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Rodríguez-Ces AM, Rapado-González Ó, Salgado-Barreira Á, Santos MA, Aroso C, Vinhas AS, López-López R, Suárez-Cunqueiro MM. Liquid Biopsies Based on Cell-Free DNA Integrity as a Biomarker for Cancer Diagnosis: A Meta-Analysis. Diagnostics (Basel) 2024; 14:1465. [PMID: 39061602 PMCID: PMC11276058 DOI: 10.3390/diagnostics14141465] [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: 05/27/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Liquid biopsies have been identified as a viable source of cancer biomarkers. We aim to evaluate the diagnostic accuracy of cell-free DNA integrity (cfDI) in liquid biopsies for cancer. A comprehensive literature search was conducted through PubMed, Embase, Web of Science, and Cochrane Library up to June 2024. Seventy-two study units from forty-six studies, comprising 4286 cancer patients, were identified and evaluated. The Quality Assessment for Studies of Diagnostic Accuracy-2 (QUADAS-2) was used to assess study quality. Meta-regression analysis was employed to investigate the underlying factors contributing to heterogeneity, alongside an evaluation of publication bias. The bivariate random-effect model was utilized to compute the primary diagnostic outcomes and their corresponding 95% confidence intervals (CIs). The pooled sensitivity, specificity, and positive and negative likelihood ratios of cfDI in cancer diagnosis were 0.70 and 0.77, 3.26 and 0.34, respectively. The overall area under the curve was 0.84, with a diagnostic odds ratio of 10.63. This meta-analysis suggested that the cfDI index has a promising potential as a non-invasive and accurate diagnostic tool for cancer. Study registration: The study was registered at PROSPERO (reference No. CRD42021276290).
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Affiliation(s)
- Ana María Rodríguez-Ces
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain; (A.M.R.-C.); (Ó.R.-G.)
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Óscar Rapado-González
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain; (A.M.R.-C.); (Ó.R.-G.)
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/CI-IPOP@RISE (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Ángel Salgado-Barreira
- Department of Public Health, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER Epidemiology and Public Health—CIBERESP), 28029 Madrid, Spain
- Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain
| | - María Arminda Santos
- UNIPRO-Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, 4585-116 Gandra, Portugal; (M.A.S.); (C.A.); (A.S.V.)
| | - Carlos Aroso
- UNIPRO-Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, 4585-116 Gandra, Portugal; (M.A.S.); (C.A.); (A.S.V.)
| | - Ana Sofia Vinhas
- UNIPRO-Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, 4585-116 Gandra, Portugal; (M.A.S.); (C.A.); (A.S.V.)
| | - Rafael López-López
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), 15706 Santiago de Compostela, Spain
| | - María Mercedes Suárez-Cunqueiro
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain; (A.M.R.-C.); (Ó.R.-G.)
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain;
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), 15706 Santiago de Compostela, Spain
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Devonshire A, Jones G, Gonzalez AF, Kofanova O, Trouet J, Pinzani P, Gelmini S, Bonin S, Foy C. Interlaboratory evaluation of quality control methods for circulating cell-free DNA extraction. N Biotechnol 2023; 78:13-21. [PMID: 37730172 DOI: 10.1016/j.nbt.2023.09.005] [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: 04/24/2023] [Revised: 09/07/2023] [Accepted: 09/17/2023] [Indexed: 09/22/2023]
Abstract
Analysis of circulating cell-free DNA (ccfDNA) isolated from liquid biopsies is rapidly being implemented into clinical practice. However, diagnostic accuracy is significantly impacted by sample quality and standardised approaches for assessing the quality of ccfDNA are not yet established. In this study we evaluated the application of nucleic acid "spike-in" control materials to aid quality control (QC) and standardisation of cfDNA isolation for use in in vitro diagnostic assays. We describe an approach for the design and characterisation of in-process QC materials, illustrating it with a spike-in material containing an exogenous Arabidopsis sequence and DNA fragments approximating to ccfDNA and genomic DNA lengths. Protocols for inclusion of the spike-in material in plasma ccfDNA extraction and quantification of its recovery by digital PCR (dPCR) were assessed for their suitability for process QC in an inter-laboratory study between five expert laboratories, using a range of blood collection devices and ccfDNA extraction methods. The results successfully demonstrated that spiking plasmid-derived material into plasma did not deleteriously interfere with endogenous ccfDNA recovery. The approach performed consistently across a range of commonly-used extraction protocols and was able to highlight differences in efficiency and variability between the methods, with the dPCR quantification assay performing with good repeatability (generally CV <5%). We conclude that initial findings demonstrate that this approach appears "fit for purpose" and spike-in recovery can be combined with other extraction QC metrics for monitoring the performance of a process over time, or in the context of external quality assessment.
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Affiliation(s)
- Alison Devonshire
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK.
| | - Gerwyn Jones
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK
| | - Ana Fernandez Gonzalez
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK
| | - Olga Kofanova
- Integrated BioBank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), 1, rue Louis Rech, L-3555 Dudelange, Luxembourg
| | - Johanna Trouet
- Integrated BioBank of Luxembourg (IBBL), Luxembourg Institute of Health (LIH), 1, rue Louis Rech, L-3555 Dudelange, Luxembourg
| | - Pamela Pinzani
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
| | - Stefania Gelmini
- Department of Clinical and Experimental Biomedical Sciences, University of Florence, Florence, Italy
| | - Serena Bonin
- DSM-Dept. Medical Sciences, University of Trieste, Trieste, Italy
| | - Carole Foy
- Molecular and Cell Biology Team, National Measurement Laboratory (NML), LGC, Teddington, Middlesex, UK
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Ma J, Teng Y, Youming H, Tao X, Fan Y. The Value of Cell-Free Circulating DNA Profiling in Patients with Skin Diseases. Methods Mol Biol 2023; 2695:247-262. [PMID: 37450124 DOI: 10.1007/978-1-0716-3346-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Liquid biopsy, also known as fluid biopsy or fluid-phase biopsy, is the sampling and analysis of the blood, cerebrospinal fluid, saliva, pleural fluid, ascites, and urine. Compared with tissue biopsy, liquid biopsy technology has the advantages of being noninvasive, having strong repeatability, enabling early diagnosis, dynamic monitoring, and overcoming tumor heterogeneity. However, interest in cfDNA and skin diseases has not expanded until recently. In this review, we present an overview of the literature related to the basic biology of cfDNA in the field of dermatology as a biomarker for early diagnosis, monitoring disease activity, predicting progression, and treatment response.
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Affiliation(s)
- Jingwen Ma
- Medical Cosmetic Center, Shanghai Skin Disease Hospital, Tongji University, Shanghai, People's Republic of China
| | - Yan Teng
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Huang Youming
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Xiaohua Tao
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Yibin Fan
- Health Management Center, Department of Dermatology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China.
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Rapado-González Ó, López-Cedrún JL, Lago-Lestón RM, Abalo A, Rubin-Roger G, Salgado-Barreira Á, López-López R, Muinelo-Romay L, Suárez-Cunqueiro MM. Integrity and quantity of salivary cell-free DNA as a potential molecular biomarker in oral cancer: A preliminary study. J Oral Pathol Med 2022; 51:429-435. [PMID: 35416334 PMCID: PMC9322526 DOI: 10.1111/jop.13299] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
Background Differences in cell‐free DNA (cfDNA) fragments have been described as a valuable tool to distinguish cancer patients from healthy individuals. We aim to investigate the concentration and integrity of cfDNA fragments in saliva from oral squamous cell carcinoma (OSCC) patients and healthy individuals in order to explore their value as diagnostic biomarkers. Methods Saliva samples were collected from a total of 34 subjects (19 OSCC patients and 15 healthy controls). The total concentration of salivary cfDNA (scfDNA) was determined using a fluorometry method and quantitative real‐time polymerase chain reaction (qPCR). To evaluate the scfDNA quantity and integrity, qPCR targeting Arthobacter luteus (ALU) sequences at three amplicons of different lengths (60, 115, and 247 bp, respectively) was carried out. ScfDNA integrity indexes (ALU115/ALU60 and ALU247/ALU60) were calculated as the ratio between the absolute concentration of the longer amplicons 115 bp and 247 bp and the total scfDNA amount (amplicon 60 bp). Results The total scfDNA concentration (ALU60) was higher in OSCC than in healthy donors, but this trend was not statistically significant. The medians of scfDNA integrity indexes, ALU115/ALU60 and ALU247/ALU60, were significantly higher in OSCC, showing area under the curve values of 0.8211 and 0.7018, respectively. Conclusion Our preliminary results suggest that scfDNA integrity indexes (ALU115/ALU60 and ALU247/ALU60) have potential as noninvasive diagnostic biomarkers for OSCC.
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Affiliation(s)
- Óscar Rapado-González
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Cáncer CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - José Luis López-Cedrún
- Department of Oral and Maxillofacial Surgery, Complexo Hospitalario Universitario de A Coruña SERGAS, A Coruña, Spain
| | - Ramón Manuel Lago-Lestón
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Alicia Abalo
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Guillermo Rubin-Roger
- Department of Oral and Maxillofacial Surgery, Complexo Hospitalario Universitario de A Coruña SERGAS, A Coruña, Spain
| | - Ángel Salgado-Barreira
- Department of Preventive Medicine, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Epidemiology, Health Public and Health Technology Assessment, Health Research Institute of Santiago de Compostela (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Rafael López-López
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
| | - Laura Muinelo-Romay
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago IDIS, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Cáncer CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - María Mercedes Suárez-Cunqueiro
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Cáncer CIBERONC, Instituto de Salud Carlos III, Madrid, Spain.,Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain
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Malignant pleural effusions for cancer genotyping: A matter of trans-pleural traffic of cell-free tumor DNA. Mol Cell Probes 2022; 61:101793. [DOI: 10.1016/j.mcp.2022.101793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/29/2022] [Accepted: 01/29/2022] [Indexed: 11/19/2022]
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The relevance of liquid biopsy in surgical oncology: The application of perioperative circulating nucleic acid dynamics in improving patient outcomes. Surgeon 2021; 20:e163-e173. [PMID: 34362650 DOI: 10.1016/j.surge.2021.06.006] [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: 01/06/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Liquid biopsy is gaining increasing clinical utility in the management of cancer patients. The main components of a liquid biopsy are circulating nucleic acids, circulating tumour cells and extracellular vesicles such as exosomes. Circulating nucleic acids including cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) in particular have been the focus of recent attention as they have demonstrated excellent potential in cancer screening, provision of prognostic information and in genomic profiling of a tumour without the need for repeated tissue biopsies. The aim of this review was to explore the current evidence in relation to the use of liquid biopsy in the perioperative setting and identify ways in which liquid biopsy may be applied in the future. METHODS This narrative review is based on a comprehensive literature search up to the 1st of June 2020 for papers relevant to the application of liquid biopsy in surgical oncology, focusing particularly on the perioperative period. RESULTS Recent evidence has demonstrated that perioperative liquid biopsy can accurately stratify patients' risk of recurrence compared to conventional biomarkers. Attention to the perioperative dynamics of liquid biopsy components can potentially provide new understanding of the complex relationship between surgery and cancer outcome. In addition, careful evaluation of liquid biopsy components in the perioperative window may provide important diagnostic and therapeutic information for cancer patients. CONCLUSION The rapidly evolving concept of the liquid biopsy has the potential to become the cornerstone for decision making around surveillance and adjuvant therapies the era of personalised medicine.
