51
|
Utility of circulating cell-free Mycobacterium tuberculosis DNA for the improved diagnosis of abdominal tuberculosis. PLoS One 2020; 15:e0238119. [PMID: 32845896 PMCID: PMC7449497 DOI: 10.1371/journal.pone.0238119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/09/2020] [Indexed: 12/13/2022] Open
Abstract
Abdominal tuberculosis (ATB) continues to pose a major diagnostic challenge for clinicians due to its nonspecific clinical presentation, variable anatomical location and lack of sensitive diagnostic tools. In spite of the development of several assays till date; no single test has proved to be adequate for ATB diagnosis. In this study, we for the first time report the detection of circulating cell-free Mycobacterium tuberculosis (M. tuberculosis) DNA (cfMTB-DNA) in ascitic fluid (AF) samples and its utility in ATB diagnosis. Sixty-five AF samples were included in the study and processed for liquid culture, cytological, biochemical and molecular assays. A composite reference standard (CRS) was formulated to categorize the patients into 'Definite ATB' (M. tuberculosis culture positive, n = 2), 'Probable ATB' (n = 16), 'Possible ATB' (n = 13) and 'Non-TB' category (n = 34). Two molecular assays were performed, namely, the novel cfMTB-DNA qPCR assay targeting M. tuberculosis devR gene and Xpert MTB/RIF assay (Xpert), and their diagnostic accuracy was assessed using CRS as reference standard. Clinical features such as fever, loss of weight, abdominal distension and positive Mantoux were found to be strongly associated with ATB disease (p<0.05). cfMTB-DNA qPCR had a sensitivity of 66.7% (95% CI:40.9,86.7) with 97.1% specificity (95% CI:84.7,99.9) in 'Definite ATB' and 'Probable ATB' group collectively. The sensitivity increased to 70.9% (95% CI:51.9,85.8) in the combined 'Definite', 'Probable' and 'Possible' ATB group with similar specificity. The cfMTB-DNA qPCR assay performed significantly better than the Xpert assay which demonstrated a poor sensitivity of ≤16.7% with 100% (95% CI:89.7,100) specificity (p<0.001). We conclude that cfMTB-DNA qPCR assay is an accurate molecular test that can provide direct evidence of M. tuberculosis etiology and has promise to pave the way for improving ATB diagnosis.
Collapse
|
52
|
Khani M, Hosseini J, Habibi M, Mirfakhraie R, Sadeghzadeh Z, Pouresmaeili F. Investigating the relationship between ccfDNA concentration, its integrity, and some individual factors in an Iranian population. Hum Antibodies 2020; 28:319-326. [PMID: 32804121 DOI: 10.3233/hab-200419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Circulating cell-free DNA (ccfDNA) increases in some pathologic conditions like cancer. We aimed to investigate the correlation between some individual factors and the ccfDNA level in peripheral blood of Iranian in relation to prostate cancer. MATERIAL AND METHOD 30 patients with prostate cancer (PCa), 40 with benign prostate hyperplasia (BPH), and 30 controls were studied. Personal information, ccfDNA concentration, and the integrity index were assessed for the correlation between the disease and different factors. The results were statistically analyzed using SPSS software. RESULTS In PCa group, no association was found between total ccfDNA, BMI, BPH background, non-cancerous diseases, medications, PCa length, and job (p-value > 0.05). But, total ccfDNA had statistical associations with weight, family history of cancer, and location (p-value < 0.05). No association was between the integrity of ccfDNA, weight, the background of BPH, and family history of cancer. But, the integrity of ccfDNA was significantly associated with BMI and PCa length (p-value < 0.05).In BPH group, no association between total ccfDNA or the integrity of ccfDNA and the assessed factors was obtained (p-value > 0.05). In the normal group, neither statistical association was found between total ccfDNA, weight, BMI, and job, nor between the integrity of ccfDNA, weight, BMI, non-cancerous disease, drug, job, and location (p-value > 0.05). But, a statistical association was found between the integrity of ccfDNA and family history of cancer in the recent group (Based on 95% CI and P-value less than 0.05). CONCLUSION ccfDNA and its integrity as possible prostate cancer biomarkers under the influence of individuals' physiological status are prone to the pathologic changes toward the disease. Further simultaneous study of the target groups could clarify this matter.
Collapse
Affiliation(s)
- Maryam Khani
- Medical Genetics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jalil Hosseini
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Habibi
- Medical Genetics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Medical Genetics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Sadeghzadeh
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farkhondeh Pouresmaeili
- Medical Genetics Department, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
53
|
Bruno DCF, Donatti A, Martin M, Almeida VS, Geraldis JC, Oliveira FS, Dogini DB, Lopes-Cendes I. Circulating nucleic acids in the plasma and serum as potential biomarkers in neurological disorders. ACTA ACUST UNITED AC 2020; 53:e9881. [PMID: 32813850 PMCID: PMC7446710 DOI: 10.1590/1414-431x20209881] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022]
Abstract
Neurological diseases are responsible for approximately 6.8 million deaths every year. They affect up to 1 billion people worldwide and cause significant disability and reduced quality of life. In most neurological disorders, the diagnosis can be challenging; it frequently requires long-term investigation. Thus, the discovery of better diagnostic methods to help in the accurate and fast diagnosis of neurological disorders is crucial. Circulating nucleic acids (CNAs) are defined as any type of DNA or RNA that is present in body biofluids. They can be found within extracellular vesicles or as cell-free DNA and RNA. Currently, CNAs are being explored as potential biomarkers for diseases because they can be obtained using non-invasive methods and may reflect unique characteristics of the biological processes involved in several diseases. CNAs can be especially useful as biomarkers for conditions that involve organs or structures that are difficult to assess, such as the central nervous system. This review presents a critical assessment of the most current literature about the use of plasma and serum CNAs as biomarkers for several aspects of neurological disorders: defining a diagnosis, establishing a prognosis, and monitoring the disease progression and response to therapy. We explored the biological origin, types, and general mechanisms involved in the generation of CNAs in physiological and pathological processes, with specific attention to neurological disorders. In addition, we present some of the future applications of CNAs as non-invasive biomarkers for these diseases.
