, Dr. H. Van der Hoffplein 1, P.O. Box 5500, 6130 MB Sittard, The Netherlands
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19
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Clinical impact of LncRNA XIST and LncRNA NEAT1 for diagnosis of high-risk group breast cancer patients. Curr Probl Cancer 2021; 45:100709. [PMID: 33602501 DOI: 10.1016/j.currproblcancer.2021.100709] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/02/2021] [Accepted: 01/11/2021] [Indexed: 12/20/2022]
Abstract
Long noncoding RNAs (lncRNAs) are evolving as contributing biomarkers for many diseases. Among these lncRNAs, X inactive-specific transcript (XIST), and nuclear paraspeckle assembly transcript 1 (NEAT1) were studied as undesirable upregulated nucleic acid markers for unfavorable prognosis of cancer. The authors aimed to investigate their role as diagnostic markers for breast cancer (BC) patients with high-risk factors. Serum samples were obtained from BC patients (n = 121), patients with benign breast lesions (n = 35), and healthy volunteers (n = 22). Assessment of lncRNA XIST, and lncRNA NEAT1 expression was performed using real time PCR. Expression levels of the investigated lncRNAs were significantly higher in BC patients as compared to the other groups. Both lncRNAs were significantly correlated with BC laterality, lymph node involvement, and clinical stages. LncRNA NEAT1 reported a significant aberrant expression with pathological types, histological grading and, hormonal status. The sensitivity of lncRNA NEAT1 was superior for detection of BC with high risk-factors as compared to lncRNA XIST. In conclusion, the detection of lncRNAs in body fluids has demonstrated a significant importance for detecting BC patients with high-risk factors, and was related to hormonal receptors, thus may be used for determining the direction of treatment strategy.
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20
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Paramathas S, Guha T, Pugh TJ, Malkin D, Villani A. Considerations for the use of circulating tumor DNA sequencing as a screening tool in cancer predisposition syndromes. Pediatr Blood Cancer 2020; 67:e28758. [PMID: 33047872 DOI: 10.1002/pbc.28758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022]
Abstract
Liquid biopsy, specifically circulating tumor DNA (ctDNA) detection, has started to revolutionize the clinical management of patients with cancer by surpassing many limitations of traditional tissue biopsies, particularly for serial testing. ctDNA sequencing has been successfully utilized for cancer detection, prognostication, and assessment of disease response and evolution. While the applications of ctDNA analysis are growing, the majority of studies to date have primarily evaluated its use as a tool for tracking a known cancer, and in most cases at advanced stage. Herein, we discuss the potential application of ctDNA for surveillance and early cancer detection in patients with a cancer predisposition syndrome.
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Affiliation(s)
- Sangeetha Paramathas
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Tanya Guha
- Institute of Medical Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Centre, Toronto, Canada.,Ontario Institute for Cancer Research, Toronto, Canada
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Institute of Medical Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Division of Haematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Anita Villani
- Division of Haematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Canada
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21
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Birkó Z, Nagy B, Klekner Á, Virga J. Novel Molecular Markers in Glioblastoma-Benefits of Liquid Biopsy. Int J Mol Sci 2020; 21:ijms21207522. [PMID: 33053907 PMCID: PMC7589793 DOI: 10.3390/ijms21207522] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022] Open
Abstract
Glioblastoma is a primary Central Nervous System (CNS) malignancy with poor survival. Treatment options are scarce and despite the extremely heterogeneous nature of the disease, clinicians lack prognostic and predictive markers to characterize patients with different outcomes. Certain immunohistochemistry, FISH, or PCR-based molecular markers, including isocitrate dehydrogenase1/2 (IDH1/2) mutations, epidermal growth factor receptor variant III (EGFRvIII) mutation, vascular endothelial growth factor overexpression (VEGF) overexpression, or (O6-Methylguanine-DNA methyltransferase promoter) MGMT promoter methylation status, are well-described; however, their clinical usefulness and accuracy is limited, and tumor tissue samples are always necessary. Liquid biopsy is a developing field of diagnostics and patient follow up in multiple types of cancer. Fragments of circulating nucleic acids are collected in various forms from different bodily fluids, including serum, urine, or cerebrospinal fluid in order to measure the quality and quantity of these markers. Multiple types of nucleic acids can be analyzed using liquid biopsy. Circulating cell-free DNA, mitochondrial DNA, or the more stable long and small non-coding RNAs, circular RNAs, or microRNAs can be identified and measured by novel PCR and next-generation sequencing-based methods. These markers can be used to detect the previously described alterations in a minimally invasive method. These markers can be used to differentiate patients with poor or better prognosis, or to identify patients who do not respond to therapy. Liquid biopsy can be used to detect recurrent disease, often earlier than using imaging modalities. Liquid biopsy is a rapidly developing field, and similarly to other types of cancer, measuring circulating tumor-derived nucleic acids from biological fluid samples could be the future of differential diagnostics, patient stratification, and follow up in the future in glioblastoma as well.
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Affiliation(s)
- Zsuzsanna Birkó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Correspondence:
| | - Bálint Nagy
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Álmos Klekner
- Department of Neurosurgery, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - József Virga
- Department of Oncology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
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22
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Fu Y, Zhang Y, Khoo BL. Liquid biopsy technologies for hematological diseases. Med Res Rev 2020; 41:246-274. [PMID: 32929726 DOI: 10.1002/med.21731] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/10/2020] [Accepted: 09/02/2020] [Indexed: 12/18/2022]
Abstract
Since the discovery of circulating tumor cells in 1869, technological advances in studying circulating biomarkers from patients' blood have made the diagnosis of nonhematologic cancers less invasive. Technological advances in the detection and analysis of biomarkers provide new opportunities for the characterization of other disease types. When compared with traditional biopsies, liquid biopsy markers, such as exfoliated bladder cancer cells, circulating cell-free DNA (cfDNA), and extracellular vesicles (EV), are considered more convenient than conventional biopsies. Liquid biopsy markers undoubtedly have the potential to influence disease management and treatment dynamics. Our main focuses of this review will be the cell-based, gene-based, and protein-based key liquid biopsy markers (including EV and cfDNA) in disease detection, and discuss the research progress of these biomarkers used in conjunction with liquid biopsy. First, we highlighted the key technologies that have been broadly adopted used in hematological diseases. Second, we introduced the latest technological developments for the specific detection of cardiovascular disease, leukemia, and coronavirus disease. Finally, we concluded with perspectives on these research areas, focusing on the role of microfluidic technology and artificial intelligence in point-of-care medical applications. We believe that the noninvasive capabilities of these technologies have great potential in the development of diagnostics and can influence treatment options, thereby advancing precision disease management.
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Affiliation(s)
- Yatian Fu
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong, China
| | - Yiyuan Zhang
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong, China
| | - Bee Luan Khoo
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong, China
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23
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Truszewska A, Wirkowska A, Gala K, Truszewski P, Krzemień-Ojak Ł, Perkowska-Ptasińska A, Mucha K, Pączek L, Foroncewicz B. Cell-free DNA profiling in patients with lupus nephritis. Lupus 2020; 29:1759-1772. [DOI: 10.1177/0961203320957717] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Increased level of cell-free DNA (cf-DNA) is associated with systemic lupus erythematosus (SLE) and might be related to disease activity. The aim of this study was to evaluate whether cfDNA integrity, size distribution and concentration of different cfDNA fractions is associated with lupus activity and kidney involvement. Methods Blood samples were collected from 43 SLE patients and 50 healthy controls. Nuclear and mitochondrial fractions of cfDNA and intracellular DNA were quantified by real-time qPCR. Sizing and quantification of total cfDNA level was performed on Bioanalyzer. Results We determined four parameters that characterized cfDNA profile: fragmentation index, ratio of intra- to extracellular mtDNA copy number, cfDNA concentration, and presence of 54–149 bp and 209–297 bp fragments. Patients with healthy-like cfDNA profile had higher eGFR ( P = 0.009) and more often no indications for kidney biopsy or less advanced lupus nephritis (LN) ( P = 0.037). In contrary, SLE patients with distinct cfDNA profile (characterized by increased cfDNA concentration and fragmentation, higher discrepancy between intra- to extracellular mtDNA copy number, and the presence of 54–149 bp and 209–297 bp fragments) had lower eGFR ( P = 0.005) and more often advanced LN or history of renal transplantation ( P = 0.001). Conclusions We showed that cfDNA profiling may help to distinguish SLE patients with renal involvement and severe disease course from patients with more favorable outcomes. We suggest cfDNA profile a promising SLE biomarker.