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Russo A, Incorvaia L, Del Re M, Malapelle U, Capoluongo E, Gristina V, Castiglia M, Danesi R, Fassan M, Giuffrè G, Gori S, Marchetti A, Normanno N, Pinto C, Rossi G, Santini D, Sartore-Bianchi A, Silvestris N, Tagliaferri P, Troncone G, Cinieri S, Beretta GD. The molecular profiling of solid tumors by liquid biopsy: a position paper of the AIOM-SIAPEC-IAP-SIBioC-SIC-SIF Italian Scientific Societies. ESMO Open 2021; 6:100164. [PMID: 34091263 PMCID: PMC8182269 DOI: 10.1016/j.esmoop.2021.100164] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023] Open
Abstract
The term liquid biopsy (LB) refers to the use of various biological fluids as a surrogate for neoplastic tissue to achieve information for diagnostic, prognostic and predictive purposes. In the current clinical practice, LB is used for the identification of driver mutations in circulating tumor DNA derived from both tumor tissue and circulating neoplastic cells. As suggested by a growing body of evidence, however, there are several clinical settings where biological samples other than tissue could be used in the routine practice to identify potentially predictive biomarkers of either response or resistance to targeted treatments. New applications are emerging as useful clinical tools, and other blood derivatives, such as circulating tumor cells, circulating tumor RNA, microRNAs, platelets, extracellular vesicles, as well as other biofluids such as urine and cerebrospinal fluid, may be adopted in the near future. Despite the evident advantages compared with tissue biopsy, LB still presents some limitations due to both biological and technological issues. In this context, the absence of harmonized procedures corresponds to an unmet clinical need, ultimately affecting the rapid implementation of LB in clinical practice. In this position paper, based on experts’ opinions, the AIOM–SIAPEC-IAP–SIBIOC–SIF Italian Scientific Societies critically discuss the most relevant technical issues of LB, the current and emerging evidences, with the aim to optimizing the applications of LB in the clinical setting. In the current clinical practice LB is used for the identification of driver mutations in circulating tumor DNA (ctDNA). New applications in tumors other than non-small-cell lung cancer (NSCLC) are emerging as useful clinical tools. Other blood derivatives, together with other biofluids, are an active field of research and may be adopted in the near future. Despite the evident advantages, liquid biopsy still presents limitations due to both biological and technological issues. Standardization of the procedures needs to be addressed to ensure widespread implementation in clinical practice.
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Affiliation(s)
- A Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy.
| | - L Incorvaia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - M Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - U Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - E Capoluongo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; CEINGE, Biotecnologie Avanzate, Naples, Italy
| | - V Gristina
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - M Castiglia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - R Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - M Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy; Veneto Institute of Oncology (IOV-IRCCS), Padua, Italy
| | - G Giuffrè
- Department of Human Pathology in Adult and Developmental Age 'Gaetano Barresi', Section of Pathology, University of Messina, Messina, Italy
| | - S Gori
- Department of Oncology, IRCCS Ospedale Sacro Cuore Don Calabria, Negrar di Valpolicella, Italy
| | - A Marchetti
- Center of Predictive Molecular Medicine, University-Foundation, CeSI Biotech Chieti, Chieti, Italy
| | - N Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | - C Pinto
- Medical Oncology Unit, Clinical Cancer Centre, IRCCS-AUSL di Reggio Emilia, Reggio Emilia, Italy
| | - G Rossi
- Pathology Unit, Ospedale Santa Maria Delle Croci, Ravenna, Italy
| | - D Santini
- Department of Medical Oncology, University Campus Biomedico, Rome, Italy
| | - A Sartore-Bianchi
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - N Silvestris
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori 'Giovanni Paolo II' of Bari, Bari, Italy; Department of Biomedical Sciences and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - P Tagliaferri
- Medical and Translational Oncology Unit, Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy
| | - G Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - S Cinieri
- Medical Oncology Division and Breast Unit, Senatore Antonio Perrino Hospital, ASL Brindisi, Brindisi, Italy
| | - G D Beretta
- Department of Oncology, Humanitas Gavazzeni, Bergamo, Italy
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Feng SN, Cen XT, Tan R, Wei SS, Sun LD. The prognostic value of circulating tumor DNA in patients with melanoma: A systematic review and meta-analysis. Transl Oncol 2021; 14:101072. [PMID: 33744725 PMCID: PMC7985561 DOI: 10.1016/j.tranon.2021.101072] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/15/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has been investigated as a potential prognostic biomarker to evaluate the therapeutic efficacy and disease progression in melanoma patients, yet results remain inconclusive. The purpose of this study was to illustrate the prognostic value of ctDNA in melanoma. OBJECTIVES To describe the clinical prognostic value of ctDNA for melanoma patients. METHODS Searched for eligible articles from Pubmed, Web of Science and Embase. Pooled hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated to evaluate the association between ctDNA at baseline or during treatment and overall survival (OS) and progression-free survival (PFS). RESULTS A total of 9 articles were obtained, involving 617 melanoma patients. The pooled HRs revealed that compared with baseline undetectable ctDNA patients, detectable ctDNA was highly correlated with poor OS (HR 2.91, 95% CI: 2.22-3.82; p < 0.001) and PFS (HR 2.75, 95% CI: 1.98-3.83; p < 0.001). A meta-analysis of these adjusted HRs was performed and confirmed that ctDNA collected at baseline was associated with poorer OS/PFS (OS: HR 3.00, 95% CI 2.19-4.11, p < 0.001/PFS: HR 2.68, 95% CI 1.77-4.06, p < 0.001). During treatment, a significant association was shown between ctDNA and poorer OS/PFS (OS: HR 6.26, 95% CI 2.48-15.80, p < 0.001; PFS: HR 4.93, 95% CI 2.36-10.33, p < 0.001). CONCLUSION Investigation and application of ctDNA will improve "liquid biopsy" and play a role in early prediction, monitoring disease progression and precise adjusting treatment strategies in melanoma patients.
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Affiliation(s)
- S N Feng
- Department of Dermatology, Zhujiang Hospital, Southern Medical University, No. 253 Gongye Avenue, Guangzhou, China
| | - X T Cen
- Department of Dermatology, Zhujiang Hospital, Southern Medical University, No. 253 Gongye Avenue, Guangzhou, China
| | - R Tan
- Department of Dermatology, Zhujiang Hospital, Southern Medical University, No. 253 Gongye Avenue, Guangzhou, China
| | - S S Wei
- Department of Dermatology, Zhujiang Hospital, Southern Medical University, No. 253 Gongye Avenue, Guangzhou, China
| | - L D Sun
- Department of Dermatology, Zhujiang Hospital, Southern Medical University, No. 253 Gongye Avenue, Guangzhou, China; Departmet of Dermatology, the Fifth Affiliated Hospital of Southern Medical University, No.566 Congcheng Avenue, Guangzhou, China.
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Mokánszki A, Bádon ES, Mónus A, Tóth L, Bittner N, Méhes G. Cell-free DNA From Pleural Effusion Samples: Is It Right for Molecular Testing in Lung Adenocarcinoma? Pathol Oncol Res 2021; 27:613071. [PMID: 34257581 PMCID: PMC8262152 DOI: 10.3389/pore.2021.613071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/19/2021] [Indexed: 12/03/2022]
Abstract
Pathogenic molecular features gained specific significance in therapeutic decisions in lung carcinoma in the past decade. Initial and follow up genetic testing requres appropriate amounts and quality of tumor derived DNA, but tumor sampling, especially for disease monitoring is generally limited. Further to the peripheral blood (PB), samples from pleural fluid, accumulating in diverse lung processes might serve as an alternative source for cell-free DNA (cfDNA) for genetic profiling. In our study, cfDNA isolated from the pleural effusion and from the PB, and genomic DNA (gDNA) obtained from tissue/cellular samples were analyzed and compared from altogether 65 patients with pulmonary disease, including 36 lung adenocarcinomas. The quantity of effusion cfDNA yield appeared to be significantly higher compared to that from simultaneously collected PB plasma (23.2 vs. 4.8 ng/μl, p < 0.05). Gene mutations could be safely demonstrated from the effusion cfDNA fraction obtained from adenocarcinoma patients, 3/36 EGFR, 9/36 KRAS and 1/36 BRAF gene variants were detected. In this series, 9/13 samples showed an effusion+/plasma-mutational status, while only 1/13 samples presented with the opposite findings (effusion-/plasma+). gDNA analysis from sediment cell blocks from the identical effusion sample was surprisingly ineffective for lung adenocarcinoma profiling due to the low DNA yield. In conclusion, the cell free supernatant of pleural effusions appears to concentrate cancer derived cfDNA and seems to be particularly suitable for serial genotyping of pulmonary adenocarcinoma.