Collapse
Affiliation(s)
- D C F Bruno
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - A Donatti
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - M Martin
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - V S Almeida
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - J C Geraldis
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - F S Oliveira
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - D B Dogini
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - I Lopes-Cendes
- Departamento de Genética Médica e Medicina Genômica, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas, SP, Brasil
| |
Collapse
|
54
|
Origin of circulating free DNA in patients with lung cancer. PLoS One 2020; 15:e0235611. [PMID: 32634139 PMCID: PMC7340299 DOI: 10.1371/journal.pone.0235611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/19/2020] [Indexed: 12/15/2022] Open
Abstract
Liquid biopsy has become widely applied in clinical medicine along with the progress in innovative technologies, such as next generation sequencing, but the origin of circulating tumor DNA (ctDNA) has not yet been precisely established. We reported bimodal peaks of long fragment circulating free DNA (cfDNA) of 5 kb and short fragment cfDNA of 170 bp in patients with advanced lung cancer, and both contained ctDNA. In this paper, we demonstrate that the total amount of cfDNA is higher when patients with lung cancer have extrathoracic metastases, and the amount of long fragment cfDNA is significantly higher in those patients. To investigate the origin of long fragment cfDNA, conditioned media isolated from lung cancer cell lines was fractionated. Long fragment cfDNA was found concomitant with extracellular vesicles (EVs), but short fragment cfDNA was not observed in any fractions. However, in peripheral blood from a metastatic animal model both fragments were detected even with those same lung cancer cell lines. In human plasma samples, long fragment cfDNA was observed in the same fraction as that from conditioned media, and short fragment cfDNA existed in the supernatant after centrifugation at 100,000g. Concentration of ctDNA in the supernatant was two times higher than that in plasma isolated by the conventional procedure. Long fragment cfDNA associated with tumor progression might therefore be released into peripheral blood, and it is possible that the long fragment cfDNA escapes degradation by co-existing with EVs. Examination of the biological characteristics of long fragment cfDNA is a logical subject of further investigation.
Collapse
|
55
|
Malentacchi F, Turrini I, Zepponi F, Fantappiè G, Sorbi F, Antonuzzo L, Fambrini M, Noci I, Pillozzi S. Mutational profile in circulating tumor DNA in a patient affected by low-risk endometrial cancer: predictable tool of relapse? Anticancer Drugs 2020; 31:1091-1095. [DOI: 10.1097/cad.0000000000000963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
56
|
Detecting Endometrial Cancer by Blood Spectroscopy: A Diagnostic Cross-Sectional Study. Cancers (Basel) 2020; 12:cancers12051256. [PMID: 32429365 PMCID: PMC7281323 DOI: 10.3390/cancers12051256] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
Endometrial cancer is the sixth most common cancer in women, with a rising incidence worldwide. Current approaches for the diagnosis and screening of endometrial cancer are invasive, expensive or of moderate diagnostic accuracy, limiting their clinical utility. There is a need for cost-effective and minimally invasive approaches to facilitate the early detection and timely management of endometrial cancer. We analysed blood plasma samples in a cross-sectional diagnostic accuracy study of women with endometrial cancer (n = 342), its precursor lesion atypical hyperplasia (n = 68) and healthy controls (n = 242, total n = 652) using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy and machine learning algorithms. We show that blood-based infrared spectroscopy has the potential to detect endometrial cancer with 87% sensitivity and 78% specificity. Its accuracy is highest for Type I endometrial cancer, the most common subtype, and for atypical hyperplasia, with sensitivities of 91% and 100%, and specificities of 81% and 88%, respectively. Our large-cohort study shows that a simple blood test could enable the early detection of endometrial cancer of all stages in symptomatic women and provide the basis of a screening tool in high-risk groups. Such a test has the potential not only to differentially diagnose endometrial cancer but also to detect its precursor lesion atypical hyperplasia—the early recognition of which may allow fertility sparing management and cancer prevention.
Collapse
|
57
|
Ungerer V, Bronkhorst AJ, Holdenrieder S. Preanalytical variables that affect the outcome of cell-free DNA measurements. Crit Rev Clin Lab Sci 2020; 57:484-507. [DOI: 10.1080/10408363.2020.1750558] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Abel J. Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| |
Collapse
|
58
|
Han D, Li R, Shi J, Tan P, Zhang R, Li J. Liquid biopsy for infectious diseases: a focus on microbial cell-free DNA sequencing. Theranostics 2020; 10:5501-5513. [PMID: 32373224 PMCID: PMC7196304 DOI: 10.7150/thno.45554] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/29/2020] [Indexed: 12/19/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) of microbial cell-free DNA (mcfDNA sequencing) is becoming an attractive diagnostic modality for infectious diseases, allowing broad-range pathogen detection, noninvasive sampling, and rapid diagnosis. At this key juncture in the translation of metagenomics into clinical practice, an integrative perspective is needed to understand the significance of emerging mcfDNA sequencing technology. In this review, we summarized the actual performance of the mcfDNA sequencing tests recently used in health care settings for the diagnosis of a variety of infectious diseases and further focused on the practice considerations (challenges and solutions) for improving the accuracy and clinical relevance of the results produced by this evolving technique. Such knowledge will be helpful for physicians, microbiologists and researchers to understand what is going on in this quickly progressing field of non-invasive pathogen diagnosis by mcfDNA sequencing and promote the routine implementation of this technique in the diagnosis of infectious disease.
Collapse
Affiliation(s)
- Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Rui Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jiping Shi
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital, Beijing, China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| |
Collapse
|
59
|
Abstract
Introduction: Lung transplantation remains an important treatment for patients with end stage lung disease. Chronic lung allograft dysfunction (CLAD) remains the greatest limiting factor for long term survival. As the diagnosis of CLAD is based on pulmonary function tests, significant lung injury is required before a diagnosis is feasible, likely when irreversible damage has already occurred. Therefore, research is ongoing for early CLAD recognition, with biomarkers making up a substantial amount of this research.Areas covered: The purpose of this review is to describe available biomarkers, focusing on those which aid in predicting CLAD and distinguishing between different CLAD phenotypes. We describe biomarkers presenting in bronchial alveolar lavage (BAL) as well as circulating in peripheral blood, both of which offer an appealing alternative to lung biopsy.Expert opinion: Development of CLAD involves complex, multiple immune and nonimmune mechanisms. Therefore, evaluation of potential CLAD biomarkers serves a dual purpose: clinically, the goal remains early detection and identification of patients at increased risk. Simultaneously, biomarkers offer insight into the different mechanisms involved in the pathophysiology of CLAD, leading to the development of possible interventions. The ultimate goal is the development of both preventive and early intervention strategies for CLAD to improve the overall survival of our lung transplant recipients.
Collapse
Affiliation(s)
- Osnat Shtraichman
- Division of Pulmonary, Allergy & Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Pulmonary institute, Rabin Medical Center, Petach Tikva, Israel; Sackler School of Medicine, Tel Aviv, Israel
| | - Joshua M Diamond
- Division of Pulmonary, Allergy & Critical Care, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
60
|
Duforestel M, Briand J, Bougras-Cartron G, Heymann D, Frenel JS, Vallette FM, Cartron PF. Cell-free circulating epimarks in cancer monitoring. Epigenomics 2020; 12:145-155. [DOI: 10.2217/epi-2019-0170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cancer numbers increasing, cases heterogeneity and the drug resistance emergence have pushed scientists to search for innovative solutions for patients and epimutations can be one. Methylated DNA, modified nucleosomes and noncoding RNAs are found in all cells, including tumor cells. They are intracellular actors but also have intercellular communication roles, being released in extracellular environment and in different body fluids. Here, we reviewed current literature on the use of these blood circulating epimarks in cancer monitoring. What stands out is that epimarkers must be considered as ‘real time’ images of the tumor, and can be isolated without invasive methods. In the future, the real challenge lies in the development of specific, sensitive, fast and clinically applicable detection and analysis methods of epimarkers.