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Affiliation(s)
- Anna Truszewska
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Wirkowska
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Gala
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Truszewski
- Department of Orthopedics and Traumatology of Musculoskeletal System, Baby Jesus Clinical Hospital, Warsaw, Poland
| | - Łucja Krzemień-Ojak
- Laboratory of the Molecular Biology of Cancer, Centre of New Technologies, Warsaw, Poland
| | | | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Leszek Pączek
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Foroncewicz
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
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24
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Heredia FL, Resto PJ, Parés-Matos EI. Fast Adhesion of Gold Nanoparticles (AuNPs) to a Surface Using Starch Hydrogels for Characterization of Biomolecules in Biosensor Applications. BIOSENSORS 2020; 10:E99. [PMID: 32824022 PMCID: PMC7460011 DOI: 10.3390/bios10080099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/29/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022]
Abstract
Gold nanoparticles (AuNPs) are the most thoroughly studied nanoparticles because of their remarkable optical properties. Color changes in assays that use AuNPs can be easily observed with the naked eye, resulting in sensitive colorimetric methods, useful for detecting a variety of biological molecules. However, while AuNPs represent an excellent nano-platform for developing analytical methods for biosensing, there are still challenges that must be overcome before colloidal AuNPs formulation can be successfully translated into practical applications. One of those challenges is the ability to immobilize AuNPs in a solid support. There are many difficulties with controlling both the cluster size and the adhesion of the coatings formed. In addition, many of the techniques employed are expensive and time-consuming, or require special equipment. Thus, a simple and inexpensive method that only requires common lab equipment for immobilizing AuNPs on a surface using Starch Hydrogels has been developed. Starch hydrogels confer a 400% increase in stability to the nanoparticles when exposed to changes in the environment while also allowing for macromolecules to interact with the AuNPs surface. Several starch derivatives were tested, including, dextrin, beta-cyclodextrin and maltodextrin, being dextrin the one that conferred the highest stability. As a proof-of-concept, a SlipChip microfluidic sensor scheme was developed to measure the concentration of DNA in a sample. The detection limit of our biosensor was found to be 25 ng/mL and 75 ng/mL for instrument and naked eye detection, respectively.
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Affiliation(s)
- Frances L. Heredia
- Department of Chemistry, University of Puerto Rico at Mayagüez, Mayagüez, PR 00680, USA;
| | - Pedro J. Resto
- Department of Mechanical Engineering, University of Puerto Rico at Mayagüez, Mayagüez, PR 00680, USA;
| | - Elsie I. Parés-Matos
- Department of Chemistry, University of Puerto Rico at Mayagüez, Mayagüez, PR 00680, USA;
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25
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Circulating cell-free DNA level predicts all-cause mortality independent of other predictors in the Health 2000 survey. Sci Rep 2020; 10:13809. [PMID: 32796872 PMCID: PMC7427793 DOI: 10.1038/s41598-020-70526-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/10/2020] [Indexed: 12/22/2022] Open
Abstract
Increased levels of circulating cell-free DNA (cf-DNA) are associated with and predict poor health outcomes. However, its predictive ability for mortality in population-based samples remains understudied. We analysed the capability of cf-DNA to predict all-cause mortality and assessed whether it adds predictive value on top of the other risk factors in the Health 2000 survey (n = 1,257, 46–76 years of age, 15-years-follow-up, 18% deceased). When analysed in a multivariate model with the other factors that independently predicted mortality in the sample (age, gender, self-rated health, smoking and plasma levels of glucose and adiponectin), increases in cf-DNA levels were associated with increased risk of mortality (hazard ratio [HR] for 0.1 µg increase in cf-DNA: 1.017, 95% confidence interval [CI] 1.008–1.026, p = 0.0003). Inclusion of cf-DNA in the model improved the model fit and discrimination. Stratifying the analysis by cardiovascular disease (CVD) status indicated that cf-DNA predicted mortality equally well in individuals with (HR 1.018, 95% CI 1.008–1.026, p = 0.002) and without (HR 1.018, 95% CI 1.001–1.035, p = 0.033) CVD. In conclusion, our study indicates that cf-DNA level predicts mortality in middle-aged and older individuals, also among those with established CVD, and adds significant value to mortality prediction. Our results thus underscore the role of cf-DNA as a viable marker of health.
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Ungerer V, Bronkhorst AJ, Holdenrieder S. Preanalytical variables that affect the outcome of cell-free DNA measurements. Crit Rev Clin Lab Sci 2020; 57:484-507. [DOI: 10.1080/10408363.2020.1750558] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Abel J. Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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27
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Nygård L, Ahlborn LB, Persson GF, Chandrananda D, Langer JW, Fischer BM, Langer SW, Gabrielaite M, Kjær A, Rosenfeld N, Mouliere F, Østrup O, Vogelius IR, Bentzen SM. Circulating cell free DNA during definitive chemo-radiotherapy in non-small cell lung cancer patients - initial observations. PLoS One 2020; 15:e0231884. [PMID: 32343749 PMCID: PMC7188247 DOI: 10.1371/journal.pone.0231884] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 04/02/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The overall aim was to investigate the change over time in circulating cell free DNA (cfDNA) in patients with locally advanced non-small cell lung cancer (NSCLC) undergoing concurrent chemo-radiotherapy. Furthermore, to assess the possibility of detecting circulating cell free tumor DNA (ctDNA) using shallow whole genome sequencing (sWGS) and size selection. METHODS Ten patients were included in a two-phase study. The first four patients had blood samples taken prior to a radiation therapy (RT) dose fraction and at 30 minutes, 1 hour and 2 hours after RT to estimate the short-term dynamics of cfDNA concentration after irradiation. The remaining six patients had one blood sample taken on six treatment days 30 minutes post treatment to measure cfDNA levels. Presence of ctDNA as indicated by chromosomal aberrations was investigated using sWGS. The sensitivity of this method was further enhanced using in silico size selection. RESULTS cfDNA concentration from baseline to 120 min after therapy was stable within 95% tolerance limits of +/- 2 ng/ml cfDNA. Changes in cfDNA were observed during therapy with an apparent qualitative difference between adenocarcinoma (average increase of 0.69 ng/ml) and squamous cell carcinoma (average increase of 4.0 ng/ml). Tumor shrinkage on daily cone beam computer tomography scans during radiotherapy did not correlate with changes in concentration of cfDNA. CONCLUSION Concentrations of cfDNA remain stable during the first 2 hours after an RT fraction. However, based on the sWGS profiles, ctDNA represented only a minor fraction of cfDNA in this group of patients. The detection sensitivity of genomic alterations in ctDNA strongly increases by applying size selection.