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Affiliation(s)
- Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Emese Sarolta Bádon
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Anikó Mónus
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Tóth
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Nóra Bittner
- Department of Pulmonology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Hinestrosa JP, Searson DJ, Lewis JM, Kinana A, Perrera O, Dobrovolskaia I, Tran K, Turner R, Balcer HI, Clark I, Bodkin D, Hoon DSB, Krishnan R. Simultaneous Isolation of Circulating Nucleic Acids and EV-Associated Protein Biomarkers From Unprocessed Plasma Using an AC Electrokinetics-Based Platform. Front Bioeng Biotechnol 2020; 8:581157. [PMID: 33224932 PMCID: PMC7674311 DOI: 10.3389/fbioe.2020.581157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/29/2020] [Indexed: 01/04/2023] Open
Abstract
The power of personalized medicine is based on a deep understanding of cellular and molecular processes underlying disease pathogenesis. Accurately characterizing and analyzing connections between these processes is dependent on our ability to access multiple classes of biomarkers (DNA, RNA, and proteins)—ideally, in a minimally processed state. Here, we characterize a biomarker isolation platform that enables simultaneous isolation and on-chip detection of cell-free DNA (cfDNA), extracellular vesicle RNA (EV-RNA), and EV-associated proteins in unprocessed biological fluids using AC Electrokinetics (ACE). Human biofluid samples were flowed over the ACE microelectrode array (ACE chip) on the Verita platform while an electrical signal was applied, inducing a field that reversibly captured biomarkers onto the microelectrode array. Isolated cfDNA, EV-RNA, and EV-associated proteins were visualized directly on the chip using DNA and RNA specific dyes or antigen-specific, directly conjugated antibodies (CD63, TSG101, PD-L1, GPC-1), respectively. Isolated material was also eluted off the chip and analyzed downstream by multiple methods, including PCR, RT-PCR, next-generation sequencing (NGS), capillary electrophoresis, and nanoparticle size characterization. The detection workflow confirmed the capture of cfDNA, EV-RNA, and EV-associated proteins from human biofluids on the ACE chip. Tumor specific variants and the mRNAs of housekeeping gene PGK1 were detected in cfDNA and RNA isolated directly from chips in PCR, NGS, and RT-PCR assays, demonstrating that high-quality material can be isolated from donor samples using the isolation workflow. Detection of the luminal membrane protein TSG101 with antibodies depended on membrane permeabilization, consistent with the presence of vesicles on the chip. Protein, morphological, and size characterization revealed that these vesicles had the characteristics of EVs. The results demonstrated that unprocessed cfDNA, EV-RNA, and EV-associated proteins can be isolated and simultaneously fluorescently analyzed on the ACE chip. The compatibility with established downstream technologies may also allow the use of the platform as a sample preparation method for workflows that could benefit from access to unprocessed exosomal, genomic, and proteomic biomarkers.
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Affiliation(s)
| | | | - Jean M Lewis
- Biological Dynamics, Inc., San Diego, CA, United States
| | - Alfred Kinana
- Biological Dynamics, Inc., San Diego, CA, United States
| | | | | | - Kevin Tran
- Departments of Translational Molecular Medicine and Sequence Center, John Wayne Cancer Institute, Santa Monica, CA, United States
| | - Robert Turner
- Biological Dynamics, Inc., San Diego, CA, United States
| | | | - Iryna Clark
- Biological Dynamics, Inc., San Diego, CA, United States
| | - David Bodkin
- Cancer Center Oncology Medical Group, La Mesa, CA, United States
| | - Dave S B Hoon
- Departments of Translational Molecular Medicine and Sequence Center, John Wayne Cancer Institute, Santa Monica, CA, United States
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Two Reliable Methodical Approaches for Non-Invasive RHD Genotyping of a Fetus from Maternal Plasma. Diagnostics (Basel) 2020; 10:diagnostics10080564. [PMID: 32764529 PMCID: PMC7460148 DOI: 10.3390/diagnostics10080564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/27/2022] Open
Abstract
Noninvasive fetal RHD genotyping is an important tool for predicting RhD incompatibility between a pregnant woman and a fetus. This study aimed to assess a methodological approach other than the commonly used one for noninvasive fetal RHD genotyping on a representative set of RhD-negative pregnant women. The methodology must be accurate, reliable, and broadly available for implementation into routine clinical practice. A total of 337 RhD-negative pregnant women from the Czech Republic region were tested in this study. The fetal RHD genotype was assessed using two methods: real-time PCR and endpoint quantitative fluorescent (QF) PCR. We used exon-7-specific primers from the RHD gene, along with internal controls. Plasma samples were analyzed and measured in four/two parallel reactions to determine the accuracy of the RHD genotyping. The RHD genotype was verified using DNA analysis from a newborn buccal swab. Both methods showed an excellent ability to predict the RHD genotype. Real-time PCR achieved its greatest accuracy of 98.6% (97.1% sensitivity and 100% specificity (95% CI)) if all four PCRs were positive/negative. The QF PCR method also achieved its greatest accuracy of 99.4% (100% sensitivity and 98.6% specificity (95% CI)) if all the measurements were positive/negative. Both real-time PCR and QF PCR were reliable methods for precisely assessing the fetal RHD allele from the plasma of RhD-negative pregnant women.
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12
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Ren S, Ren XD, Guo LF, Qu XM, Shang MY, Dai XT, Huang Q. Urine cell-free DNA as a promising biomarker for early detection of non-small cell lung cancer. J Clin Lab Anal 2020; 34:e23321. [PMID: 32281142 PMCID: PMC7439414 DOI: 10.1002/jcla.23321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/26/2022] Open
Abstract
Background While blood‐derived cell‐free DNA has been shown to be a candidate biomarker able to provide diagnostic and prognostic insight in cancer patients, little is known regarding the potential application of urine cell‐free DNA (ucfDNA) in diagnosis of cancer. Thus, the aim of this study was to investigate ucfDNA concentration and integrity index as potential biomarkers for early detection of non‐small‐cell lung cancer (NSCLC). Methods Urine samples were collected from 35 healthy controls and 55 NSCLC patients at various tumor node metastasis (TNM) stages. Two long interspersed nuclear element 1 (LINE1) fragments (LINE1‐97 and 266 bp) were quantified via quantitative real‐time PCR (qPCR). DNA integrity index was calculated as the ratio of LINE1‐266/LINE‐97. Results LINE1 fragments concentrations of ucfDNA (LINE1‐97, 266 bp) were significantly higher in NSCLC patients with stage III/IV than in stage I/II and in healthy controls. The receiver operating characteristic (ROC) curves for discriminating patients with stage III/IV from healthy controls had areas under the curves (AUC) of 0.84 and 0.886, respectively. Moreover, ucfDNA integrity LINE1‐266/97 was significantly higher in patients with stage III/IV than in stage I/II and in healthy controls. The AUC of ROC curve for discriminating patients with stage III/IV from healthy controls was 0.800. Furthermore, LINE1‐266 fragment concentration was significantly higher in lymph node metastasis (LNM)‐positive patients relative to LNM‐negative patients. The ROC curve for discriminating LNM‐positive from LNM‐negative patients had an AUC of 0.822. Conclusion UcfDNA could serve as a promising biomarker for early detection of NSCLC.
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Affiliation(s)
- Sai Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Xiao-Dong Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Li-Fang Guo
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Xue-Mei Qu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Mei-Yun Shang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Xiao-Tian Dai
- Department of Pulmonology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
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Salvianti F, Massi D, De Giorgi V, Gori A, Pazzagli M, Pinzani P. Evaluation of the liquid biopsy for the detection of BRAFV600E mutation in metastatic melanoma patients. Cancer Biomark 2020; 26:271-279. [PMID: 31524142 DOI: 10.3233/cbm-181647] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Circulating tumor cells (CTCs) and circulating cell free DNA (ccfDNA) represent a liquid biopsy of a tumor allowing real time disease monitoring especially in advanced stages of cancer, but their analysis is technically challenging. OBJECTIVE We aimed to demonstrate the feasibility of two different technical approaches to detect the BRAFV600E mutation in the liquid biopsy of 20 metastatic melanoma patients by using both the enriched CTC fraction and circulating ccfDNA from the same blood sample. METHODS We detected CTCs by a filtration method in 20 metastatic melanoma patients and detected the BRAFV600E variant on CTCs and ccfDNA by an allele-specific qPCR assay; the mutated samples were confirmed by ICE-COLD PCR followed by Sanger sequencing. RESULTS We found CTCs in 70% of the samples, and identified the BRAFV600E variant on CTCs. We correlated the results with those obtained on ccfDNA from the same blood draw. We found some discordant results between CTCs and ccfDNA. CONCLUSIONS Our results underline the importance of investigating both CTCs and ccfDNA in a liquid biopsy approach to melanoma patients.
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Affiliation(s)
- Francesca Salvianti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Italy
| | - Daniela Massi
- Division of Pathology, Department of Health Sciences (DSS), University of Florence, Italy
| | - Vincenzo De Giorgi
- Division of Dermatology, Department of Health Sciences (DSS), University of Florence, Italy
| | - Alessia Gori
- Division of Dermatology, Department of Health Sciences (DSS), University of Florence, Italy
| | - Mario Pazzagli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Italy
| | - Pamela Pinzani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Italy
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Tuchalska-Czuroń J, Lenart J, Augustyniak J, Durlik M. Clinical value of tissue DNA integrity index in pancreatic cancer. Surgeon 2020; 18:269-279. [PMID: 32156475 DOI: 10.1016/j.surge.2019.10.008] [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: 06/25/2019] [Revised: 10/08/2019] [Accepted: 10/28/2019] [Indexed: 10/24/2022]
Abstract
BACKGROUND DNA integrity index as a blood biomarker is associated with the prognosis of cancer patients. AIMS The primary goal of the study was to examine tissue DNA integrity index (DII) in a group of pancreatic cancer (PC) tumor tissues and control adjacent pancreatic tissues. We also aimed to test the relationship between the tumor tissue DII and the clinicopathological parameters and the overall survival. METHODS In the prospective study, DII was calculated using: the Alu 247/115 ratio, the LINE1 300/79 ratio and the average of the above values, based on the data obtained by real-time PCR. The tumors samples (n = 42) originated from the patients with pathologically confirmed pancreatic ductal adenocarcinoma and the control adjacent pancreatic tissue specimens (n = 32) were received from surgical margins. RESULTS Specimens from the tumors pathologically marked as R1 (microscopic residual tumor) had a significantly higher LINE1 300/79 ratio values than specimens from adjacent normal pancreatic tissue (P<0.05). ROC curve analysis revealed that LINE1 300/79 ratio is a good parameter to distinguish between R0 and R1 tumors (AUC = 0.703, P<0.05). CONCLUSIONS This is the first study exploring the tissue DNA integrity index (DII) in pancreatic cancer. LINE1 DII can be used as auxiliary parameter for objective evaluation of margin status.