Collapse
Affiliation(s)
- Manon Duforestel
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Joséphine Briand
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Gwenola Bougras-Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
| | - Dominique Heymann
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
| | - Jean-Sébastien Frenel
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- Department of Medical Oncology, Institut de Cancérologie de l'Ouest Site René Gauducheau, Saint Herblain, France
| | - François M Vallette
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- LabEX IGO, Université de Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France
- Equipe Apoptose et Progression tumorale, LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Niches & Epigenetics of Tumors Network from Cancéropôle Grand Ouest
- EpiSAVMEN Network (Région Pays de la Loire)
- LabEX IGO, Université de Nantes, France
| |
Collapse
|
61
|
Gupta R, Othman T, Chen C, Sandhu J, Ouyang C, Fakih M. Guardant360 Circulating Tumor DNA Assay Is Concordant with FoundationOne Next-Generation Sequencing in Detecting Actionable Driver Mutations in Anti-EGFR Naive Metastatic Colorectal Cancer. Oncologist 2019; 25:235-243. [PMID: 32162812 DOI: 10.1634/theoncologist.2019-0441] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Direct comparisons between Guardant360 (G360) circulating tumor DNA (ctDNA) and FoundationOne (F1) tumor biopsy genomic profiling in metastatic colorectal cancer (mCRC) are limited. We aim to assess the concordance across overlapping genes tested in both F1 and G360 in patients with mCRC. MATERIALS AND METHODS We retrospectively analyzed 75 patients with mCRC who underwent G360 and F1 testing. We evaluated the concordance among gene mutations tested by both G360 and F1 among three categories of patients: untreated, treated without, and treated with EGFR inhibitors, while considering the clonal and/or subclonal nature of each genomic alteration. RESULTS There was a high rate of concordance in APC, TP53, KRAS, NRAS, and BRAF mutations in the treatment-naive and non-anti-EGFR-treated cohorts. There was increased discordance in the anti-EGFR treated patients in three drivers of anti-EGFR resistance: KRAS, NRAS, and EGFR somatic mutations. Based on percentage of ctDNA, discordant somatic mutations were mostly subclonal instead of clonal and may have limited clinical significance. Most discordant amplifications noted on G360 showed the magnitude below the top decile, occurred in all three cohorts of patients, and were of unknown clinical significance. Serial ctDNA in anti-EGFR treated patients showed the emergence of multiple new alterations that affected the EGFR pathway: EGFR and RAS mutations and MET, RAS, and BRAF amplifications. CONCLUSION G360 Next-Generation Sequencing platform may be used as an alternative to F1 to detect targetable somatic alterations in non-anti-EGFR treated mCRC, but larger prospective studies are needed to further validate our findings. IMPLICATIONS FOR PRACTICE Genomic analysis of tissue biopsy is currently the optimal method for identifying DNA genomic alterations to help physicians target specific genes but has many disadvantages that may be mitigated by a circulating free tumor DNA (ctDNA) assay. This study showed a high concordance rate in certain gene mutations in patients who were treatment naive and treated with non-anti-EGFR therapy prior to ctDNA testing. This suggests that ctDNA genomic analysis may potentially be used as an alternative to tumor biopsy to identify appropriate patients for treatment selection in mCRC, but larger prospective studies are needed to further validate concordance among tissue and ctDNA tumor profiling.
Collapse
Affiliation(s)
- Rohan Gupta
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, California, USA
| | - Tamer Othman
- Department of Internal Medicine, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Chen Chen
- Center for Informatics, City of Hope National Medical Center, Duarte, California, USA
| | - Jaideep Sandhu
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, California, USA
| | - Ching Ouyang
- Center for Informatics, City of Hope National Medical Center, Duarte, California, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope National Medical Center, Duarte, California, USA
| | - Marwan Fakih
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, California, USA
| |
Collapse
|
62
|
Abstract
The technique of cell-free DNA (cfDNA) analysis, also called liquid biopsy, has been developed over the past several years to serve as a minimal residual disease tool, as has already been done with reliability and robustness in acute leukemias. This technique has important theoretical advantages, including the simplicity of acquiring blood samples, which can easily be repeated over time, its noninvasive and quantitative nature, which provides results consistent with the results obtained from tumor genomic DNA, and its speed and low cost. cfDNA analysis, as the leading tool to quantify somatic mutations, is a major technological leap in the noninvasive management of lymphomas. This technology may empower monitoring and treatment adjustment in real time and enable the quick detection of refractory lymphomas and resistance to routine therapies. Here, we summarize the results that have established the clinical relevance of cfDNA in diagnostic and prognostic stratification and the monitoring of lymphoma treatments.
Collapse
Affiliation(s)
- Vincent Camus
- Department of Hematology, Centre Henri Becquerel, 1 Rue D'Amiens, 76038 Rouen Cedex, France
| | - Fabrice Jardin
- Department of Hematology, Centre Henri Becquerel, 1 Rue D'Amiens, 76038 Rouen Cedex, France
| |
Collapse
|
63
|
Dekaliuk M, Qiu X, Troalen F, Busson P, Hildebrandt N. Discrimination of the V600E Mutation in BRAF by Rolling Circle Amplification and Förster Resonance Energy Transfer. ACS Sens 2019; 4:2786-2793. [PMID: 31577130 DOI: 10.1021/acssensors.9b01420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The quantification of very low concentrations of circulating tumor DNA (ctDNA) biomarkers from liquid biopsies has become an important requirement for clinical diagnostics and personalized medicine. In particular, the simultaneous detection of wild-type (WT) dsDNA and their cancer-related counterparts presenting single-point mutations with simple, sensitive, specific, and reproducible technologies is paramount for ctDNA assays in clinical practice. Here, we present the development and evaluation of an amplified dsDNA assay based on a combination of isothermal rolling circle amplification (RCA) and time-gated Förster resonance energy transfer (TG-FRET) between a Tb donor and two dye (Cy3.5 and Cy5.5) acceptors. The RCA-FRET assay is free of washing and separation steps and can quantify both WT and mutated (MT) (V600E) dsDNA in the BRAF gene from a single sample in the 75 fM to 4.5 pM (4.5 × 105 to 2.7 × 107 copies) concentration range. This assay includes all steps from denaturation of the dsDNA targets to the final duplexed quantification of WT and MT targets. High assay performance at different dsDNA sequence lengths and high target specificity even in the presence of a large excess of nonspecific cell-free DNA from human plasma samples demonstrated the applicability to clinical samples. The RCA-FRET single-point mutation sensor has the potential to become an important complementary technique for analyzing liquid biopsies in advanced cancer diagnostics.