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Affiliation(s)
- Lotte Nygård
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lise B. Ahlborn
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Gitte F. Persson
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, England, United Kingdom
| | - Jonathan W. Langer
- Department of Clinical Physiology, Nuclear Medicine & PET and Cluster for Molecular Imaging, Rigshospitalet and University of Copenhagen, Copenhagen, Denmark
| | - Barbara M. Fischer
- Department of Clinical Physiology, Nuclear Medicine & PET and Cluster for Molecular Imaging, Rigshospitalet and University of Copenhagen, Copenhagen, Denmark
- PET Centre, School of Biomedical Engineering and Imaging Sciences, Kings College London, St Thomas' Hospital, London, England, United Kingdom
| | - Seppo W. Langer
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Miglė Gabrielaite
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Andreas Kjær
- Department of Clinical Physiology, Nuclear Medicine & PET and Cluster for Molecular Imaging, Rigshospitalet and University of Copenhagen, Copenhagen, Denmark
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, England, United Kingdom
| | - Florent Mouliere
- Department of Pathology, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ivan R. Vogelius
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Søren M. Bentzen
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, University of Maryland Greenebaum Comprehensive Cancer Center, and University of Maryland School of Medicine, Baltimore, MD, United States of America
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28
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Yan W, Xu T, Zhu H, Yu J. Clinical Applications of Cerebrospinal Fluid Circulating Tumor DNA as a Liquid Biopsy for Central Nervous System Tumors. Onco Targets Ther 2020; 13:719-731. [PMID: 32158224 PMCID: PMC6986252 DOI: 10.2147/ott.s229562] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/11/2020] [Indexed: 12/19/2022] Open
Abstract
Central nervous system (CNS) malignancies are associated with poor prognosis, as well as exceptional morbidity and mortality, likely as a result of low rates of early diagnosis and limited knowledge of the tumor growth and resistance mechanisms, dissemination, and evolution in the CNS. Monitoring patients with CNS malignancies for treatment response and tumor recurrence can be challenging because of the difficulty and risks of brain biopsies and the low specificity and sensitivity of the less invasive methodologies that are currently available. Therefore, there is an urgent need to detect and validate reliable and minimally invasive biomarkers for CNS tumors that can be used separately or in combination with current clinical practices. The circulating tumor DNA (ctDNA) of cerebrospinal fluid (CSF) samples can outline the genetic landscape of entire CNS tumors effectively and is a promising, suitable biomarker, though its role in managing CNS malignancies has not been studied extensively. This review summarizes recent studies that explore the diagnostic, prognostic, and predictive roles of CSF-ctDNA as a liquid biopsy with primary and metastatic CNS malignancies.
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Affiliation(s)
- Weiwei Yan
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China.,Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, People's Republic of China
| | - Tingting Xu
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, People's Republic of China
| | - Hui Zhu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, People's Republic of China
| | - Jinming Yu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, People's Republic of China
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29
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Shepard CR. TLR9 in MAFLD and NASH: At the Intersection of Inflammation and Metabolism. Front Endocrinol (Lausanne) 2020; 11:613639. [PMID: 33584545 PMCID: PMC7880160 DOI: 10.3389/fendo.2020.613639] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
Toll-Like Receptor 9 (TLR9) is an ancient receptor integral to the primordial functions of inflammation and metabolism. TLR9 functions to regulate homeostasis in a healthy system under acute stress. The literature supports that overactivation of TLR9 under the chronic stress of obesity is a critical driver of the pathogenesis of NASH and NASH-associated fibrosis. Research has focused on the core contributions of the parenchymal and non-parenchymal cells in the liver, adipose, and gut compartments. TLR9 is activated by endogenous circulating mitochondrial DNA (mtDNA). Chronically elevated circulating levels of mtDNA, caused by the stress of overnutrition, are observed in obesity, metabolic dysfunction-associated fatty liver disease (MAFLD), and NASH. Clinical evidence is supportive of TLR9 overactivation as a driver of disease. The role of TLR9 in metabolism and energy regulation may have an underappreciated contribution in the pathogenesis of NASH. Antagonism of TLR9 in NASH and NASH-associated fibrosis could be an effective therapeutic strategy to target both the inflammatory and metabolic components of such a complex disease.
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30
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Early detection of cancer using circulating tumor DNA: biological, physiological and analytical considerations. Crit Rev Clin Lab Sci 2019:1-17. [PMID: 31865831 DOI: 10.1080/10408363.2019.1700902] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early diagnosis of cancer improves the efficacy of curative therapies. However, due to the difficulties involved in distinguishing between small early-stage tumors and normal biological variation, early detection of cancer is an extremely challenging task and there are currently no clinically validated biomarkers for a pan-cancer screening test. It is thus of particular significance that increasing evidence indicates the potential of circulating tumor DNA (ctDNA) molecules, which are fragmented segments of DNA shed from tumor cells into adjacent body fluids and the circulatory system, to serve as molecular markers for early cancer detection and thereby allow early intervention and improvement of therapeutic and survival outcomes. This is possible because ctDNA molecules bear cancer-specific fragmentation patterns, nucleosome depletion motifs, and genetic and epigenetic alterations, as distinct from plasma DNA originating from non-cancerous tissues/cells. Compared to traditional biomarkers, ctDNA analysis therefore presents the distinctive advantage of detecting tumor-specific alterations. However, based on a thorough survey of the literature, theoretical and empirical evidence suggests that current ctDNA analysis strategies, which are mainly based on DNA mutation detection, do not demonstrate the necessary diagnostic sensitivity and specificity that is required for broad clinical implementation in a screening context. Therefore, in this review we explain the biological, physiological, and analytical challenges toward the development of clinically meaningful ctDNA tests. In addition, we explore some approaches that can be implemented in order to increase the sensitivity and specificity of ctDNA assays.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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31
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Shi Y, Zhang Y, Zhang L, Ma JL, Zhou T, Li ZX, Liu WD, Li WQ, Deng DJ, You WC, Pan KF. Telomere Length of Circulating Cell-Free DNA and Gastric Cancer in a Chinese Population at High-Risk. Front Oncol 2019; 9:1434. [PMID: 31921685 PMCID: PMC6928050 DOI: 10.3389/fonc.2019.01434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 12/02/2019] [Indexed: 12/27/2022] Open
Abstract
Background: Telomeres have long been found to be involved in cancer development, while little was known about the dynamic changes of telomere length in carcinogenesis process. Methods: The present study longitudinally investigated telomere alterations of cell-free DNA (cfDNA) in 86 gastric cancer (GC) subjects recruited through a 16-year prospective cohort with 2–4 serums collected before each GC-diagnosis from baseline and three follow-up time-points (a total of 276 samples). As the control, 86 individual-matched cancer-free subjects were enrolled with 276 serums from the matched calendar year. Results: In the 73 pairs of baseline serums from GC and control subjects, shortened telomeres showed increased subsequent GC risk [odds ratio (OR) = 9.17, 95% CI: 2.72–31.25 for 1 unit shortening]. In each baseline gastric lesion category, higher risks of GC progression were also found with shortened cfDNA telomeres; ORs per 1 unit shortening were 6.99 (95% CI: 1.63–30.30) for mild gastric lesions, 6.06 (95% CI: 1.89–19.61) for intestinal metaplasia and 15.63 (95% CI: 1.91–125.00) for dysplasia. With all measurements from baseline and follow-up time-points, shortened telomeres also showed significant association with GC risk (OR = 7.37, 95% CI: 2.06–26.32 for 1 unit shortening). In temporal trend analysis, shortened telomeres were found in GC subjects compared to corresponding controls more than 3 years ahead of GC-diagnosis (most P < 0.05), while no significant difference was found between two groups within 3 years approaching to GC-diagnosis. Conclusion: Our findings suggest that telomere shortening may be associated with gastric carcinogenesis, which supports further etiological study and potential biomarker for risk stratification.