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Affiliation(s)
- Julia Tuchalska-Czuroń
- Department of Surgical Research and Transplantology, Medical Research Centre Polish Academy of Sciences, Warsaw, Poland; Diagnostic Radiology Department, Central Clinical Hospital of the MSWiA in Warsaw, Poland.
| | - Jacek Lenart
- Department of Neurochemistry, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Justyna Augustyniak
- Department of Neurochemistry, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Marek Durlik
- Department of Surgical Research and Transplantology, Medical Research Centre Polish Academy of Sciences, Warsaw, Poland; Department of Gastroenterological Surgery and Transplantation Medicine, Centre of Postgraduate Medical Education, Warsaw, Poland; Clinical Department of Gastroenterological Surgery and Transplantation Medicine, Central Clinical Hospital of the MSWiA in Warsaw, Poland
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15
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Chen A, Li J, Wang L, Huang Q, Zhu J, Wen S, Lyu J, Wu W. Comparison of paired cerebrospinal fluid and serum cell-free mitochondrial and nuclear DNA with copy number and fragment length. J Clin Lab Anal 2020; 34:e23238. [PMID: 32052892 PMCID: PMC7307366 DOI: 10.1002/jcla.23238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 01/11/2020] [Accepted: 01/21/2020] [Indexed: 12/22/2022] Open
Abstract
Background Most studies on cell‐free DNA (cfDNA) were only for single body fluids; however, the differences in cfDNA distribution between two body fluids are rarely reported. Hence, in this work, we compared the differences in cfDNA distribution between cerebrospinal fluid (CSF) and serum of patients with brain‐related diseases. Methods The fragment length of cfDNA was determined by using Agilent 2100 Bioanalyzer. The copy numbers of cell‐free mitochondrial DNA (cf‐mtDNA) and cell‐free nuclear DNA (cf‐nDNA) were determined by using real‐time quantitative PCR (qPCR) and droplet digital PCR (ddPCR) with three pairs of mitochondrial ND1 and nuclear GAPDH primers, respectively. Results There were short (~60 bp), medium (~167 bp), and long (>250 bp) cfDNA fragment length distributions totally obtained from CSF and serum using Agilent 2100 Bioanalyzer. The results of both qPCR and ddPCR confirmed the existence of these three cfDNA fragment ranges in CSF and serum. According to qPCR, the copy numbers of long cf‐mtDNA, medium, and long cf‐nDNA in CSF were significantly higher than in paired serum. In CSF, only long cf‐mtDNA's copy numbers were higher than long cf‐nDNA. But in serum, the copy numbers of medium and long cf‐mtDNA were higher than the corresponding cf‐nDNA. Conclusion The cf‐nDNA and cf‐mtDNA with different fragment lengths differentially distributed in the CSF and serum of patients with brain disorders, which might serve as a biomarker of human brain diseases.
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Affiliation(s)
- Aolong Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jun Li
- Department of Clinical Laboratory, Wenzhou People's Hospital, Wenzhou, China
| | - Lei Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qin Huang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jiajin Zhu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shumeng Wen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Hangzhou Medical College, Hangzhou, China
| | - Wenhe Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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Kozak K, Kowalik A, Gos A, Wasag B, Lugowska I, Jurkowska M, Krawczynska N, Kosela-Paterczyk H, Switaj T, Teterycz P, Klimczak A, Siedlecki JA, Chlopek M, Kalisz J, Limon J, Rutkowski P. Cell-free DNA BRAF V600E measurements during BRAF inhibitor therapy of metastatic melanoma: long-term analysis. TUMORI JOURNAL 2020; 106:300891619900928. [PMID: 32026754 DOI: 10.1177/0300891619900928] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE We assessed the status of the BRAF V600E mutation in cell-free circulating tumor DNA (cfDNA) isolated from the plasma of patients with metastatic melanoma treated with the BRAF inhibitor vemurafenib, collected at different time points during therapy to evaluate the sensitivity and specificity of quantitative polymerase chain reaction and droplet digital polymerase chain reaction (ddPCR) and the correlation between the level of plasma cfDNA p.V600E and the long-term clinical outcome. METHODS cfDNA in patients with BRAF-mutated melanoma (n = 62) was analyzed at baseline and at 4-8 weeks from the start of vemurafenib therapy. BRAF mutations were assessed using tumor tissue-derived DNA and circulating cfDNA from plasma samples. Quantification of BRAF V600E was performed in cfDNA using ddPCR. RESULTS cfDNA V600E was detected in the plasma of 48/62 (77%) patients at baseline and in 18/62 (29%) patients after 4-8 weeks of treatment. Patients positive for BRAF mutations in cfDNA at baseline had shorter progression-free survival (PFS) and overall survival (OS) compared with patients with undetectable cfDNA BRAF mutations. Undetectable cfDNA p.V600E at baseline and after 4-8 weeks of therapy was associated with the best prognosis. When treated as a continuous variable, the log-transformed concentration of baseline cfDNA p.V600E was significantly associated with both PFS and OS. This effect was retained in the multivariate OS Cox model adjusted for Eastern Cooperative Oncology Group performance status, the presence of brain metastases, patient age, and previous systemic treatment. CONCLUSIONS Monitoring of plasma BRAF p.V600E cfDNA concentrations in patients with metastatic melanoma on targeted therapy may have prognostic value. Undetectable cfDNA p.V600E before and during treatment was associated with a favorable prognosis.
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Affiliation(s)
- Katarzyna Kozak
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Artur Kowalik
- Department of Molecular Diagnostics, Holy Cross Cancer Centre, Kielce, Poland
| | - Aleksandra Gos
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Bartosz Wasag
- Department of Molecular Biology, Medical University of Gdansk, Gdansk, Poland
| | - Iwona Lugowska
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | | | - Natalia Krawczynska
- Department of Molecular Biology, Medical University of Gdansk, Gdansk, Poland
| | - Hanna Kosela-Paterczyk
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Tomasz Switaj
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Paweł Teterycz
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Anna Klimczak
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Małgorzata Chlopek
- Department of Molecular Diagnostics, Holy Cross Cancer Centre, Kielce, Poland
| | - Joanna Kalisz
- Department of Molecular Diagnostics, Holy Cross Cancer Centre, Kielce, Poland
| | - Janusz Limon
- Department of Molecular Biology, Medical University of Gdansk, Gdansk, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
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Thakur S, Tobey A, Daley B, Auh S, Walter M, Patel D, Nilubol N, Kebebew E, Patel A, Jensen K, Vasko V, Klubo-Gwiezdzinska J. Limited Utility of Circulating Cell-Free DNA Integrity as a Diagnostic Tool for Differentiating Between Malignant and Benign Thyroid Nodules With Indeterminate Cytology (Bethesda Category III). Front Oncol 2019; 9:905. [PMID: 31620364 PMCID: PMC6759775 DOI: 10.3389/fonc.2019.00905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/30/2019] [Indexed: 12/17/2022] Open
Abstract
Background: Analysis of plasma circulating cell-free DNA integrity (cfDI) has emerged as a promising tool in the diagnosis of malignant vs. benign tumors. There is limited data on the role of cfDI in thyroid cancer. The goal of this study was to analyze cfDI as a biomarker of malignancy in patients with cytologically indeterminate thyroid nodules. Methods: The cfDI was measured in the plasma of patients with cytologically indeterminate thyroid nodules. All patients underwent plasma collection within 24–72 h before surgical treatment for thyroid nodules. Additionally, samples were collected from seven patients via the vein draining the thyroid and peripheral vein during surgery. Quantitative real-time PCR was performed on the isolated cell-free DNA using two different primer sets (115 and 247 bp) to amplify consensus ALU sequences. The cfDI was calculated as the ratio of ALU247 to ALU115. Results: All data are given as median [25th−75th percentile]. The study group consisted of 67 patients with 100 nodules, 80.6% (54/67) women, aged 43 [33-60] years. There was no difference in cfDI between 29 patients with benign nodules (0.49 [0.41–0.59]) and 38 patients with malignant lesions (0.45 [0.36–0.57], p = 0.19). There was no difference in cfDI in the vein draining the thyroid (0.47 [0.24–1.05]) and peripheral vein (0.48 [0.36–0.56], p = 0.44). In comparison to thyroid cancer patients, patients with benign nodules were characterized by significantly higher concentrations of ALU115 (1,064 [529–2,960] vs. 411 [27–1,049] ng/ml; p = 0.002) and ALU247 (548 [276–1,894] vs. 170 [17-540] ng/ml; p = 0.0005), most likely because benign tumors were larger (3, [1.8–4.1 cm]) than malignant lesions (0.7 [0.23–1.45], p < 0.0001). Women had significantly lower cfDI (0.45 [0.27–0.54]) than men (0.56 [0.44–0.8], p = 0.011). Conclusion: The cfDI measured in the vein draining the thyroid is similar to the cfDI measured in the antecubital vein, validating cfDI measurements by peripheral liquid biopsy. Analysis of cfDI needs to be stratified by patients gender. In contrast to its diagnostic utility in aggressive cancers, cfDI has limited utility as a biomarker of malignancy in cytologically indeterminate thyroid nodules.
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Affiliation(s)
- Shilpa Thakur
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Andrew Tobey
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Brianna Daley
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sungyoung Auh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Mary Walter
- Core for Clinical Laboratory Services, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Dhaval Patel
- Cancer Center - Froedtert Hospital, Milwaukee, WI, United States
| | - Naris Nilubol
- Endocrine Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Electron Kebebew
- Division of General Surgery, Endocrine Oncology Research Laboratory, Department of Surgery, Stanford Medicine, School of Medicine, Stanford, CA, United States
| | - Aneeta Patel
- Department of Pediatric Endocrinology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Kirk Jensen
- Department of Pediatric Endocrinology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Vasyl Vasko
- Department of Pediatric Endocrinology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Joanna Klubo-Gwiezdzinska
- Metabolic Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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Abstract
The study of cell-free DNA (cfDNA) is often challenging due to genomic DNA contamination, low concentration, and high fragmentation. Therefore, it is important to optimize pre-analytical and analytical procedures in order to maximize the performance of cfDNA-based analyses.In this chapter, we report the most common methods for the correct collection, centrifugation, storage, and DNA isolation from cell-free biological sources such as plasma, urines, cerebrospinal fluid, and pleural effusion fluid.