Collapse
Affiliation(s)
- Mariia Dekaliuk
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
- Department of Neurochemistry, O. V. Palladin Institute of Biochemistry, Kyiv, 01030, Ukraine
| | - Xue Qiu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
| | - Frédéric Troalen
- Gustave Roussy, Université Paris-Saclay, CNRS, UMR 8126, 94805 Villejuif, France
| | - Pierre Busson
- Gustave Roussy, Université Paris-Saclay, CNRS, UMR 8126, 94805 Villejuif, France
- Université Paris-Sud, Université Paris-Saclay, 94270 Le Kremlin-Bicêtre, France
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay Cedex, France
- Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont Saint-Aignan, France
| |
Collapse
|
64
|
Fiala C, Kulasingam V, Diamandis EP. Circulating Tumor DNA for Early Cancer Detection. J Appl Lab Med 2019; 3:300-313. [PMID: 33636948 DOI: 10.1373/jalm.2018.026393] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/22/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Cancer cells release circulating tumor DNA (ctDNA) into the bloodstream, which can now be quantified and examined using novel high-throughput sequencing technologies. This has led to the emergence of the "liquid biopsy," which proposes to analyze this genetic material and extract information on a patient's cancer using a simple blood draw. CONTENT ctDNA has been detected in many advanced cancers. It has also been proven to be a highly sensitive indicator of relapse and prognosis. Sequencing the genetic material has also led to the discovery of mutations targetable by existing therapies. Although ctDNA screening is more expensive, it is showing promise against circulating tumor cells and traditional cancer biomarkers. ctDNA has also been detected in other bodily fluids, including cerebrospinal fluid, urine, saliva, and stool. The utility of ctDNA for early cancer detection is being studied. However, a blood test for cancer faces heavy obstacles, such as extremely low ctDNA concentrations in early-stage disease and benign mutations caused by clonal hematopoiesis, causing both sensitivity and specificity concerns. Nonetheless, companies and academic laboratories are highly active in developing such a test. CONCLUSION Currently, ctDNA is unlikely to perform at the high level of sensitivity and specificity required for early diagnosis and population screening. However, ctDNA in blood and other fluids has important clinical applications for cancer monitoring, prognosis, and selection of therapy that require further investigation.
Collapse
Affiliation(s)
- Clare Fiala
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
| | - Eleftherios P Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada
| |
Collapse
|
65
|
van Helden EJ, Angus L, Menke-van der Houven van Oordt CW, Heideman DAM, Boon E, van Es SC, Radema SA, van Herpen CML, de Groot DJA, de Vries EGE, Jansen MPHM, Sleijfer S, Verheul HMW. RAS and BRAF mutations in cell-free DNA are predictive for outcome of cetuximab monotherapy in patients with tissue-tested RAS wild-type advanced colorectal cancer. Mol Oncol 2019; 13:2361-2374. [PMID: 31350822 PMCID: PMC6822250 DOI: 10.1002/1878-0261.12550] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 05/09/2019] [Accepted: 07/17/2019] [Indexed: 12/15/2022] Open
Abstract
In metastatic colorectal cancer, RAS and BRAF mutations cause resistance to anti‐EGFR therapies, such as cetuximab. Heterogeneity in RAS and BRAF mutations might explain nonresponse in a subset of patients receiving cetuximab. Analyzing mutations in plasma‐derived circulating tumor DNA (ctDNA) could provide a more comprehensive overview of the mutational landscape as compared to analyses of primary and/or metastatic tumor tissue. Therefore, this prospective multicenter study followed 34 patients with metastatic colorectal cancer who were tissue‐tested as RAS wild‐type (exons 2–4) during routine work‐up and received third‐line cetuximab monotherapy. BRAF mutation status was also tested but did not exclude patients from therapy. At baseline and upon disease progression, cell‐free DNA (cfDNA) was isolated for targeted next‐generation sequencing (NGS). At 8 weeks, we determined that patients had benefited from treatment. NGS of cfDNA identified three patients with RAS mutations not detected in tumor tissue during routine work‐up. Another six patients had a BRAF or rare RAS mutation in ctDNA and/or tumor tissue. Relative to patients without mutations in RAS/BRAF, patients with mutations at baseline had shorter progression‐free survival [1.8 versus 4.9 months (P < 0.001)] and overall survival [3.1 versus 9.4 months (P = 0.001)]. In patients with clinical benefit (progressive disease after 8 weeks), ctDNA testing revealed previously undetected mutations in RAS/BRAF (71%) and EGFR (47%), which often emerged polyclonally. Our results indicate that baseline NGS of ctDNA can identify additional RAS mutation carriers, which could improve patient selection for anti‐EGFR therapies. Acquired resistance, in patients with initial treatment benefit, is mainly explained by polyclonal emergence of RAS,BRAF, and EGFR mutations in ctDNA.
Collapse
Affiliation(s)
- Erik J van Helden
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
| | - Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Daniëlle A M Heideman
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
| | - Eline Boon
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Suzanne C van Es
- Department of Medical Oncology, University Medical Center Groningen, The Netherlands
| | - Sandra A Radema
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carla M L van Herpen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Derk Jan A de Groot
- Department of Medical Oncology, University Medical Center Groningen, The Netherlands
| | | | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, The Netherlands
| |
Collapse
|
66
|
Franceschini T, Giunchi F, Montironi R, Scarpelli M, Lopez-Beltran A, Cheng L, Fiorentino M. Liquid biopsies in urological cancers: what we need to know before starting using them. Expert Rev Mol Diagn 2019; 20:135-139. [PMID: 31509027 DOI: 10.1080/14737159.2019.1665508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | | | | | | | | | - Liang Cheng
- Department of Pathology, Indiana University, Indianapolis, IN, USA
| | | |
Collapse
|
67
|
Stelcer E, Konkol M, Głȩboka A, Suchorska WM. Liquid Biopsy in Oligometastatic Prostate Cancer-A Biologist's Point of View. Front Oncol 2019; 9:775. [PMID: 31475117 PMCID: PMC6702517 DOI: 10.3389/fonc.2019.00775] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/31/2019] [Indexed: 12/13/2022] Open
Abstract
Prostate cancer (PCa) is the main cause of cancer-related mortality in males and the diagnosis, treatment, and care of these patients places a great burden on healthcare systems globally. Clinically, PCa is highly heterogeneous, ranging from indolent tumors to highly aggressive disease. In many cases treatment-generally either radiotherapy (RT) or surgery-can be curative. Several key genetic and demographic factors such as age, family history, genetic susceptibility, and race are associated with a high incidence of PCa. While our understanding of PCa, which is mainly based on the tools of molecular biology-has improved dramatically in recent years, efforts to better understand this complex disease have led to the identification of a new type of PCa-oligometastatic PCa. Oligometastatic disease should be considered an individual, heterogeneous entity with distinct metastatic phenotypes and, consequently, wide prognostic variability. In general, patients with oligometastatic disease typically present less biologically aggressive tumors whose metastatic potential is more limited and which are slow-growing. These patients are good candidates for more aggressive treatment approaches. The main aim of the presented review was to evaluate the utility of liquid biopsy for diagnostic purposes in PCa and for use in monitoring disease progression and treatment response, particularly in patients with oligometastatic PCa. Liquid biopsies offer a rapid, non-invasive approach whose use t is expected to play an important role in routine clinical practice to benefit patients. However, more research is needed to resolve the many existing discrepancies with regard to the definition and isolation method for specific biomarkers, as well as the need to determine the most appropriate markers. Consequently, the current priority in this field is to standardize liquid biopsy-based techniques. This review will help to improve understanding of the biology of PCa, particularly the recently defined condition known as "oligometastatic PCa". The presented review of the body of evidence suggests that additional research in molecular biology may help to establish novel treatments for oligometastatic PCa. In the near future, the treatment of PCa will require an interdisciplinary approach involving active cooperation among clinicians, physicians, and biologists.