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Affiliation(s)
- Yu Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yang Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Lian Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jun-Ling Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Tong Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Zhe-Xuan Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, China
| | | | - Wen-Qing Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Da-Jun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Wei-Cheng You
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Kai-Feng Pan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital and Institute, Beijing, China
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Pan Y, Long W, Liu Q. Current Advances and Future Perspectives of Cerebrospinal Fluid Biopsy in Midline Brain Malignancies. Curr Treat Options Oncol 2019; 20:88. [PMID: 31784837 DOI: 10.1007/s11864-019-0689-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
OPINION STATEMENT Malignancies arising in midline brain structures, including lymphomas, teratomas, germinomas, diffuse midline gliomas, and medulloblastomas typically respond to systemic therapies, and excessive surgical excision can result in serious complications, so that total surgical removal is not routinely performed. Identifying tumor specific biomarkers that can facilitate diagnosis at early stage and allow for dynamic surveillance of the tumor is of great clinical importance. However, existing standard methods for biopsy of these brain neoplasms are high risk, time consuming, and costly. Thus, less invasive and more rapid diagnosis tests are urgently needed to detect midline brain malignancies. Currently, tools for cerebrospinal biopsy of midline brain malignancies mainly include circulating tumor DNA, circulating tumor cells, and extracellular vesicles. Circulating tumor DNA achieved minimally invasive biopsy in several brain malignancies and has advantages in detecting tumor-specific mutations. In the field of tumor heterogeneity, circulating tumor cells better reflect the genome of tumors than surgical biopsy specimens. They can be applied for the diagnosis of leptomeningeal metastasis. Extracellular vesicles contain lots of genetic information about cancer cells, so they have potential in finding therapeutic targets and studying tumor invasion and metastasis.
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Affiliation(s)
- Yimin Pan
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Wenyong Long
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qing Liu
- Department of Neurosurgery in Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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Stiel L, Mayeur-Rousse C, Helms J, Meziani F, Mauvieux L. First visualization of circulating neutrophil extracellular traps using cell fluorescence during human septic shock-induced disseminated intravascular coagulation. Thromb Res 2019; 183:153-158. [PMID: 31678710 DOI: 10.1016/j.thromres.2019.09.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/18/2022]
Abstract
Disseminated intravascular coagulation (DIC) is a severe complication of septic shock. Polymorphonuclear neutrophils (PMNs) may play a key role in septic shock-induced DIC via the release of neutrophils extracellular traps (NETs). NETs capture invading pathogens, but also act as a pro-coagulant surface at the interface between immunity and thrombosis. During septic shock-induced DIC, neutrophil activation may result in excessive NET formation. Herein, we originally report the presence of circulating NETs in human blood during septic shock-induced DIC. To investigate NET formation during shock-induced DIC neutrophils were isolated from patients in septic shock associated with (n = 3) or without (n = 3) DIC. Neutrophils from healthy donors (n = 3) were stimulated in vitro with ionomycin as NET formation positive controls. PMNs smears were stained with mouse anti-human FITC anti-myeloperoxidase antibody and the blue-fluorescent DAPI nucleic acid stain. NETs were identified as elongated extracellular DNA fibers associated to myeloperoxidase detected by immunofluorescence. NETs were unambiguously observed in PMNs from septic shock patients with DIC but not from patients without DIC. NETs features in DIC+ patients were undistinguishable from those observed in ionomycin-induced PMNs from healthy donors. Fluorescence images of NETs were associated to extracellular cytoplasmic expansions. Our data report for the first time the direct visualization of circulating NETs in patients with septic shock-induced DIC. The in vivo relevance of previously reported indirect markers of NETosis (neutrophil side fluorescence) is confirmed.
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Affiliation(s)
- Laure Stiel
- Université de Strasbourg (UNISTRA), Faculté de Médecine; Hôpitaux universitaires de Strasbourg, Nouvel Hôpital Civil, Service de Médecine Intensive Réanimation, Strasbourg, France; UMR 1260, Regenerative Nano Medecine, INSERM, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Caroline Mayeur-Rousse
- Laboratoire d'hématologie cellulaire, Hôpitaux universitaires de Strasbourg, Strasbourg, France
| | - Julie Helms
- Université de Strasbourg (UNISTRA), Faculté de Médecine; Hôpitaux universitaires de Strasbourg, Nouvel Hôpital Civil, Service de Médecine Intensive Réanimation, Strasbourg, France; ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx TRANSPLANTEX, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération Hospitalo-Universitaire (FHU) OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Ferhat Meziani
- Université de Strasbourg (UNISTRA), Faculté de Médecine; Hôpitaux universitaires de Strasbourg, Nouvel Hôpital Civil, Service de Médecine Intensive Réanimation, Strasbourg, France; UMR 1260, Regenerative Nano Medecine, INSERM, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Laurent Mauvieux
- Laboratoire d'hématologie cellulaire, Hôpitaux universitaires de Strasbourg, Strasbourg, France; INSERM UMR 1113: Interface Recherche Fondamentale et Appliquée en Cancérologie (IRFAC), Strasbourg, France.
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Jeremic I, Djuric O, Nikolic M, Vlajnic M, Nikolic A, Radojkovic D, Bonaci-Nikolic B. Neutrophil extracellular traps-associated markers are elevated in patients with systemic lupus erythematosus. Rheumatol Int 2019; 39:1849-1857. [PMID: 31444555 DOI: 10.1007/s00296-019-04426-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/12/2019] [Indexed: 01/21/2023]
Abstract
Neutrophil extracellular traps (NETs) are the main source of autoantigens in systemic lupus erythematosus (SLE). The aim of this study was to evaluate the clinical importance of NETs-associated markers in SLE. We compared NETs-associated markers in SLE patients (n = 111) with healthy controls (n = 50). Moreover, in 35 patients with drug-naïve SLE (n = 35), we investigated correlation between NETs-associated markers [DNase I concentration, myeloperoxidase (MPO) activity, anti-MPO antibodies, cell-free DNA (cfDNA), NETolytic activity] with serological parameters [anti-dsDNA antibodies, C3, C4 and B-cell activating factor (BAFF) levels] and disease activity measured by modified SLE Disease Activity Index (M-SLEDAI-2K). In comparison with healthy controls, SLE patients had higher cfDNA, MPO activity, anti-MPO antibodies (p < 0.001), BAFF and DNase I concentration (p < 0.01). Contrary, NETolytic activity was lower in SLE patients (p < 0.05), despite higher concentration of DNase I. MPO activity and cfDNA levels showed correlation with DNase I concentration (p < 0.001, p < 0.01, respectively). BAFF levels correlated with cfDNA, DNase I concentration and MPO activity (p < 0.05). Anti-dsDNA antibodies showed correlation with MPO activity (p < 0.01), cfDNA and BAFF levels (p < 0.001). Anti-dsDNA and C3 levels were independent predictors of M-SLEDAI-2K in multivariate analysis (p < 0.01). We demonstrated that sera of SLE patients have decreased NETolytic activity, leading to increased levels of various NETs-associated markers, which correlate with anti-dsDNA antibodies in drug-naïve SLE. We showed that BAFF participates in a complex relationship between NETosis and anti-dsDNA antibodies production. These findings have important implications for a better understanding of SLE pathogenesis and development of therapy that inhibits NETs persistence and disease progression.
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Affiliation(s)
- Ivica Jeremic
- School of Medicine, Institute of Rheumatology, University of Belgrade, Resavska 69, Belgrade, 11000, Serbia.
| | - Olivera Djuric
- School of Medicine, Institute of Epidemiology, University of Belgrade, Belgrade, Serbia
| | - Milos Nikolic
- School of Medicine, Clinic of Dermatovenereology, Clinical Centre of Serbia, University of Belgrade, Belgrade, Serbia
| | - Marina Vlajnic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Nikolic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Dragica Radojkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Branka Bonaci-Nikolic
- School of Medicine, Clinic of Allergy and Immunology, University of Belgrade, Belgrade, Serbia
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Hübner A, Wachsmuth M, Schröder R, Li M, Eis-Hübinger AM, Madea B, Stoneking M. Sharing of heteroplasmies between human liver lobes varies across the mtDNA genome. Sci Rep 2019; 9:11219. [PMID: 31375696 PMCID: PMC6677727 DOI: 10.1038/s41598-019-47570-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/16/2019] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial DNA (mtDNA) heteroplasmy (intra-individual variation) varies among different human tissues and increases with age, suggesting that the majority of mtDNA heteroplasmies are acquired, rather than inherited. However, the extent to which heteroplasmic sites are shared across a tissue remains an open question. We therefore investigated heteroplasmy in two liver samples (one from each primary lobe) from 83 Europeans, sampled at autopsy. Minor allele frequencies (MAF) at heteroplasmic sites were significantly correlated between the two liver samples from an individual, with significantly more sharing of heteroplasmic sites in the control region than in the non-control region. We show that this increased sharing for the control region cannot be explained by recent mutations at just a few specific heteroplasmic sites or by the possible presence of 7S DNA. Moreover, we carried out simulations to show that there is significantly more sharing than would be predicted from random genetic drift from a common progenitor cell. We also observe a significant excess of non-synonymous vs. synonymous heteroplasmies in the protein-coding region, but significantly more sharing of synonymous heteroplasmies. These contrasting patterns for the control vs. the non-control region, and for non-synonymous vs. synonymous heteroplasmies, suggest that selection plays a role in heteroplasmy sharing.