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Affiliation(s)
- Filippo Martignano
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
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Lin J, Ma L, Zhang D, Gao J, Jin Y, Han Z, Lin D. Tumour biomarkers-Tracing the molecular function and clinical implication. Cell Prolif 2019; 52:e12589. [PMID: 30873683 PMCID: PMC6536410 DOI: 10.1111/cpr.12589] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/19/2018] [Accepted: 01/10/2019] [Indexed: 12/19/2022] Open
Abstract
In recent years, with the increase in cancer mortality caused by metastasis, and with the development of individualized and precise medical treatment, early diagnosis with precision becomes the key to decrease the death rate. Since detecting tumour biomarkers in body fluids is the most non‐invasive way to identify the status of tumour development, it has been widely investigated for the usage in clinic. These biomarkers include different expression or mutation in microRNAs (miRNAs), circulating tumour DNAs (ctDNAs), proteins, exosomes and circulating tumour cells (CTCs). In the present article, we summarized and discussed some updated research on these biomarkers. We overviewed their biological functions and evaluated their multiple roles in human and small animal clinical treatment, including diagnosis of cancers, classification of cancers, prognostic and predictive values for therapy response, monitors for therapy efficacy, and anti‐cancer therapeutics. Biomarkers including different expression or mutation in miRNAs, ctDNAs, proteins, exosomes and CTCs provide more choice for early diagnosis of tumour detection at early stage before metastasis. Combination detection of these tumour biomarkers may provide higher accuracy at the lowest molecule combination number for tumour early detection. Moreover, tumour biomarkers can provide valuable suggestions for clinical anti‐cancer treatment and execute monitoring of treatment efficiency.
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Affiliation(s)
- Jiahao Lin
- The Clinical Department, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lie Ma
- Department of Respiratory Disease, The Navy General Hospital of PLA, Beijing, China
| | - Di Zhang
- The Clinical Department, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiafeng Gao
- The Clinical Department, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yipeng Jin
- The Clinical Department, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhihai Han
- Department of Respiratory Disease, The Navy General Hospital of PLA, Beijing, China
| | - Degui Lin
- The Clinical Department, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Ivanov M, Chernenko P, Breder V, Laktionov K, Rozhavskaya E, Musienko S, Baranova A, Mileyko V. Utility of cfDNA Fragmentation Patterns in Designing the Liquid Biopsy Profiling Panels to Improve Their Sensitivity. Front Genet 2019; 10:194. [PMID: 30915108 PMCID: PMC6422983 DOI: 10.3389/fgene.2019.00194] [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: 10/19/2018] [Accepted: 02/25/2019] [Indexed: 01/05/2023] Open
Abstract
Genotyping of cell-free DNA (cfDNA) in plasma samples has the potential to allow for a noninvasive assessment of tumor biology, avoiding the inherent shortcomings of tissue biopsy. Next generation sequencing (NGS), a leading technology for liquid biopsy analysis, continues to be hurdled with several major issues with cfDNA samples, including low cfDNA concentration and high fragmentation. In this study, by employing Ion Torrent PGM semiconductor technology, we performed a comparison between two multi-biomarker amplicon-based NGS panels characterized by a substantial difference in average amplicon length. In course of the analysis of the peripheral blood from 13 diagnostic non-small cell lung cancer patients, equivalence of two panels, in terms of overall diagnostic sensitivity and specificity was shown. A pairwise comparison of the allele frequencies for the same somatic variants obtained from the pairs of panel-specific amplicons, demonstrated an identical analytical sensitivity in range of 140 to 170 bp amplicons in size. Further regression analysis between amplicon length and its coverage, illustrated that NGS sequencing of plasma cfDNA equally tolerates amplicons with lengths in the range of 120 to 170 bp. To increase the sensitivity of mutation detection in cfDNA, we performed a computational analysis of the features associated with genome-wide nucleosome maps, evident from the data on the prevalence of cfDNA fragments of certain sizes and their fragmentation patterns. By leveraging the support vector machine-based machine learning approach, we showed that a combination of nucleosome map associated features with GC content, results in the increased accuracy of prediction of high inter-sample sequencing coverage variation (areas under the receiver operating curve: 0.75, 95% CI: 0.750–0.752 vs. 0.65, 95% CI: 0.63–0.67). Thus, nucleosome-guided fragmentation should be utilized as a guide to design amplicon-based NGS panels for the genotyping of cfDNA samples.
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Affiliation(s)
- Maxim Ivanov
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Valery Breder
- N.N. Blokhin Russian Cancer Research Center, Moscow, Russia
| | | | - Ekaterina Rozhavskaya
- Atlas Oncology Diagnostics, Ltd., Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Ancha Baranova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Atlas Oncology Diagnostics, Ltd., Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia.,School of Systems Biology, George Mason University, Fairfax, VA, United States
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Rushton JG, Ertl R, Klein D, Tichy A, Nell B. Circulating cell-free DNA does not harbour a diagnostic benefit in cats with feline diffuse iris melanomas. J Feline Med Surg 2019; 21:124-132. [PMID: 29529957 PMCID: PMC10814613 DOI: 10.1177/1098612x18762017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
OBJECTIVES Feline diffuse iris melanoma (FDIM) is the most common malignant primary intraocular tumour in cats, with reported metastases rates between 19% and 63%. Currently, the only available diagnostic tool for a tentative diagnosis is histopathological examination of the enucleated eye. Therefore, the veterinary ophthalmologist is often faced with the dilemma of whether to enucleate an oftentimes visual eye or to continue monitoring, with the risk of metastases developing. In the past, cell-free DNA (cfDNA) gained more attention in human medicine, especially in the field of oncology. Prior studies have shown the use of cfDNA as diagnostic or prognostic markers in canine and human cancer patients. Therefore, the aim of this study was to investigate cfDNA concentration and integrity in cats with FDIMs compared with cats with benign iris naevi and without ocular abnormalities. METHODS cfDNA from plasma of cats with iris melanoma (n = 34), iris naevus (n = 30) and without ocular abnormalities (n = 32) were extracted. Primer and probes for feline amyloid beta precursor protein ( APP) and beta actin ( ACTB) were designed for amplicons of various lengths and quantitative PCRs of extracted cfDNA were performed to measure cfDNA concentration and integrity of the plasma samples. Differences of cfDNA concentrations and integrity levels between the three groups (iris melanoma, iris naevi and controls) were analysed using the Mann-Whitney U-test. RESULTS cfDNA concentration and integrity analysis revealed no significant differences between the cats with iris melanoma, iris naevus or the control group ( P >0.01). Cats with metastases showed similar cfDNA concentration and integrity to cats without metastases. CONCLUSIONS AND RELEVANCE cfDNA concentration and integrity seem to be insufficient as a diagnostic or prognostic marker in cats with FDIMs.
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Affiliation(s)
- Jessica G Rushton
- Department for Companion Animals and Horses, Vetmeduni Vienna, Vienna, Austria
| | - Reinhard Ertl
- VetCore Facility for Research, Vetmeduni Vienna, Vienna, Austria
| | - Dieter Klein
- VetCore Facility for Research, Vetmeduni Vienna, Vienna, Austria
| | - Alexander Tichy
- Department of Biomedical Sciences, Vetmeduni Vienna, Vienna, Austria
| | - Barbara Nell
- Department for Companion Animals and Horses, Vetmeduni Vienna, Vienna, Austria
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23
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Comparison of 4 commercial kits for the extraction of circulating DNA from plasma. Cancer Genet 2018; 228-229:143-150. [DOI: 10.1016/j.cancergen.2018.02.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 02/16/2018] [Indexed: 12/21/2022]
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24
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Sumbal S, Javed A, Afroze B, Zulfiqar HF, Javed F, Noreen S, Ijaz B. Circulating tumor DNA in blood: Future genomic biomarkers for cancer detection. Exp Hematol 2018; 65:17-28. [PMID: 29940219 DOI: 10.1016/j.exphem.2018.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/06/2018] [Accepted: 06/14/2018] [Indexed: 12/12/2022]
Abstract
Cancer is characterized by Darwinian evolution and is a primary cause of mortality and morbidity around the globe. Over the preceding decade, the treatment of cancer has been markedly improved by many targeted therapies, but these treatments have given birth to new challenges and issues. Clonal evolution and tumor heterogeneity present a significant challenge in designing cancer therapies. Fortunately, these restrictions have been overcome by technological advancements allowing us to track both genetic and epigenetic aberrations. Cell-free circulating tumor DNA (ctDNA) analysis, or "liquid biopsy" from a blood sample, provides the opportunity to track the genetic landscape of cancerous lesions. This review focuses on ctDNA analysis as a noninvasive method and versatile biomarker for cancer treatment and technological advancements for ctDNA analysis. This method may able to cope with all the challenges associated with previous cancer therapies and has the potential to monitor minimal residual disease, tumor burden, and therapy response and provide rapid detection of relapse. However, there are many challenges that still need to be addressed. Future prognosis, diagnosis, and analysis of ctDNA require reproducibility and accuracy of results, which are not possible without the validation and optimization of procedures. Integrated digital error suppression has thus far shown promise in the detection of ctDNA in cancer.
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Affiliation(s)
- Sumbal Sumbal
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan
| | - Aneeqa Javed
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan
| | - Bakht Afroze
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan
| | | | - Faqeeha Javed
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan
| | - Sobia Noreen
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan
| | - Bushra Ijaz
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, Pakistan.
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25
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Tang Z, Li L, Shen L, Shen X, Ju S, Cong H. Diagnostic Value of Serum Concentration and Integrity of Circulating Cell-Free DNA in Breast Cancer: A Comparative Study With CEA and CA15-3. Lab Med 2018; 49:323-328. [PMID: 29701836 DOI: 10.1093/labmed/lmy019] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Zijie Tang
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Li Li
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Lei Shen
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xianjuan Shen
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Shaoqing Ju
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Hui Cong
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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26
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Ponti G, Maccaferri M, Manfredini M, Kaleci S, Mandrioli M, Pellacani G, Ozben T, Depenni R, Bianchi G, Pirola GM, Tomasi A. The value of fluorimetry (Qubit) and spectrophotometry (NanoDrop) in the quantification of cell-free DNA (cfDNA) in malignant melanoma and prostate cancer patients. Clin Chim Acta 2018; 479:14-19. [DOI: 10.1016/j.cca.2018.01.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/13/2017] [Accepted: 01/04/2018] [Indexed: 11/26/2022]
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27
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Glebova KV, Veiko NN, Nikonov AA, Porokhovnik LN, Kostuyk SV. Cell-free DNA as a biomarker in stroke: Current status, problems and perspectives. Crit Rev Clin Lab Sci 2018; 55:55-70. [PMID: 29303618 DOI: 10.1080/10408363.2017.1420032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
There is currently no proposed stroke biomarker with consistent application in clinical practice. A number of studies have examined cell-free DNA (cfDNA), which circulates in biological fluids during stroke, as a potential biomarker of this disease. The data available suggest that dynamically-determined levels of blood cfDNA may provide new prognostic information for assessment of stroke severity and outcome. However, such an approach has its own difficulties and limitations. This review covers the potential role of cfDNA as a biomarker in stroke, and includes evidence from both animal models and clinical studies, protocols used to analyze cfDNA, and hypotheses on the origin of cfDNA.