Collapse
Affiliation(s)
- Ewelina Stelcer
- Radiobiology Laboratory, Greater Poland Cancer Centre, Poznan, Poland
- Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marek Konkol
- Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland
- Radiation Oncology Department, Greater Poland Cancer Centre, Poznan, Poland
| | | | - Wiktoria Maria Suchorska
- Radiobiology Laboratory, Greater Poland Cancer Centre, Poznan, Poland
- Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland
| |
Collapse
|
68
|
Kaczor-Urbanowicz KE, Wei F, Rao SL, Kim J, Shin H, Cheng J, Tu M, Wong DTW, Kim Y. Clinical validity of saliva and novel technology for cancer detection. Biochim Biophys Acta Rev Cancer 2019; 1872:49-59. [PMID: 31152821 PMCID: PMC6692231 DOI: 10.1016/j.bbcan.2019.05.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/05/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022]
Abstract
Cancer, a local disease at an early stage, systemically evolves as it progresses by triggering alterations in surrounding microenvironment, disturbing immune surveillance and further disseminating its molecular contents into circulation. This pathogenic characteristic of cancer makes the use of biofluids such as blood/serum/plasma, urine, tear and cerebrospinal fluids credible surrogates harboring tumor tissue-derived molecular alterations for the detection of cancer. Most importantly, a number of recent reports have credentialed the clinical validity of saliva for the detection of systemic diseases including cancers. In this review, we discussed the validity of saliva as credible biofluid and clinical sample type for the detection of cancers. We have presented the molecular constituents of saliva that could mirror the systemic status of our body and recent findings of salivaomics associated with cancers. Recently, liquid biopsy to detect cancer-derived circulating tumor DNA has emerged as a credible cancer-detection tool with potential benefits in screening, diagnosis and also risk management of cancers. We have further presented the clinical validity of saliva for liquid biopsy of cancers and a new technology platform based on electrochemical detection of cancer-derived ctDNA in saliva with superior sensitivity and point-of-care potential. The clinical utilities of saliva for the detection of cancers have been evidenced, but biological underpinning on the existence of molecular signatures of cancer-origin in saliva, such as via exosomal distribution, should be addressed in detail.
Collapse
Affiliation(s)
- Karolina Elżbieta Kaczor-Urbanowicz
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America; UCLA's Section of Orthodontics, UCLA School of Dentistry, University of California at Los Angeles, United States of America
| | - Fang Wei
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America
| | - Shannon Liu Rao
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America
| | - Jinseok Kim
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America
| | - Heebum Shin
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America
| | - Jordan Cheng
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America
| | - Michael Tu
- EZLife Bio Inc., 21250 Califa St #101, Woodland Hills, CA 9367, United States of America
| | - David T W Wong
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America; UCLA's Jonsson Comprehensive Cancer Center, United States of America.
| | - Yong Kim
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America; UCLA's Jonsson Comprehensive Cancer Center, United States of America.
| |
Collapse
|
69
|
Quantitative Methylation-Specific PCR: A Simple Method for Studying Epigenetic Modifications of Cell-Free DNA. Methods Mol Biol 2019; 1909:137-162. [PMID: 30580429 DOI: 10.1007/978-1-4939-8973-7_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aberrant DNA methylation of cell-free circulating DNA (cfDNA) has recently gained attention for its use as biomarker in cancer diagnosis, prognosis, and prediction of therapeutic response. Quantification of cfDNA methylation levels requires methods with high sensitivity and specificity due to low amounts of cfDNA available in plasma, high degradation of cfDNA, and/or contamination with genomic DNA. To date, several approaches for measuring cfDNA methylation have been established, including quantitative methylation-specific PCR (qMSP), which represents a simple, fast, and cost-effective technique that can be easily implemented into clinical practice. In this chapter, we provide a detailed protocol for SYBR Green qMSP analysis which is currently used in our laboratory for cfDNA methylation detection. Useful information regarding successful qMSP primers design are also provided.
Collapse
|
70
|
Abstract
Since its discovery in human blood plasma about 70 years ago, circulating cell-free DNA (cfDNA) has become an attractive subject of research as noninvasive disease biomarker. The interest in clinical applications has gained an exponential increase, making it a popular and potential target in a wide range of research areas.cfDNA can be found in different body fluids, both in healthy and not healthy subjects. The recent and rapid development of new molecular techniques is promoting the study and the identification of cfDNA, holding the key to minimally invasive diagnostics, improving disease monitoring, clinical decision, and patients' outcome.cfDNA has already given a huge impact on prenatal medicine, and it could become, in the next future, the standard of care also in other fields, from oncology to transplant medicine and cardiovascular diseases.
Collapse
Affiliation(s)
- Rossella Ranucci
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy.
| |
Collapse
|
71
|
Cell-Free DNA in the Liquid Biopsy Context: Role and Differences Between ctDNA and CTC Marker in Cancer Management. Methods Mol Biol 2019; 1909:47-73. [PMID: 30580422 DOI: 10.1007/978-1-4939-8973-7_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid biopsy is a new diagnostic concept to investigate the molecular features of solid tumors by blood, saliva, urine, and any other body fluids which show a source of potential biomarkers. In cancer patients, it is a simple and less invasive mean, representing a sustainable alternative to interrogate all tumor cells longitudinally, quantifying and characterizing the biological materials (DNAs, RNAs, proteins) which originate from cancer tissues. Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) analysis from a simple blood draw received enormous attention for the related clinical research results. A rich scientific literature demonstrates that liquid biopsy is a valid instrument to assess the tumor biomarkers in real time and profile the cancer genotype in diagnostic and prognostic field, as well to quantify minimal residual disease, during patient follow-up. This could be a breakthrough for a companion diagnostic and personalized medicine. Liquid biopsy needs further implementation in the methodological aspects as well as cost-based assessment. The number of new molecular diagnostic assays increases day by day, but the standards for their adoption and clinical validation are still to be achieved.