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Affiliation(s)
- Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.
| | - Manja Wachsmuth
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Anna Maria Eis-Hübinger
- Institut für Virologie, Universitätsklinikum Bonn, Sigmund-Freud-Str. 25, D-53105, Bonn, Germany
| | - Burkhard Madea
- Institut für Rechtsmedizin, Universitätsklinikum Bonn, Stiftsplatz 12, D-53111, Bonn, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.
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Oxidized Cell-Free DNA Role in the Antioxidant Defense Mechanisms under Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:1245749. [PMID: 31360293 PMCID: PMC6644271 DOI: 10.1155/2019/1245749] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/08/2019] [Indexed: 12/15/2022]
Abstract
The present study focuses on the investigation of the oxidized cell-free DNA (cfDNA) properties in several experimental models, including cultured cerebellum cells, peripheral blood lymphocytes (PBL), plasma, and hippocampus under an acute and chronic unpredictable stress model in rats. Firstly, our study shows that Spectrum Green fluorescence-labeled oxidized cfDNA fragments were transferred into the cytoplasm of 80% of the cerebellum culture cells; meanwhile, the nonoxidized cfDNA fragments do not pass into the cells. Oxidized cfDNA stimulates the antioxidant mechanisms and induction of transcription factor NRF2 expression, followed by an activation of NRF2 signaling pathway genes-rise of Nrf2 and Hmox1 gene expression and consequently NRF2 protein synthesis. Secondly, we showed that stress increases plasma cfDNA concentration in rats corresponding with the duration of the stress exposure. At the same time, our study did not reveal any significant changes of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) level in PBL of rats under acute or chronic stress, probably due to the significantly increased Nrf2 expression, that we found in such conditions. 8-oxodG is one of the most reliable markers of DNA oxidation. We also found an increased level of 8-oxodG in the hippocampal homogenates and hippocampal dentate gyrus in rats subjected to acute and chronic stress. Taken together, our data shows that oxidized cfDNA may play a significant role in systemic and neuronal physiological mechanisms of stress and adaptation.
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Abstract
Since its discovery in human blood plasma about 70 years ago, circulating cell-free DNA (cfDNA) has become an attractive subject of research as noninvasive disease biomarker. The interest in clinical applications has gained an exponential increase, making it a popular and potential target in a wide range of research areas.cfDNA can be found in different body fluids, both in healthy and not healthy subjects. The recent and rapid development of new molecular techniques is promoting the study and the identification of cfDNA, holding the key to minimally invasive diagnostics, improving disease monitoring, clinical decision, and patients' outcome.cfDNA has already given a huge impact on prenatal medicine, and it could become, in the next future, the standard of care also in other fields, from oncology to transplant medicine and cardiovascular diseases.
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Affiliation(s)
- Rossella Ranucci
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy.
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38
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Shi X, Duose DY, Mehrotra M, Harmon MA, Hu P, Wistuba II, Kopetz S, Luthra R. Non-invasive genotyping of metastatic colorectal cancer using circulating cell free DNA. Cancer Genet 2019; 237:82-89. [PMID: 31447070 DOI: 10.1016/j.cancergen.2019.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/03/2019] [Accepted: 06/09/2019] [Indexed: 02/07/2023]
Abstract
Circulating cell-free DNA (ccfDNA) in plasma provides an easily accessible source of circulating tumor DNA (ctDNA) for detecting actionable genomic alterations that can be used to guide colorectal cancer (CRC) treatment and surveillance. The goal of this study was to test the feasibility of using a traditional amplicon-based next-generation sequencing (NGS) on Ion Torrent platform to detect low-frequency alleles in ctDNA and compare it with a digital NGS assay specifically designed to detect low-frequency variants (as low as 0.1%) to provide evidence for the standard care of CRC. The study cohort consisted of 48 CRC patients for whom matched samples of formalin-fixed, paraffin-embedded tumor tissue, plasma, and peripheral blood mononuclear cells were available. DNA samples from different sources were sequenced on different platforms using commercial protocols. Our results demonstrate that the ccfDNA sequencing with the traditional NGS can be reliably used in an integrated workflow to detect low-frequency somatic variants in CRC. We found a high degree of concordance between traditional NGS and digital NGS in profiling mutant alleles in ccfDNA. These findings suggest that the traditional NGS is a viable alternative to digital sequencing of ccfDNA at allele frequency above 1%. ccfDNA sequencing can not only provide real-time monitoring of CRC, but also lay the basis for its application as a clinical diagnostic test to guide personalized therapy.
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Affiliation(s)
- Xuemei Shi
- Diagnostic Genetics, School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Blvd., Houston, TX 77030, United States
| | - Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Michael A Harmon
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Peter Hu
- Diagnostic Genetics, School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Blvd., Houston, TX 77030, United States
| | - Scott Kopetz
- Department of GI Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Rajyalakshmi Luthra
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Blvd., Houston, TX 77030, United States; Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States.
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39
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Phuong NTN, Manh DH, Dumre SP, Mizukami S, Weiss LN, Van Thuong N, Ha TTN, Phuc LH, Van An T, Tieu TM, Kamel MG, Morra ME, Huong VTQ, Huy NT, Hirayama K. Plasma cell-free DNA: a potential biomarker for early prediction of severe dengue. Ann Clin Microbiol Antimicrob 2019; 18:10. [PMID: 30871553 PMCID: PMC6419393 DOI: 10.1186/s12941-019-0309-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/22/2019] [Indexed: 12/30/2022] Open
Abstract
Background Considerable progress has been made in dengue management, however the lack of appropriate predictors of severity has led to huge number of unwanted admissions mostly decided on the grounds of warning signs. Apoptosis related mediators, among others, are known to correlate with severe dengue (SD) although no predictive validity is established. The objective of this study was to investigate the association of plasma cell-free DNA (cfDNA) with SD, and evaluate its prognostic value in SD prediction at acute phase. Methods This was a hospital-based prospective cohort study conducted in Vietnam. All the recruited patients were required to be admitted to the hospital and were strictly monitored for various laboratory and clinical parameters (including progression to SD) until discharged. Plasma samples collected during acute phase (6–48 h before defervescence) were used to estimate the level of cfDNA. Results Of the 61 dengue patients, SD patients (n = 8) developed shock syndrome in 4.8 days (95% CI 3.7–5.4) after the fever onset. Plasma cfDNA levels before the defervescence of SD patients were significantly higher than the non-SD group (p = 0.0493). From the receiver operating characteristic (ROC) curve analysis, a cut-off of > 36.9 ng/mL was able to predict SD with a good sensitivity (87.5%), specificity (54.7%), and area under the curve (AUC) (0.72, 95% CI 0.55–0.88; p = 0.0493). Conclusions Taken together, these findings suggest that cfDNA could serve as a potential prognostic biomarker of SD. Studies with cfDNA kinetics and its combination with other biomarkers and clinical parameters would further improve the diagnostic ability for SD. Electronic supplementary material The online version of this article (10.1186/s12941-019-0309-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nguyen Thi Ngoc Phuong
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.,Health Innovation Course, School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Dao Huy Manh
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.,Global Leader Nurturing Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Shyam Prakash Dumre
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Shusaku Mizukami
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Lan Nguyen Weiss
- Department of Immunology and Microbiology, Pasteur Institute, Ho Chi Minh City, Vietnam
| | - Nguyen Van Thuong
- Department of Immunology and Microbiology, Pasteur Institute, Ho Chi Minh City, Vietnam
| | - Tran Thi Ngoc Ha
- Department of Immunology and Microbiology, Pasteur Institute, Ho Chi Minh City, Vietnam
| | - Le Hong Phuc
- Nguyen Dinh Chieu Hospital, Ben Tre Province, Vietnam
| | - Tran Van An
- Nguyen Dinh Chieu Hospital, Ben Tre Province, Vietnam
| | - Thuan Minh Tieu
- Online research Club (www.onlineresearchclub.org/), Nagasaki, Japan.,Faculty of Health Sciences, McMaster University, Hamilton, Canada
| | - Mohamed Gomaa Kamel
- Online research Club (www.onlineresearchclub.org/), Nagasaki, Japan.,Faculty of Medicine, Minia University, Minia, Egypt
| | - Mostafa Ebraheem Morra
- Online research Club (www.onlineresearchclub.org/), Nagasaki, Japan.,Faculty of Medicine, Alazhar University, Cairo, 11884, Egypt
| | - Vu Thi Que Huong
- Department of Immunology and Microbiology, Pasteur Institute, Ho Chi Minh City, Vietnam
| | - Nguyen Tien Huy
- Evidence Based Medicine Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam. .,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, 70000, Vietnam. .,Department of Clinical Product Development, Institute of Tropical Medicine (NEKKEN), School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, 852-8523, Japan.