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Affiliation(s)
- Kristina V Glebova
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
| | - Natalya N Veiko
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
| | - Aleksey A Nikonov
- b Department of Neurology, Neurosurgery and Medical Genetics , Pirogov Russian National Research Medical University , Moscow , Russia
| | - Lev N Porokhovnik
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
| | - Svetlana V Kostuyk
- a Laboratory of Molecular Biology , Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russia
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28
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Gangadhar TC, Savitch SL, Yee SS, Xu W, Huang AC, Harmon S, Lieberman DB, Soucier D, Fan R, Black TA, Morrissette JJD, Salathia N, Waters J, Zhang S, Toung J, van Hummelen P, Fan JB, Xu X, Amaravadi RK, Schuchter LM, Karakousis GC, Hwang WT, Carpenter EL. Feasibility of monitoring advanced melanoma patients using cell-free DNA from plasma. Pigment Cell Melanoma Res 2018; 31:73-81. [PMID: 28786531 PMCID: PMC5742050 DOI: 10.1111/pcmr.12623] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/31/2017] [Indexed: 12/24/2022]
Abstract
To determine the feasibility of liquid biopsy for monitoring of patients with advanced melanoma, cell-free DNA was extracted from plasma for 25 Stage III/IV patients, most (84.0%) having received previous therapy. DNA concentrations ranged from 0.6 to 390.0 ng/ml (median = 7.8 ng/ml) and were positively correlated with tumor burden as measured by imaging (Spearman rho = 0.5435, p = .0363). Using ultra-deep sequencing for a 61-gene panel, one or more mutations were detected in 12 of 25 samples (48.0%), and this proportion did not vary significantly for patients on or off therapy at the time of blood draw (52.9% and 37.5% respectively; p = .673). Sixteen mutations were detected in eight different genes, with the most frequent mutations detected in BRAF, NRAS, and KIT. Allele fractions ranged from 1.1% to 63.2% (median = 29.1%). Among patients with tissue next-generation sequencing, nine of 11 plasma mutations were also detected in matched tissue, for a concordance of 81.8%.
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Affiliation(s)
- Tara C. Gangadhar
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Samantha L. Savitch
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Stephanie S. Yee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Wei Xu
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Alexander C. Huang
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Institue for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Parker Institute of Immunotherapy at the University of Pennsylvania
| | - Shannon Harmon
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - David B. Lieberman
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Devon Soucier
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ryan Fan
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Taylor A. Black
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Jennifer J. D. Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | | | | | | | | | | | | | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Ravi K. Amaravadi
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Lynn M. Schuchter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | - Wei-Ting Hwang
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Biostatistics & Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Erica L. Carpenter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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Cheng J, Tang Q, Cao X, Burwinkel B. Cell-Free Circulating DNA Integrity Based on Peripheral Blood as a Biomarker for Diagnosis of Cancer: A Systematic Review. Cancer Epidemiol Biomarkers Prev 2017; 26:1595-1602. [DOI: 10.1158/1055-9965.epi-17-0502] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/13/2017] [Accepted: 08/07/2017] [Indexed: 11/16/2022] Open
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Mehrotra M, Singh RR, Chen W, Huang RS, Almohammedsalim AA, Barkoh BA, Simien CM, Hernandez M, Behrens C, Patel KP, Routbort MJ, Broaddus RR, Medeiros LJ, Wistuba II, Kopetz S, Luthra R. Study of Preanalytic and Analytic Variables for Clinical Next-Generation Sequencing of Circulating Cell-Free Nucleic Acid. J Mol Diagn 2017; 19:514-524. [DOI: 10.1016/j.jmoldx.2017.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 02/10/2017] [Accepted: 03/06/2017] [Indexed: 12/19/2022] Open
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Integrity and Quantity of Total Cell-Free DNA in the Diagnosis of Thyroid Cancer: Correlation with Cytological Classification. Int J Mol Sci 2017; 18:ijms18071350. [PMID: 28672797 PMCID: PMC5535843 DOI: 10.3390/ijms18071350] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/19/2017] [Accepted: 06/22/2017] [Indexed: 01/04/2023] Open
Abstract
Cell-free DNA (cfDNA) quantity and quality in plasma has been investigated as a non-invasive biomarker in cancer. Previous studies have demonstrated increased cfDNA amount and length in different types of cancer with respect to healthy controls. The present study aims to test the hypothesis that the presence of longer DNA strands circulating in plasma can be considered a biomarker for tumor presence in thyroid cancer. We adopted a quantitative real-time PCR (qPCR) approach based on the quantification of two amplicons of different length (67 and 180 bp respectively) to evaluate the integrity index 180/67. Cell-free DNA quantity and integrity were higher in patients affected by nodular thyroid diseases than in healthy controls. Importantly, cfDNA integrity index was higher in patients with cytological diagnosis of thyroid carcinoma (Thy4/Thy5) than in subjects with benign nodules (Thy2). Therefore, cfDNA integrity index 180/67 is a suitable parameter for monitoring cfDNA fragmentation in thyroid cancer patients and a promising circulating biomarker in the diagnosis of thyroid nodules.
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32
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Eltorgoman AE, Badr E, Kombr Y, Yousif M. Pleural fluid DNA integrity index as a diagnostic marker of malignant pleural effusion. Br J Biomed Sci 2017; 74:148-151. [PMID: 28537492 DOI: 10.1080/09674845.2017.1297215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- A E Eltorgoman
- a Faculty of Science, Department of Organic Chemistry , Menoufia University , Shebin Elkom city , Egypt
| | - Eae Badr
- b Faculty of Medicine, Department of Medical Biochemistry , Menoufia University , Shebin Elkom city , Egypt
| | - Yfae Kombr
- c Faculty of Science, Department of Biochemistry , Menoufia University , Shebin Elkom city , Egypt
| | - M Yousif
- d Faculty of Medicine, Department of Chest , Menoufia University , Shebin Elkom city , Egypt
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Chen D, Pan S, Xie E, Gao L, Xu H, Xia W, Xu T, Huang P. Development and Evaluation of a Duplex Real-Time PCR Assay With a Novel Internal Standard for Precise Quantification of Plasma DNA. Ann Lab Med 2017; 37:18-27. [PMID: 27834061 PMCID: PMC5107613 DOI: 10.3343/alm.2017.37.1.18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/25/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
Background Circulating levels of cell-free DNA increase in many pathologic conditions. However, notable discrepancies in the quantitative analysis of cell-free DNA from a large number of laboratories have become a considerable pitfall, hampering its clinical application. Methods We designed a novel recombinant DNA fragment that could be applied as an internal standard in a newly developed and validated duplex real-time PCR assay for the quantitative analysis of total cell-free plasma DNA, which was tested in 5,442 healthy adults and 200 trauma patients. Results Compared with two traditional methods, this novel assay showed a lower detection limit of 0.1 ng/mL, lower intra- and inter-assay CVs, and higher accuracy in the recovery test. The median plasma DNA concentration of healthy males (20.3 ng/mL, n=3,092) was significantly higher than that of healthy females (16.1 ng/mL, n=2,350) (Mann-Whitney two-sample rank sum test, P<0.0001). The reference intervals of plasma DNA concentration were 0-45.8 ng/mL and 0-52.5 ng/mL for healthy females and males, respectively. The plasma DNA concentrations of the majority of trauma patients (96%) were higher than the upper normal cutoff values and were closely related to the corresponding injury severity scores (R2=0.916, P<0.0001). Conclusions This duplex real-time PCR assay with a new internal standard could eliminate variation and allow for more sensitive, repeatable, accurate, and stable quantitative measurements of plasma DNA, showing promising application in clinical diagnosis.
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Affiliation(s)
- Dan Chen
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shiyang Pan
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Erfu Xie
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Gao
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Huaguo Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenying Xia
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ting Xu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Peijun Huang
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Pu WY, Zhang R, Xiao L, Wu YY, Gong W, Lv XD, Zhong FY, Zhuang ZX, Bai XM, Li K, Xing CG. Prediction of cancer progression in a group of 73 gastric cancer patients by circulating cell-free DNA. BMC Cancer 2016; 16:943. [PMID: 27938352 PMCID: PMC5148873 DOI: 10.1186/s12885-016-2977-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/29/2016] [Indexed: 12/12/2022] Open
Abstract
Background Circulating cell-free DNA (ccf-DNA) in plasma may contain both specific and non-specific of tumor markers. The concentration and integrity of ccf-DNA may be clinical useful for detecting and predicting cancer progression. Methods Plasma samples from 40 healthy controls and 73 patients with gastric cancers (two stage 0, 17 stage I, 11 stage II, 33 stage III, and 10 stage IV according to American Joint Committee on Cancer stage) were assessed respectively. qPCR targeting the Alu repeats was performed using two different sets of primers amplifying the long and short segments. DNA integrity was calculated as a ratio of the long to the short fragments of Alu repeats. Results Plasma DNA concentration was significantly higher in patients with stage III and IV gastric cancers than in healthy controls (p = 0.028 and 0.029 respectively). The receiver operating characteristic (ROC) curve for discriminating patients with stage III and IV gastric cancers from healthy controls had an area under the curve (AUC) of 0.744 (95% CI, 0.64 to 0.85). Circulating cell-free DNA concentration increased within 21 days following surgery and dropped by 3 months after surgery. Conclusions Concentration of ccf-DNA is a promising molecular marker for assessing gastric cancer progression. Trial registration Current Controlled Trials ChiCTR-DDT-12002848, 8 October 2012. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2977-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wang-Yang Pu
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Rong Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Li Xiao
- Molecular Medicine Center, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yong-You Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Wei Gong
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Xiao-Dong Lv
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Feng-Yun Zhong
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Zhi-Xiang Zhuang
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Xu-Ming Bai
- Department of Interventional Radiology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Kai Li
- Department of Molecular Diagnostics and Biopharmaceutics, College of Pharmaceutical Science, Soochow University, Suzhou, 215004, China.
| | - Chun-Gen Xing
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China.