Collapse
|
72
|
Advances in liquid biopsy using circulating tumor cells and circulating cell-free tumor DNA for detection and monitoring of breast cancer. Clin Exp Med 2019; 19:271-279. [PMID: 31190187 DOI: 10.1007/s10238-019-00563-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 06/03/2019] [Indexed: 12/17/2022]
Abstract
Overview the progress of liquid biopsy using circulating tumor cells (CTCs) and circulating cell-free tumor DNA (cfDNA) to detect and monitor breast cancer. Based on numerous research efforts, the potential value of CTCs and cfDNA in the clinical aspects of cancer has become clear. With the development of next-generation sequencing analysis and newly developed technologies, many technical issues have been resolved, making liquid biopsy widely used in clinical practice. They can be powerful tools for dynamic monitoring of tumor progression and therapeutic efficacy. In the field of breast cancer, liquid biopsy is a research hot spot in recent years, playing a key role in monitoring breast cancer metastasis, predicting disease recurrence and assessing clinical drug resistance. Liquid biopsy has the advantages of noninvasive, high sensitivity, high specificity and real-time dynamic monitoring. Still application is far from reality, but the research and application prospects of CTCs and cfDNA in breast cancer are still worth exploring and discovering. This article reviews the main techniques and applications of CTCs and cfDNA in breast cancer.
Collapse
|
73
|
Fares J, Kanojia D, Rashidi A, Ahmed AU, Balyasnikova IV, Lesniak MS. Diagnostic Clinical Trials in Breast Cancer Brain Metastases: Barriers and Innovations. Clin Breast Cancer 2019; 19:383-391. [PMID: 31262686 DOI: 10.1016/j.clbc.2019.05.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/08/2019] [Accepted: 05/27/2019] [Indexed: 01/05/2023]
Abstract
Optimal treatment of breast cancer brain metastases (BCBM) is often hampered by limitations in diagnostic abilities. Developing innovative tools for BCBM diagnosis is vital for early detection and effective treatment. In this study we explored the advances in trial for the diagnosis of BCBM, with review of the literature. On May 8, 2019, we searched ClinicalTrials.gov for interventional and diagnostic clinical trials involving BCBM, without limiting for date or location. Information on trial characteristics, experimental interventions, results, and publications were collected and analyzed. In addition, a systematic review of the literature was conducted to explore published studies related to BCBM diagnosis. Only 9 diagnostic trials explored BCBM. Of these, 1 trial was withdrawn because of low accrual numbers. Three trials were completed; however, none had published results. Modalities in trial for BCBM diagnosis entailed magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), PET-CT, nanobodies, and circulating tumor cells (CTCs), along with a collection of novel tracers and imaging biomarkers. MRI continues to be the diagnostic modality of choice, whereas CT is best suited for acute settings. Advances in PET and PET-CT allow the collection of metabolic and functional information related to BCBM. CTC characterization can help reflect on the molecular foundations of BCBM, whereas cell-free DNA offers new genetic material for further exploration in trials. The integration of machine learning in BCBM diagnosis seems inevitable as we continue to aim for rapid and accurate detection and better patient outcomes.
Collapse
Affiliation(s)
- Jawad Fares
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Deepak Kanojia
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Aida Rashidi
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Atique U Ahmed
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Irina V Balyasnikova
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Maciej S Lesniak
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL.
| |
Collapse
|
74
|
Chin RI, Chen K, Usmani A, Chua C, Harris PK, Binkley MS, Azad TD, Dudley JC, Chaudhuri AA. Detection of Solid Tumor Molecular Residual Disease (MRD) Using Circulating Tumor DNA (ctDNA). Mol Diagn Ther 2019; 23:311-331. [PMID: 30941670 PMCID: PMC6561896 DOI: 10.1007/s40291-019-00390-5] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Circulating tumor DNA (ctDNA) is a component of cell-free DNA that is shed by malignant tumors into the bloodstream and other bodily fluids. Levels of ctDNA are typically low, particularly in patients with localized disease, requiring highly sophisticated methods for detection and quantification. Multiple liquid biopsy methods have been developed for ctDNA analysis in solid tumor malignancies and are now enabling detection and assessment of earlier stages of disease, post-treatment molecular residual disease (MRD), resistance to targeted systemic therapy, and tumor mutational burden. Understanding ctDNA biology, mechanisms of release, and clearance and size characteristics, in conjunction with the application of molecular barcoding and targeted error correction, have increased the sensitivity and specificity of ctDNA detection techniques. Combinatorial approaches including integration of ctDNA data with circulating protein biomarkers may further improve assay sensitivity and broaden the scope of ctDNA applications. Circulating viral DNA may be utilized to monitor disease in some virally induced malignancies. In spite of increasingly accurate methods of ctDNA detection, results need to be interpreted with caution given that somatic mosaicisms such as clonal hematopoiesis of indeterminate potential (CHIP) may give rise to genetic variants in the bloodstream unrelated to solid tumors, and the limited concordance observed between different commercial platforms. Overall, highly precise ctDNA detection and quantification methods have the potential to transform clinical practice via non-invasive monitoring of solid tumor malignancies, residual disease detection at earlier timepoints than standard clinical and/or imaging surveillance, and treatment personalization based on real-time assessment of the tumor genomic landscape.
Collapse
Affiliation(s)
- Re-I Chin
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kevin Chen
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Abul Usmani
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Chanelle Chua
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Peter K Harris
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael S Binkley
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tej D Azad
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan C Dudley
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA.
- Alvin J. Siteman Cancer Center, Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
75
|
Toward the Development of a Circulating Free DNA-Based In Vitro Diagnostic Test for Infectious Diseases: a Review of Evidence for Tuberculosis. J Clin Microbiol 2019; 57:JCM.01234-18. [PMID: 30404942 PMCID: PMC6440766 DOI: 10.1128/jcm.01234-18] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The detection of circulating free DNA (cfDNA) has transformed the field of oncology and prenatal diagnostics. Clinical application of cfDNA for disease diagnosis and monitoring, however, is relatively recent in the field of infectious disease. The detection of circulating free DNA (cfDNA) has transformed the field of oncology and prenatal diagnostics. Clinical application of cfDNA for disease diagnosis and monitoring, however, is relatively recent in the field of infectious disease. The potential of cfDNA as a noninvasive diagnostic and monitoring tool is especially promising for tuberculosis (TB), as it enables the detection of both pulmonary and extrapulmonary TB from easily accessible urine and/or blood samples from any age group. However, despite the potential of cfDNA detection to identify TB, very few studies are described in the literature to date. A comprehensive search of the literature identified 15 studies that report detecting Mycobacterium tuberculosis DNA in the blood and urine of TB patients with nongenitourinary disease, but in only six of them were the methodological steps considered suitable for cfDNA isolation and detection. The sensitivities and specificities for the diagnosis of pulmonary and extrapulmonary TB cases reported in these six studies are highly variable, falling in the range of 29% to 79% and 67% to 100%, respectively. While most studies could not meet the performance requirements of the high-priority target product profiles (TPP) published by the World Health Organization (WHO), the study results nonetheless show promise for a point-of-care detection assay. Better designed prospective studies, using appropriate samples, will be required to validate cfDNA as a TB biomarker.