| | - Kenji Hirayama
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan. .,Global Leader Nurturing Program, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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40
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Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100087. [PMID: 30923679 PMCID: PMC6425120 DOI: 10.1016/j.bdq.2019.100087] [Citation(s) in RCA: 367] [Impact Index Per Article: 61.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023]
Abstract
An increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, physical properties, and dynamics in circulation. The latter knowledge is crucial for interpreting the associations between changes in the baseline characteristics of cfDNA and the clinical manifestations of cancer. In this review we explore recent advancements and highlight the current gaps in our knowledge concerning each point of contact between cfDNA analysis and the different stages of cancer management.
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Affiliation(s)
| | | | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße. 36, D-80636, Munich, Germany
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Drainage of Tumor-Derived DNA into Sentinel Lymph Nodes in Breast Cancer Patients. Pathol Oncol Res 2019; 25:1635-1643. [PMID: 30805870 DOI: 10.1007/s12253-019-00618-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/15/2019] [Indexed: 01/01/2023]
Abstract
Circulating tumor DNA (ctDNA) is released from cancer cells by apoptosis or other mechanisms, and as tumor tissue contains both blood and lymphatic vessels, ctDNA can spread to local lymph nodes (LNs). We aimed to detect the tumor-derived free DNA in metastasis-free LNs in patients with breast cancers harboring the PIK3CA-H1047R mutation. One hundred twenty-three patients were evaluated and the PIK3CA-H1047R mutation was assayed in sentinel LNs (SLNs), non-SLNs without metastasis, and serum by digital PCR. The mutant DNA was more frequent in metastasis-free SLNs (21.6%) than in metastasis-free non-SLNs (8.6%; P = 0.038), and patients with mutation-positive SLNs were more likely to be positive for serum mutant DNA. Apoptosis in primary breast tumors was determined by TUNEL assay. The apoptotic index was significantly higher (P = 0.003) in patients with mutation-positive SLNs without metastasis (mean, 1.17%) than those with mutation-negative SLNs without metastasis (mean, 0.79%). It was also significantly higher (P = 0.006) in those with mutation-positive serum (mean, 1.41%) than in those with mutation-negative serum (mean, 0.86%). Furthermore, fragment size of PIK3CA-H1047R mutant DNA in metastatic-free SLN lysate used for the one-step nucleic acid amplification (OSNA) assay was short (<500 bp). These results support the theory that DNA is released from the primary tumor via apoptotic fragmentation. In conclusion, ctDNA is detectable in metastasis-free LNs and significantly more frequent in SLNs from patients with breast tumors harboring a high apoptotic index, consistent with drainage of ctDNA from apoptotic primary tumor cells into SLNs.
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Delmonico L, Costa MASM, Fournier MV, Romano SDO, Nascimento CMD, Barbosa AS, Moreira ADS, Scherrer LR, Ornellas MHF, Alves G. Mutation profiling in the PIK3CA, TP53, and CDKN2A genes in circulating free DNA and impalpable breast lesions. Ann Diagn Pathol 2019; 39:30-35. [PMID: 30634138 DOI: 10.1016/j.anndiagpath.2018.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 12/21/2018] [Accepted: 12/30/2018] [Indexed: 01/05/2023]
Abstract
Breast impalpable lesions have become a clinical dilemma because they are small, presenting a heterogeneous cellular phenotype. The aim of this study was to evaluate the mutational profile of the PIK3CA, TP53, and CDKN2A genes, comparing the mammary tissue with the respective circulating free DNA (cfDNA). The PIK3CA, TP53, and CDKN2A genes were sequenced (PCR-Sanger) in 58 women with impalpable lesions (49 malignant and 9 benign) with the respective cfDNA. The chi-square or Fisher's exact test was used to evaluate statistical significance between the clinical variables and mutational profile. A total of 51 out of 58 samples generated successful mutation profiles in both breast lesion and cfDNA. Of the 37 mutations detected, 10 (27%) and 16 (43%) mutations were detected in benign and malignant breast lesions, respectively, while 2 (5%) and 9 (24%) were found in cfDNA of women with benign and malignant lesions, respectively. The lymph node involvement with mutations in the PIK3CA in malignant lesions (P = 0.001), and the relationship between mutations in PIK3CA, comparing ductal tumors with benign lesions (P = 0.05), were statistically significant. This study detected different mutations in PIK3CA, TP53, and CDKN2A genes, which represent, in part, the heterogeneity of impalpable lesions. The results confirm that more studies should be conducted on the functional role of cfDNA in the impalpable lesions.
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Affiliation(s)
- Lucas Delmonico
- Circulating Biomarkers Laboratory, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil; Graduate Program in Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil.
| | | | | | | | | | | | - Aline Dos Santos Moreira
- Laboratory of Functional Genomics and Bioinformatics, PTDIS/FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | | | - Maria Helena Faria Ornellas
- Circulating Biomarkers Laboratory, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil; Graduate Program in Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Gilda Alves
- Circulating Biomarkers Laboratory, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil; Graduate Program in Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil.
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Baysa A, Fedorov A, Kondratov K, Ruusalepp A, Minasian S, Galagudza M, Popov M, Kurapeev D, Yakovlev A, Valen G, Kostareva A, Vaage J, Stensløkken KO. Release of Mitochondrial and Nuclear DNA During On-Pump Heart Surgery: Kinetics and Relation to Extracellular Vesicles. J Cardiovasc Transl Res 2018; 12:184-192. [PMID: 30542983 DOI: 10.1007/s12265-018-9848-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/18/2018] [Indexed: 12/12/2022]
Abstract
During heart surgery with cardiopulmonary bypass (CPB), the release of mitochondrial (mtDNA) and nuclear DNA (nDNA) and their association to extracellular vesicles were investigated. In patients undergoing elective coronary artery bypass grafting (CABG, n = 12), blood was sampled before, during, and after surgery from peripheral artery, pulmonary artery, and the coronary sinus. Plasma was separated in three fractions: microvesicles, exosomes, and supernatant. mtDNA and nDNA were measured by qPCR. mtDNA and nDNA levels increased after start of surgery, but before CPB, and increased further during CPB. mtDNA copy number was about 1000-fold higher than nDNA. mtDNA was predominantly localized to the vesicular fractions in plasma, whereas nDNA was predominantly in the supernatant. The amount of free mtDNA increased after surgery. There was no net release or disappearance of DNAs across the pulmonary, systemic, or coronary circulation. Extracellular DNAs, in particular mtDNA, may be important contributors to the whole-body inflammation during CPB.