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Skrypkina I, Tsyba L, Onyshchenko K, Morderer D, Kashparova O, Nikolaienko O, Panasenko G, Vozianov S, Romanenko A, Rynditch A. Concentration and Methylation of Cell-Free DNA from Blood Plasma as Diagnostic Markers of Renal Cancer. DISEASE MARKERS 2016; 2016:3693096. [PMID: 27725787 PMCID: PMC5048037 DOI: 10.1155/2016/3693096] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 12/13/2022]
Abstract
The critical point for successful treatment of cancer is diagnosis at early stages of tumor development. Cancer cell-specific methylated DNA has been found in the blood of cancer patients, indicating that cell-free DNA (cfDNA) circulating in the blood is a convenient tumor-associated DNA marker. Therefore methylated cfDNA can be used as a minimally invasive diagnostic marker. We analysed the concentration of plasma cfDNA and methylation of six tumor suppressor genes in samples of 27 patients with renal cancer and 15 healthy donors as controls. The cfDNA concentrations in samples from cancer patients and healthy donors was measured using two different methods, the SYBR Green I fluorescence test and quantitative real-time PCR. Both methods revealed a statistically significant increase of cfDNA concentrations in cancer patients. Hypermethylation on cfDNA was detected for the LRRC3B (74.1%), APC (51.9%), FHIT (55.6%), and RASSF1 (62.9%) genes in patients with renal cancer. Promoter methylation of VHL and ITGA9 genes was not found on cfDNA. Our results confirmed that the cfDNA level and methylation of CpG islands of RASSF1A, FHIT, and APC genes in blood plasma can be used as noninvasive diagnostic markers of cancer.
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Affiliation(s)
- Inessa Skrypkina
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Liudmyla Tsyba
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Kateryna Onyshchenko
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Dmytro Morderer
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Olena Kashparova
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Oleksii Nikolaienko
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Grigory Panasenko
- Department of Molecular Oncogenetics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
| | - Sergii Vozianov
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Alina Romanenko
- Institute of Urology, National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Alla Rynditch
- Department of Functional Genomics, Institute of Molecular Biology and Genetics of the National Academy of Science of Ukraine, Kyiv, Ukraine
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36
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Basnet S, Zhang ZY, Liao WQ, Li SH, Li PS, Ge HY. The Prognostic Value of Circulating Cell-Free DNA in Colorectal Cancer: A Meta-Analysis. J Cancer 2016; 7:1105-13. [PMID: 27326254 PMCID: PMC4911878 DOI: 10.7150/jca.14801] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) is a promising candidate biomarker for detection, monitoring and survival prediction of colorectal cancer (CRC). However, its prognostic significance for patients with CRC remains controversial. To derive a precise estimation of the prognostic significance of cfDNA, a meta-analysis was performed. METHODS We made a systematic search in data base of the Science Citation Index Embase and Pubmed for studies reporting prognostic data of cfDNA in CRC patients. The data of cfDNA on recurrences-free survival (RFS) and overall survival (OS) were extracted and measured in hazard rates (HRs) and 95% confident intervals (CIs). Subgroup analyses were carried out as well. Finally, the meta-analysis is accompanied with nine studies including 19 subunits. RESULTS The pooled HRs with 95% CIs revealed strong associations between cfDNA and RFS (HR [95%CI]=2.78[2.08-3.72], I(2)=32.23%, n=7) along with OS (HR [95%CI]=3.03[2.51-3.66], I(2)=29.24%, n=12) in patients with CRC. Entire subgroup analyses indicated strong prognostic value of cfDNA irrespective tumor stage, study size, tumor markers, detection methods and marker origin. CONCLUSIONS All the results exhibits that appearance of cfDNA in blood is an indicator for adverse RFS and OS in CRC patients.
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Affiliation(s)
- Shiva Basnet
- 1. Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhen-yu Zhang
- 1. Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wen-qiang Liao
- 1. Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shu-heng Li
- 1. Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ping-shu Li
- 2. Department of Research Administration, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hai-yan Ge
- 1. Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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37
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Kamel AM, Teama S, Fawzy A, El Deftar M. Plasma DNA integrity index as a potential molecular diagnostic marker for breast cancer. Tumour Biol 2016; 37:7565-72. [PMID: 26684805 DOI: 10.1007/s13277-015-4624-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/10/2015] [Indexed: 12/11/2022] Open
Abstract
Plasma DNA integrity index is increased in various malignancies including breast cancer, the most common cancer in women worldwide; early detection is crucial for successful treatment. Current screening methods fail to detect many cases of breast cancer at an early stage. In this study, we evaluated the level of plasma DNA integrity index in 260 females (95 with breast cancer, 95 with benign breast lesions, and 70 healthy controls) to verify its potential value in discriminating malignant from benign breast lesions. The criteria of the American Joint Committee on Cancer were used for staging of breast cancer patients. DNA integrity index was measured by real-time PCR. DNA integrity index was significantly higher in breast cancer than in benign breast patients and healthy subjects (P = <0.001). DNA integrity index is correlated with TNM stage. Given 100 % specificity, the highest sensitivity achieved in detecting cancer group was 85.3 % at 0.55 DNA integrity index cutoff. In conclusion, the plasma DNA integrity index may be a promising molecular diagnostic marker of malignancy in breast lesions.
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MESH Headings
- Adult
- Aged
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Breast/metabolism
- Breast/pathology
- Breast Neoplasms/blood
- Breast Neoplasms/diagnosis
- Breast Neoplasms/genetics
- Carcinoma, Ductal, Breast/blood
- Carcinoma, Ductal, Breast/diagnosis
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Lobular/blood
- Carcinoma, Lobular/diagnosis
- Carcinoma, Lobular/genetics
- Case-Control Studies
- DNA, Neoplasm/blood
- DNA, Neoplasm/genetics
- Female
- Follow-Up Studies
- Humans
- Middle Aged
- Neoplasm Grading
- Neoplasm Staging
- Plasma/chemistry
- Prognosis
- ROC Curve
- Real-Time Polymerase Chain Reaction
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Affiliation(s)
- Azza M Kamel
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Fom El-Khalig Square, Kasr El-Aini Street, 11796, Cairo, Egypt.
| | - Salwa Teama
- Medical Research Center, Molecular Biology Unit, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | - Amal Fawzy
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Fom El-Khalig Square, Kasr El-Aini Street, 11796, Cairo, Egypt
| | - Mervat El Deftar
- Department of Pathology, Tissue culture & Cytogenetic unit, National Cancer Institute, Cairo University, Cairo, Egypt
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38
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Latchana N, Ganju A, Howard JH, Carson WE. MicroRNA dysregulation in melanoma. Surg Oncol 2016; 25:184-9. [PMID: 27566021 DOI: 10.1016/j.suronc.2016.05.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 05/19/2016] [Indexed: 01/06/2023]
Abstract
Melanoma is the deadliest form of skin cancer. Current challenges facing the management of melanoma include accurate prediction of individuals who will respond to adjuvant therapies as well as early detection of recurrences. These and other challenges have prompted investigation into biomarkers that could be used as diagnostic, prognostic and therapeutic aids. MicroRNAs (miRs) are small 19-22 nucleotide RNA inhibitors of protein translation. Over 800 different miRs are present within cells and importantly miR expression profiles may vary across different cells types and stages of malignancy. Unique expression profiles have been described for malignant melanoma; however, this work has yet to be translated into routine clinical practice. We highlight pertinent studies involving common miRs implicated in the oncogenesis of melanoma including miR-21, miR-125b, miR-150, miR-155, miR-205, and miR-211. In particular, emphasis is placed upon differential expression across different stages of melanoma progression, prognostic implications and potential mechanistic involvement. Focused efforts on inhibition of these miRs could be the most efficient method of translating preclinical endeavors into clinically meaningful applications.
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Affiliation(s)
- Nicholas Latchana
- Department of Surgery, The Ohio State University, Columbus, OH 43210, USA.
| | - Akaansha Ganju
- Department of Surgery, The Ohio State University, Columbus, OH 43210, USA.
| | - J Harrison Howard
- Department of Surgery, The Ohio State University, Columbus, OH 43210, USA.
| | - William E Carson
- Department of Surgery, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Virology, Immunology and Medical Genetics, The Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH 43210, USA.
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39
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El-Gayar D, El-Abd N, Hassan N, Ali R. Increased Free Circulating DNA Integrity Index as a Serum Biomarker in Patients with Colorectal Carcinoma. Asian Pac J Cancer Prev 2016; 17:939-944. [DOI: 10.7314/apjcp.2016.17.3.939] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
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40
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Qin Z, Ljubimov VA, Zhou C, Tong Y, Liang J. Cell-free circulating tumor DNA in cancer. CHINESE JOURNAL OF CANCER 2016; 35:36. [PMID: 27056366 PMCID: PMC4823888 DOI: 10.1186/s40880-016-0092-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/01/2016] [Indexed: 02/07/2023]
Abstract
Cancer is a common cause of death worldwide. Despite significant advances in cancer treatments, the morbidity and mortality are still enormous. Tumor heterogeneity, especially intratumoral heterogeneity, is a significant reason underlying difficulties in tumor treatment and failure of a number of current therapeutic modalities, even of molecularly targeted therapies. The development of a virtually noninvasive “liquid biopsy” from the blood has been attempted to characterize tumor heterogeneity. This review focuses on cell-free circulating tumor DNA (ctDNA) in the bloodstream as a versatile biomarker. ctDNA analysis is an evolving field with many new methods being developed and optimized to be able to successfully extract and analyze ctDNA, which has vast clinical applications. ctDNA has the potential to accurately genotype the tumor and identify personalized genetic and epigenetic alterations of the entire tumor. In addition, ctDNA has the potential to accurately monitor tumor burden and treatment response, while also being able to monitor minimal residual disease, reducing the need for harmful adjuvant chemotherapy and allowing more rapid detection of relapse. There are still many challenges that need to be overcome prior to this biomarker getting wide adoption in the clinical world, including optimization, standardization, and large multicenter trials.
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Affiliation(s)
- Zhen Qin
- Department of Medicine, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California, 90048, USA.,School of Life Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, P. R. China
| | - Vladimir A Ljubimov
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Cuiqi Zhou
- Department of Medicine, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California, 90048, USA
| | - Yunguang Tong
- Department of Medicine, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, California, 90048, USA. .,Department of Pathology, Xinxiang Medical University, Xinxiang, 453003, Henan, P. R. China.
| | - Jimin Liang
- School of Life Science and Technology, Xidian University, Xi'an, 710126, Shaanxi, P. R. China.