Collapse
|
76
|
Fonseca FLA, Alves BDCA. The Rediscovery of the DNA Molecule in Liquid Biopsies in Cancer. Am J Med Sci 2019; 357:449-450. [PMID: 30846187 DOI: 10.1016/j.amjms.2019.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Fernando Luiz Affonso Fonseca
- Laboratório de Análises Clínicas, Faculdade de Medicina do ABC, Santo André, São Paulo, Brazil; Universidade Federal de São Paulo, Diadema, São Paulo, Brazil.
| | | |
Collapse
|
77
|
Wasenang W, Chaiyarit P, Proungvitaya S, Limpaiboon T. Serum cell-free DNA methylation of OPCML and HOXD9 as a biomarker that may aid in differential diagnosis between cholangiocarcinoma and other biliary diseases. Clin Epigenetics 2019; 11:39. [PMID: 30832707 PMCID: PMC6399934 DOI: 10.1186/s13148-019-0634-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 02/18/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cholangiocarcinoma (CCA) is a fatal cancer of the bile duct epithelial cell lining. The misdiagnosis of CCA and other biliary diseases may occur due to the similarity of clinical manifestations and blood tests resulting in inappropriate or delayed treatment. Thus, an accurate and less-invasive method for differentiating CCA from other biliary diseases is inevitable. METHODS We quantified methylation of OPCML, HOXA9, and HOXD9 in serum cell-free DNA (cfDNA) of CCA patients and other biliary diseases using methylation-sensitive high-resolution melting (MS-HRM). Their potency as differential biomarkers between CCA and other biliary diseases was also evaluated by using receiver operating characteristic (ROC) curves. RESULTS The significant difference of methylation levels of OPCML and HOXD9 was observed in serum cfDNA of CCA compared to other biliary diseases. Assessment of serum cfDNA methylation of OPCML and HOXD9 as differential biomarkers of CCA and other biliary diseases showed the area under curve (AUC) of 0.850 (0.759-0.941) for OPCML which sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy were 80.00%, 90.00%, 88.88%, 81.81%, and 85.00%, respectively. The AUC of HOXD9 was 0.789 (0.686-0.892) with sensitivity, specificity, PPV, NPV, and accuracy of 67.50%, 90.00%, 87.09%, 73.46%, and 78.75%, respectively. The combined marker between OPCML and HOXD9 showed sensitivity, specificity, PPV, and NPV of 62.50%, 100%, 100%, and 72.72%, respectively, which may be helpful to prevent a misdiagnosis between CCA and other biliary diseases. CONCLUSIONS Our findings suggest the application of serum cfDNA methylation of OPCML and HOXD9 for differential diagnosis of CCA and other biliary diseases due to its less invasiveness and clinically practical method which may benefit the patients by preventing the misdiagnosis of CCA and avoiding unnecessary surgical intervention.
Collapse
Affiliation(s)
- Wiphawan Wasenang
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
- Biomedical Sciences, Graduate School, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Ponlatham Chaiyarit
- Research Group of Chronic Inflammatory Oral Diseases and Systemic Diseases Associated with Oral Health, Department of Oral Diagnosis, Faculty of Dentistry, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Siriporn Proungvitaya
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Temduang Limpaiboon
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, 40002, Thailand.
- Cholangiocarcinoma Research Institute, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| |
Collapse
|
78
|
Gwak H, Kim J, Cha S, Cheon Y, Kim SI, Kwak B, Hyun KA, Jung HI. On-chip isolation and enrichment of circulating cell-free DNA using microfluidic device. BIOMICROFLUIDICS 2019; 13:024113. [PMID: 31110597 PMCID: PMC6491348 DOI: 10.1063/1.5100009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Circulating cell-free DNA (cfDNA), containing cancer-specific DNAs derived from tumor cells, plays an important role in real-time monitoring of disease progression. Due to the abnormal growth of cancer and the promotion of cancer cell apoptosis by chemotherapy, the higher cfDNA concentration than healthy individuals is closely correlated with the diagnosis and treatment of cancer. Also, the mutation detection in tumor cell-derived cfDNA can be used to predict tumor progression. Human blood contains many blood cells (red blood cells, white blood cells, and platelets), proteins, extracellular vesicles, and so on. These blood components act as the inhibitors when the cfDNA is analyzed using polymerase chain reaction. So, analysis of cfDNA using whole blood directly may affect the sensitivity of the analysis or result in false-negative. The conventional methods of cfDNA isolation, such as silica absorption and polymer-mediated enrichment, are labor-intensive and time-consuming processes that can also lead to the loss of cfDNA in cumbersome procedures. Here, we designed an integrated microfluidic chip capable of on-chip cfDNA extracting to reduce sample loss and processing time. Our proposed device minimizes the number of experimental steps from 5 to 1, the total processing time from 42 to 19 min, and the required volume of washing reagents from 2 to 0.4 ml for cfDNA enrichment compared to the conventional method.
Collapse
Affiliation(s)
- Hogyeong Gwak
- School of Mechanical Engineering, Yonsei University, Seoul 03722, South Korea
| | - Junmoo Kim
- School of Mechanical Engineering, Yonsei University, Seoul 03722, South Korea
| | - Sunyeong Cha
- School of Biological Sciences and Chemistry, Sungshin Women’s University, Seoul 01133, South Korea
| | - Yong–Pil Cheon
- School of Biological Sciences and Chemistry, Sungshin Women’s University, Seoul 01133, South Korea
| | - Seung-Il Kim
- College of Medicine, Yonsei University, Seoul 03722, South Korea
| | - Bongseop Kwak
- College of Medicine, Dongguk University, Goyangsi, Gyeonggi-do 10326, South Korea
| | - Kyung-A Hyun
- School of Mechanical Engineering, Yonsei University, Seoul 03722, South Korea
| | - Hyo-Il Jung
- School of Mechanical Engineering, Yonsei University, Seoul 03722, South Korea
| |
Collapse
|
79
|
A Study of Pre-Analytical Variables and Optimization of Extraction Method for Circulating Tumor DNA Measurements by Digital Droplet PCR. Cancer Epidemiol Biomarkers Prev 2019; 28:909-916. [DOI: 10.1158/1055-9965.epi-18-0586] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/13/2018] [Accepted: 02/25/2019] [Indexed: 11/16/2022] Open
|
80
|
Li W, Cui X, Huo Q, Qi Y, Sun Y, Tan M, Kong Q. Profile of HBV Integration in the Plasma DNA of Hepatocellular Carcinoma Patients. Curr Genomics 2019; 20:61-68. [PMID: 31015792 PMCID: PMC6446477 DOI: 10.2174/1389202919666181002144336] [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: 07/01/2018] [Revised: 08/14/2018] [Accepted: 09/20/2018] [Indexed: 12/11/2022] Open
Abstract
Background: Hepatitis B Viral (HBV) infection is one of the major causes of Hepatocellular Carcinoma (HCC). Mounting evidence had provided that the HBV integration might be a critical con-tributor of HCC carcinogenesis. Objective and Methods: To explore the profile of HBV integration in the plasma DNA, the method of next-generation sequencing, HBV capture and bioinformatics had been employed to screen for HBV in-tegration sites in the plasma samples. Results: In the initial experiment, a total of 87 breakpoints were detected in the 20 plasma samples. The distribution of breakpoints showed that there was significant enrichment of breakpoints in the region of intron. Furthermore, the HBV breakpoints were prone to occur in the region of X protein (1,700-2,000bp) in the plasma samples. The pathway analysis had revealed that the HBV integrations sites were specifically enriched in the cancer pathway. Conclusion: Altogether, our results had provided direct evidence for the HBV integration in plasma DNA, and they might be potentially useful for future HCC prognosis and diagnosis.