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Affiliation(s)
- Anton Baysa
- Division of Physiology, Department of Molecular Medicine, Institute of Basic Medical Science, University of Oslo, Postbox 1103, Blindern, 0317, Oslo, Norway
- Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Anton Fedorov
- Almazov National Medical Research Centre, Saint Petersburg, Russia
- Department of Cytology and Histology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Kirill Kondratov
- Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Arno Ruusalepp
- Department of Cardiac Surgery, Tartu University Hospital, Tartu, Estonia
| | - Sarkis Minasian
- Almazov National Medical Research Centre, Saint Petersburg, Russia
| | | | - Maxim Popov
- Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Dmitry Kurapeev
- Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Alexey Yakovlev
- Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Guro Valen
- Division of Physiology, Department of Molecular Medicine, Institute of Basic Medical Science, University of Oslo, Postbox 1103, Blindern, 0317, Oslo, Norway
- Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Anna Kostareva
- Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Jarle Vaage
- Institute of Clinical Medicine, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Kåre-Olav Stensløkken
- Division of Physiology, Department of Molecular Medicine, Institute of Basic Medical Science, University of Oslo, Postbox 1103, Blindern, 0317, Oslo, Norway.
- Center for Heart Failure Research, University of Oslo, Oslo, Norway.
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Rohanizadegan M. Analysis of circulating tumor DNA in breast cancer as a diagnostic and prognostic biomarker. Cancer Genet 2018; 228-229:159-168. [PMID: 29572011 PMCID: PMC6108954 DOI: 10.1016/j.cancergen.2018.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 01/15/2018] [Accepted: 02/16/2018] [Indexed: 12/17/2022]
Abstract
Despite all the advances in diagnosis and treatment of breast cancer, a large number of patients suffer from late diagnosis or recurrence of their disease. Current available imaging modalities do not reveal micrometastasis and tumor biopsy is an invasive method to detect early stage or recurrent cancer, signifying the need for an inexpensive, non-invasive diagnostic modality. Cell-free tumor DNA (ctDNA) has been tried for early detection and targeted therapy of breast cancer, but its diagnostic and prognostic utility is still under investigation. This review summarizes the existing evidence on the use of ctDNA specifically in breast cancer, including detection methods, diagnostic accuracy, role in genetics and epigenetics evaluation of the tumor, and comparison with other biomarkers. Current evidence suggests that increasing levels of ctDNA in breast cancer can be of significant diagnostic value for early detection of breast cancer although the sensitivity and specificity of the methods is still suboptimal. Additionally, ctDNA allows for characterizing the tumor in a non-invasive way and monitor the response to therapy, although discordance of ctDNA results with direct biopsy (i.e. due to tumor heterogeneity) is still considered a notable limitation.
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Affiliation(s)
- Mersedeh Rohanizadegan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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Peng L, Yang Y, Guo R, Mao Y, Xu C, Chen Y, Sun Y, Ma J, Tang L. Relationship between pretreatment concentration of plasma Epstein-Barr virus DNA and tumor burden in nasopharyngeal carcinoma: An updated interpretation. Cancer Med 2018; 7:5988-5998. [PMID: 30378277 PMCID: PMC6308091 DOI: 10.1002/cam4.1858] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/26/2018] [Accepted: 10/15/2018] [Indexed: 12/27/2022] Open
Abstract
Background Pretreatment plasma Epstein‐Barr virus (EBV) DNA is an important tumor marker and prognostic factor in nasopharyngeal carcinoma (NPC). This study aimed to clarify the relationship between plasma EBV DNA level and tumor burden. Materials and Methods Pretreatment tumor burden was measured by radiologically delineated volumes, including nasopharynx tumor volume (GTVnx) and malignant nodes volume (GTVnd); pretreatment level of plasma EBV DNA was quantified by quantitative polymerase chain reaction. The relationship between natural logarithm of EBV DNA (ln‐DNA) and square root of tumor volume (sq‐GTV) was analyzed by Pearson correlation coefficient and partial correlation coefficient. Correlations in subgroups of tumor and nodal stages were also analyzed. A linear regression model was constructed to evaluate the contribution of tumor volumes to plasma EBV DNA. The prognostic effects of EBV DNA independent of tumor burden were evaluated. Results Two thousand two hundred and forty nine nonmetastatic NPC patients with detectable plasma EBV DNA were included in correlation analyses. Ln‐DNA showed significant correlation with sq‐GTVnx (r = 0.171) and sq‐GTVnd (r = 0.339) separately. Together, sq‐GTVnx and sq‐GTVnd could only explain 12.9% of the ln‐DNA. Tumor and nodal stages of disease could clearly influence the strength of relationship in subgroup analysis. After excluding confounding volume information, EBV DNA still can predict death and distant metastasis, but not locoregional relapse. Conclusion This study suggests that plasma EBV DNA is not only an index of tumor burden, but may also reflect other tumor features, such as accessibility to circulation, angiogenesis, tumor cell kinetics, metabolic activity, and metastatic potential, among others.
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Affiliation(s)
- Liang Peng
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapySun Yat‐sen University Cancer CentreGuangzhouChina
| | - Yi Yang
- Department of Medical OncologyGuizhou Provincial People’s HospitalGuiyangChina
| | - Rui Guo
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapySun Yat‐sen University Cancer CentreGuangzhouChina
| | - Yan‐Ping Mao
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapySun Yat‐sen University Cancer CentreGuangzhouChina
| | - Cheng Xu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapySun Yat‐sen University Cancer CentreGuangzhouChina
| | - Yu‐Pei Chen
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapySun Yat‐sen University Cancer CentreGuangzhouChina
| | - Ying Sun
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapySun Yat‐sen University Cancer CentreGuangzhouChina
| | - Jun Ma
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapySun Yat‐sen University Cancer CentreGuangzhouChina
| | - Ling‐Long Tang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapySun Yat‐sen University Cancer CentreGuangzhouChina
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Grölz D, Hauch S, Schlumpberger M, Guenther K, Voss T, Sprenger-Haussels M, Oelmüller U. Liquid Biopsy Preservation Solutions for Standardized Pre-Analytical Workflows-Venous Whole Blood and Plasma. CURRENT PATHOBIOLOGY REPORTS 2018; 6:275-286. [PMID: 30595972 PMCID: PMC6290703 DOI: 10.1007/s40139-018-0180-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW Liquid biopsy analyses based on circulating cell-free nucleic acids, circulating tumor cells or other diseased cells from organs, and exosomes or other microvesicles in blood offer new means for non-invasive diagnostic applications. The main goal of this review is to explain the importance of preserving whole blood specimens after blood draw for use as liquid biopsies, and to summarize preservation solutions that are currently available. RECENT FINDINGS Despite the great potential of liquid biopsies for diagnostics and disease management, besides non-invasive prenatal testing (NIPT), only a few liquid biopsy applications are fully implemented for routine in vitro diagnostic testing. One major barrier is the lack of standardized pre-analytical workflows, including the collection of consistent quality blood specimens and the generation of good-quality plasma samples therefrom. Broader use of liquid biopsies in clinical routine applications therefore requires improved pre-analytical procedures to enable high-quality specimens to obtain unbiased analyte profiles (DNA, RNA, proteins, etc.) as they are in the patient's body. SUMMARY A growing number of stabilizing reagents and dedicated blood collection tubes are available for the post-collection preservation of circulating cell-free DNA (ccfDNA) profiles in whole blood. In contrast, solutions for the preservation of circulating tumor cells (CTC) that enable both, enumeration and molecular analyses are rare. Solutions for extracellular vesicle (EV) populations, including exosomes, do not yet exist.