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41
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Huang SK, Hoon DSB. Liquid biopsy utility for the surveillance of cutaneous malignant melanoma patients. Mol Oncol 2016; 10:450-63. [PMID: 26778792 PMCID: PMC5307330 DOI: 10.1016/j.molonc.2015.12.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/04/2015] [Accepted: 12/08/2015] [Indexed: 01/01/2023] Open
Abstract
Cutaneous melanoma is one of the highest incident-rate cancers with increasing prevalence in Western societies. Despite the advent of new approved therapeutics, the 5-year overall survival rate of stage IV melanoma patients remains below 15%. Current treatments for late stage disease have shown higher efficacy when treated at a lower disease burden. Thus, blood-based biomarkers capable of detecting melanoma prior to clinically evident distant metastasis, will improve the treatment and outcomes for melanoma patients. To that end, effective treatment of melanoma necessitates identification of patients at risk for developing distant metastases. Furthermore, employing blood biomarkers that monitor cancer progression over the course of treatment is a promising solution to post-treatment drug resistance often developed in melanoma patients. Non-invasive blood biomarker assays allow for regular dynamic monitoring of disease. "Liquid Biopsy" of blood, which exploits circulating tumor cells (CTCs), cell-free circulating tumor DNA (ctDNA) and cell-free circulating microRNA (cmiRNA), has been shown to detect prognostic factors for relapse in AJCC stage III and stage IV melanoma patients. Moreover, molecular characterization of CTC and analysis of various forms of ctDNA present promising potential in development of individualized therapy for melanoma patients. New approaches such as massive parallel sequencing (MPS) provide a comprehensive view of the disease progression, allowing for the selection of therapeutic options for individual patients. With advancements of improving molecular assays, liquid biopsy analysis as a powerful, routine clinical assay for melanoma patients, is highly promising prospective.
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Affiliation(s)
- Sharon K Huang
- Department of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, United States
| | - Dave S B Hoon
- Department of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404, United States.
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42
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Diagnostic and prognostic potential of circulating cell-free genomic and mitochondrial DNA fragments in clear cell renal cell carcinoma patients. Clin Chim Acta 2016; 452:109-19. [DOI: 10.1016/j.cca.2015.11.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 01/05/2023]
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43
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Aarthy R, Mani S, Velusami S, Sundarsingh S, Rajkumar T. Role of Circulating Cell-Free DNA in Cancers. Mol Diagn Ther 2015; 19:339-50. [PMID: 26400814 DOI: 10.1007/s40291-015-0167-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Liquid biopsy is a term used to describe non-invasive tests, which provide information about disease conditions through analysis of circulating cell-free DNA and circulating tumor cells from peripheral blood samples. In patients with cancer, the concentration of cell-free DNA increases, and structural, sequence, and epigenetic changes to DNA can be observed through the disease process and during therapy. Furthermore, cell-free DNA released by the tumor contains the same variants as those in the tumor cells. Therefore, cell-free DNA allows non-invasive assessment of cancer in real time. This review summarizes the origin of cell-free DNA, recent advancements in the detection of cell-free DNA, a possible role in metastasis, and its importance as a non-invasive diagnostic assay for cancer.
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Affiliation(s)
- Raghu Aarthy
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Samson Mani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India
| | - Sridevi Velusami
- Department of Surgical Oncology, Cancer Institute (WIA), Chennai, India
| | | | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600036, India.
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44
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Bronkhorst AJ, Aucamp J, Pretorius PJ. Cell-free DNA: Preanalytical variables. Clin Chim Acta 2015; 450:243-53. [DOI: 10.1016/j.cca.2015.08.028] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/17/2015] [Accepted: 08/30/2015] [Indexed: 12/11/2022]
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45
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Comprehensive evaluation of methods to isolate, quantify, and characterize circulating cell-free DNA from small volumes of plasma. Anal Bioanal Chem 2015; 407:6873-8. [DOI: 10.1007/s00216-015-8846-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/03/2015] [Accepted: 06/10/2015] [Indexed: 12/21/2022]
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46
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Abstract
Many methods have been developed for DNA integrity assessment including electrophoresis-based procedures, quantitative PCR, and, more recently, microfluidics-based procedures. DNA integrity evaluation can be employed for characterizing biological samples quality before extensive genomic analysis and also finds applications in reproductive medicine, prenatal diagnostics, or cancer research. In this chapter, we will focus on the assessment of DNA integrity in cancer research. In particular, we will present the application of the determination of DNA integrity for tracking of circulating tumor DNA. Finally, we will conclude by illustrating the potential innovative application of DNA integrity as a biomarker in clinical research, especially for prognostic purposes, patient follow-up, or early diagnosis.
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47
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Alegre E, Sammamed M, Fernández-Landázuri S, Zubiri L, González Á. Circulating biomarkers in malignant melanoma. Adv Clin Chem 2015; 69:47-89. [PMID: 25934359 DOI: 10.1016/bs.acc.2014.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Melanoma is an aggressive tumor with increasing incidence worldwide. Biomarkers are valuable tools to minimize the cost and improve efficacy of treatment of this deadly disease. Serological markers have not widely been introduced in routine clinical practice due to their insufficient diagnostic sensitivity and specificity. It is likely that the lack of objective responses with traditional treatment hinder biomarker research and development in melanoma. Recently, new drugs and therapies have, however, emerged in advanced melanoma with noticeable objective response ratio and survival. In this new scenario, serological tumor markers should be revisited. In addition, other potential circulating biomarkers such as cell-free DNA, exosomes, microRNA, and circulating tumor cells have also been identified. In this review, we summarize classical and emerging tumor markers and discuss their possible roles in emerging therapeutics.
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Affiliation(s)
- Estibaliz Alegre
- Laboratory of Biochemistry, University Clinic of Navarra, Pamplona, Spain
| | - Miguel Sammamed
- Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain; Department of Oncology, University Clinic of Navarra, Pamplona, Spain
| | | | - Leyre Zubiri
- Department of Oncology, University Clinic of Navarra, Pamplona, Spain
| | - Álvaro González
- Laboratory of Biochemistry, University Clinic of Navarra, Pamplona, Spain.
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48
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Fleischhacker M, Schmidt B. Extracellular Nucleic Acids and Cancer. ADVANCES IN PREDICTIVE, PREVENTIVE AND PERSONALISED MEDICINE 2015. [DOI: 10.1007/978-94-017-9168-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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49
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Hao TB, Shi W, Shen XJ, Qi J, Wu XH, Wu Y, Tang YY, Ju SQ. Circulating cell-free DNA in serum as a biomarker for diagnosis and prognostic prediction of colorectal cancer. Br J Cancer 2014; 111:1482-9. [PMID: 25157833 PMCID: PMC4200099 DOI: 10.1038/bjc.2014.470] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/07/2014] [Accepted: 07/16/2014] [Indexed: 12/15/2022] Open
Abstract
Background: To verify whether the concentrations and integrity index of circulating cell-free DNA (ccf-DNA) in serum may be clinically useful for the diagnosis and progression monitoring of colorectal cancer (CRC) patients. Methods: Serum samples were collected from 104 with primary CRC, 85 with operated CRC, 16 with recurrent/metastatic CRC, 63 patients with intestinal polyps and 110 normal controls. Long (247 bp) and short (115 bp) DNA fragments in serum were detected by real-time quantitative PCR by amplifying the ALU repeats (ALU-qPCR). Serum carcinoembryonic antigen (CEA) level was detected by ARCHITECT assay. Results: The median absolute serum ALU115 and ALU247/115 in primary CRC group was significantly higher than those in intestinal polyp and normal control groups (both P<0.0001), in recurrent/metastatic CRC was significantly higher compared with primary CRC (P=0.0021, P=0.0018) or operated CRC (P<0.0001, respectively) and during follow-up, ALU115 and ALU247/115 were increased before surgery and decreased significantly after surgery. Conclusions: Combined detection of ALU115, ALU247/115 and CEA could improve the diagnostic efficiency for CRC. Serum DNA concentrations and integrity index may be valuable in early complementary diagnosis and monitoring of progression and prognosis of CRC.
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Affiliation(s)
- T B Hao
- Medical School of Nantong University, Nantong 226000, Jiangsu Province, China
| | - W Shi
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu Province, China
| | - X J Shen
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu Province, China
| | - J Qi
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu Province, China
| | - X H Wu
- Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu Province, China
| | - Y Wu
- Medical School of Nantong University, Nantong 226000, Jiangsu Province, China
| | - Y Y Tang
- Medical School of Nantong University, Nantong 226000, Jiangsu Province, China
| | - S Q Ju
- 1] Surgical Comprehensive Laboratory, Affiliated Hospital of Nantong University, Nantong 226000, Jiangsu Province, China [2] Center of Laboratory Medicine, Affiliated Hospital of Nantong University, 20 Xisi Street, Nantong 226000, Jiangsu Province, China
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50
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Tug S, Helmig S, Menke J, Zahn D, Kubiak T, Schwarting A, Simon P. Correlation between cell free DNA levels and medical evaluation of disease progression in systemic lupus erythematosus patients. Cell Immunol 2014; 292:32-9. [PMID: 25243646 DOI: 10.1016/j.cellimm.2014.08.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/07/2014] [Accepted: 08/12/2014] [Indexed: 12/20/2022]
Abstract
High levels of cell free DNA (cfDNA) in human blood plasma have been described in patients with autoimmune diseases. The aim of this study was to determine the levels of cfDNA in systemic lupus erythematosus (SLE) patients and to assess fluctuations of cfDNA concentrations compared to the course of disease progression under standard treatment. Therefore, nuclear cfDNA concentrations in plasma were measured in 59 SLE patients and 59 healthy controls. Follow-up blood plasma was collected from 27 of the 59 SLE patients. Patients were characterised by clinical parameters (antinuclear antibodies (ANA), anti-dsDNA-antibodies, C3, C4, and CRP), SLE disease activity index (SLEDAI) and medical therapy. Our results showed that cfDNA concentrations were significantly higher in SLE patients compared to healthy individuals. Levels of cfDNA assessed in serial samples correlated significantly with the medical evaluation of disease activity in SLE patients. Our results could implicate cfDNA as a global marker for disease activity.
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Affiliation(s)
- Suzan Tug
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Susanne Helmig
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Julia Menke
- Department of Rheumatology and Clinical Immunology, University Medical Centre of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Daniela Zahn
- Institute of Psychology, Health Psychology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Thomas Kubiak
- Institute of Psychology, Health Psychology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Andreas Schwarting
- Department of Rheumatology and Clinical Immunology, University Medical Centre of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany.
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