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Affiliation(s)
- Daniel Grölz
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | - Siegfried Hauch
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | | | - Kalle Guenther
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | - Thorsten Voss
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | | | - Uwe Oelmüller
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
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Panditharatna E, Kilburn LB, Aboian MS, Kambhampati M, Gordish-Dressman H, Magge SN, Gupta N, Myseros JS, Hwang EI, Kline C, Crawford JR, Warren KE, Cha S, Liang WS, Berens ME, Packer RJ, Resnick AC, Prados M, Mueller S, Nazarian J. Clinically Relevant and Minimally Invasive Tumor Surveillance of Pediatric Diffuse Midline Gliomas Using Patient-Derived Liquid Biopsy. Clin Cancer Res 2018; 24:5850-5859. [PMID: 30322880 DOI: 10.1158/1078-0432.ccr-18-1345] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/27/2018] [Accepted: 08/30/2018] [Indexed: 01/07/2023]
Abstract
PURPOSE Pediatric diffuse midline glioma (DMG) are highly malignant tumors with poor clinical outcomes. Over 70% of patients with DMG harbor the histone 3 p.K27M (H3K27M) mutation, which correlates with a poorer clinical outcome, and is also used as a criterion for enrollment in clinical trials. Because complete surgical resection of DMG is not an option, biopsy at presentation is feasible, but rebiopsy at time of progression is rare. While imaging and clinical-based disease monitoring is the standard of care, molecular-based longitudinal characterization of these tumors is almost nonexistent. To overcome these hurdles, we examined whether liquid biopsy allows measurement of disease response to precision therapy. EXPERIMENTAL DESIGN We established a sensitive and specific methodology that detects major driver mutations associated with pediatric DMGs using droplet digital PCR (n = 48 subjects, n = 110 specimens). Quantification of circulating tumor DNA (ctDNA) for H3K27M was used for longitudinal assessment of disease response compared with centrally reviewed MRI data. RESULTS H3K27M was identified in cerebrospinal fluid (CSF) and plasma in 88% of patients with DMG, with CSF being the most enriched for ctDNA. We demonstrated the feasibility of multiplexing for detection of H3K27M, and additional driver mutations in patient's tumor and matched CSF, maximizing the utility of a single source of liquid biome. A significant decrease in H3K27M plasma ctDNA agreed with MRI assessment of tumor response to radiotherapy in 83% (10/12) of patients. CONCLUSIONS Our liquid biopsy approach provides a molecularly based tool for tumor characterization, and is the first to indicate clinical utility of ctDNA for longitudinal surveillance of DMGs.
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Affiliation(s)
- Eshini Panditharatna
- Rese arch Center for Genetic Medicine, Children's National Health System, Washington, D.C.,Institute for Biomedical Sciences, George Washington University School of Medicine and Health Sciences, Washington, D.C
| | - Lindsay B Kilburn
- Center for Cancer and Blood Disorders, Children's National Health System, Washington D.C.,Brain Tumor Institute, Children's National Health System, Washington, D.C
| | - Mariam S Aboian
- Departments of Neurology, Pediatrics and Neurosurgery, University of California, San Francisco School of Medicine, San Francisco, California
| | - Madhuri Kambhampati
- Rese arch Center for Genetic Medicine, Children's National Health System, Washington, D.C
| | | | - Suresh N Magge
- Division of Neurosurgery, Children's National Health System, Washington, D.C
| | - Nalin Gupta
- Department of Neurological Surgery and Pediatrics, University of California San Francisco, San Francisco, California
| | - John S Myseros
- Division of Neurosurgery, Children's National Health System, Washington, D.C
| | - Eugene I Hwang
- Center for Cancer and Blood Disorders, Children's National Health System, Washington D.C.,Brain Tumor Institute, Children's National Health System, Washington, D.C
| | - Cassie Kline
- Pediatric Hematology-Oncology and Neurology, UCSF Benioff Children's Hospital, San Francisco, California
| | - John R Crawford
- Department of Neurosciences, UC San Diego School of Medicine, La Jolla, California
| | | | - Soonmee Cha
- Department of Radiology, University of California, San Francisco School of Medicine, San Francisco, California
| | - Winnie S Liang
- Translational Genomics Research Institute, Phoenix, Arizona
| | | | - Roger J Packer
- Brain Tumor Institute, Children's National Health System, Washington, D.C
| | - Adam C Resnick
- Center for Data-Driven Discovery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael Prados
- Departments of Neurology, Pediatrics and Neurosurgery, University of California, San Francisco School of Medicine, San Francisco, California
| | - Sabine Mueller
- Departments of Neurology, Pediatrics and Neurosurgery, University of California, San Francisco School of Medicine, San Francisco, California
| | - Javad Nazarian
- Rese arch Center for Genetic Medicine, Children's National Health System, Washington, D.C. .,Center for Cancer and Blood Disorders, Children's National Health System, Washington D.C.,Brain Tumor Institute, Children's National Health System, Washington, D.C.,Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C
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Nagler M, Insam H, Pietramellara G, Ascher-Jenull J. Extracellular DNA in natural environments: features, relevance and applications. Appl Microbiol Biotechnol 2018; 102:6343-6356. [PMID: 29858957 PMCID: PMC6061472 DOI: 10.1007/s00253-018-9120-4] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/15/2018] [Accepted: 05/19/2018] [Indexed: 01/13/2023]
Abstract
Extracellular DNA (exDNA) is abundant in many habitats, including soil, sediments, oceans and freshwater as well as the intercellular milieu of metazoa. For a long time, its origin has been assumed to be mainly lysed cells. Nowadays, research is collecting evidence that exDNA is often secreted actively and is used to perform a number of tasks, thereby offering an attractive target or tool for biotechnological, medical, environmental and general microbiological applications. The present review gives an overview on the main research areas dealing with exDNA, depicts its inherent origins and functions and deduces the potential of existing and emerging exDNA-based applications. Furthermore, it provides an overview on existing extraction methods and indicates common pitfalls that should be avoided whilst working with exDNA.
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Affiliation(s)
- Magdalena Nagler
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria.
| | - Heribert Insam
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria
| | - Giacomo Pietramellara
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università degli Studi di Firenze, Piazzale delle Cascine 18, 50144, Florence, Italy
| | - Judith Ascher-Jenull
- Universität Innsbruck, Institute of Microbiology, Technikerstr. 25d, 6020, Innsbruck, Austria
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Università degli Studi di Firenze, Piazzale delle Cascine 18, 50144, Florence, Italy
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50
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Nevel KS, Wilcox JA, Robell LJ, Umemura Y. The Utility of Liquid Biopsy in Central Nervous System Malignancies. Curr Oncol Rep 2018; 20:60. [PMID: 29876874 DOI: 10.1007/s11912-018-0706-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW Liquid biopsy is a sampling of tumor cells or tumor nucleotides from biofluids. This review explores the roles of liquid biopsy for evaluation and management of patients with primary and metastatic CNS malignancies. RECENT FINDINGS Circulating tumor cell (CTC) detection has emerged as a relatively sensitive and specific tool for diagnosing leptomeningeal metastases. Circulating tumor DNA (ctDNA) detection can effectively demonstrate genetic markup of CNS tumors in the cerebrospinal fluid, though its role in managing CNS malignancies is less well-defined. The value of micro RNA (miRNA) detection in CNS malignancies is unclear at this time. Current standard clinical tools for the diagnosis and monitoring of CNS malignancies have limitations, and liquid biopsy may help address clinical practice and knowledge gaps. Liquid biopsy offers exciting potential for the diagnosis, prognosis, and treatment of CNS malignancies, but each modality needs to be studied in large prospective trials to better define their use.
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Affiliation(s)
- Kathryn S Nevel
- Department of Neurology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Jessica A Wilcox
- Department of Neurology, NewYork-Presbyterian Hospital, Weill Cornell Medical Center, 520 E 70th St, Starr Pavilion 607, New York, NY, 10021, USA
| | - Lindsay J Robell
- Department of Neurology, University of Michigan, 1914 Taubman Center, 1500 E. Medical Center Dr., SPC 5316, Ann Arbor, MI, 48109-5316, USA
| | - Yoshie Umemura
- Department of Neurology, University of Michigan, 1914 Taubman Center, 1500 E. Medical Center Dr., SPC 5316, Ann Arbor, MI, 48109-5316, USA.
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