Collapse
Affiliation(s)
- Weiyang Li
- 1Jining Medical University, Jining, Shandong272067, China; 2Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, Shandong272067, China; 3Southern University of Science and Technology, Shenzhen518055, China; 4Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen518002, China; 5Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA19104, USA; 6BGI College, University of Chinese Academy of Sciences, Shenzhen518083, China
| | - Xiaofang Cui
- 1Jining Medical University, Jining, Shandong272067, China; 2Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, Shandong272067, China; 3Southern University of Science and Technology, Shenzhen518055, China; 4Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen518002, China; 5Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA19104, USA; 6BGI College, University of Chinese Academy of Sciences, Shenzhen518083, China
| | - Qing Huo
- 1Jining Medical University, Jining, Shandong272067, China; 2Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, Shandong272067, China; 3Southern University of Science and Technology, Shenzhen518055, China; 4Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen518002, China; 5Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA19104, USA; 6BGI College, University of Chinese Academy of Sciences, Shenzhen518083, China
| | - Yanwei Qi
- 1Jining Medical University, Jining, Shandong272067, China; 2Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, Shandong272067, China; 3Southern University of Science and Technology, Shenzhen518055, China; 4Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen518002, China; 5Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA19104, USA; 6BGI College, University of Chinese Academy of Sciences, Shenzhen518083, China
| | - Yuhui Sun
- 1Jining Medical University, Jining, Shandong272067, China; 2Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, Shandong272067, China; 3Southern University of Science and Technology, Shenzhen518055, China; 4Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen518002, China; 5Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA19104, USA; 6BGI College, University of Chinese Academy of Sciences, Shenzhen518083, China
| | - Meihua Tan
- 1Jining Medical University, Jining, Shandong272067, China; 2Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, Shandong272067, China; 3Southern University of Science and Technology, Shenzhen518055, China; 4Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen518002, China; 5Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA19104, USA; 6BGI College, University of Chinese Academy of Sciences, Shenzhen518083, China
| | - Qingsheng Kong
- 1Jining Medical University, Jining, Shandong272067, China; 2Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, Shandong272067, China; 3Southern University of Science and Technology, Shenzhen518055, China; 4Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center, Shenzhen518002, China; 5Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA19104, USA; 6BGI College, University of Chinese Academy of Sciences, Shenzhen518083, China
| |
Collapse
|
81
|
Circulating cell-free DNA in breast cancer: size profiling, levels, and methylation patterns lead to prognostic and predictive classifiers. Oncogene 2019; 38:3387-3401. [PMID: 30643192 DOI: 10.1038/s41388-018-0660-y] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/11/2018] [Accepted: 12/07/2018] [Indexed: 12/24/2022]
Abstract
Blood circulating cell-free DNA (ccfDNA) is a suggested biosource of valuable clinical information for cancer, meeting the need for a minimally-invasive advancement in the route of precision medicine. In this paper, we evaluated the prognostic and predictive potential of ccfDNA parameters in early and advanced breast cancer. Groups consisted of 150 and 16 breast cancer patients under adjuvant and neoadjuvant therapy respectively, 34 patients with metastatic disease and 35 healthy volunteers. Direct quantification of ccfDNA in plasma revealed elevated concentrations correlated to the incidence of death, shorter PFS, and non-response to pharmacotherapy in the metastatic but not in the other groups. The methylation status of a panel of cancer-related genes chosen based on previous expression and epigenetic data (KLK10, SOX17, WNT5A, MSH2, GATA3) was assessed by quantitative methylation-specific PCR. All but the GATA3 gene was more frequently methylated in all the patient groups than in healthy individuals (all p < 0.05). The methylation of WNT5A was statistically significantly correlated to greater tumor size and poor prognosis characteristics and in advanced stage disease with shorter OS. In the metastatic group, also SOX17 methylation was significantly correlated to the incidence of death, shorter PFS, and OS. KLK10 methylation was significantly correlated to unfavorable clinicopathological characteristics and relapse, whereas in the adjuvant group to shorter DFI. Methylation of at least 3 or 4 genes was significantly correlated to shorter OS and no pharmacotherapy response, respectively. Classification analysis by a fully automated, machine learning software produced a single-parametric linear model using ccfDNA plasma concentration values, with great discriminating power to predict response to chemotherapy (AUC 0.803, 95% CI [0.606, 1.000]) in the metastatic group. Two more multi-parametric signatures were produced for the metastatic group, predicting survival and disease outcome. Finally, a multiple logistic regression model was constructed, discriminating between patient groups and healthy individuals. Overall, ccfDNA emerged as a highly potent predictive classifier in metastatic breast cancer. Upon prospective clinical evaluation, all the signatures produced could aid accurate prognosis.
Collapse
|
82
|
Abstract
Cell-free DNA integrity (cfDNAi) could be a valuable biomarker for solid tumors, to define prognosis and response to therapy. Several elements have been studied for cfDNAi, such as specific genes involved in cancer progression or repetitive DNA sequences as surrogate markers for the whole circulating DNA.However, the lack of a standardized method for cfDNAi evaluation remains one of its main critical issues. Apoptotic index (AI) and integrity index (II) of cfDNA could be useful biomarkers to identify the patients likely to recur, progress, or relapse, which is an urgent need in translational research in oncology.Here it is provided an adequate method of cfDNAi analysis: a cheap and reproducible tool, robust and performable in all laboratories using a real-time PCR instrument.
Collapse
|
83
|
van Dessel LF, Vitale SR, Helmijr JCA, Wilting SM, van der Vlugt-Daane M, Oomen-de Hoop E, Sleijfer S, Martens JWM, Jansen MPHM, Lolkema MP. High-throughput isolation of circulating tumor DNA: a comparison of automated platforms. Mol Oncol 2018; 13:392-402. [PMID: 30516338 PMCID: PMC6360376 DOI: 10.1002/1878-0261.12415] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/09/2018] [Accepted: 11/19/2018] [Indexed: 01/06/2023] Open
Abstract
The emerging interest in circulating tumor DNA (ctDNA) analyses for clinical trials has necessitated the development of a high-throughput method for fast, reproducible, and efficient isolation of ctDNA. Currently, the majority of ctDNA studies use the manual QIAamp (QA) platform to isolate DNA from blood. The purpose of this study was to compare two competing automated DNA isolation platforms [Maxwell (MX) and QIAsymphony (QS)] to the current 'gold standard' QA to facilitate high-throughput processing of samples in prospective trials. We obtained blood samples from healthy blood donors and metastatic cancer patients for plasma isolation. Total cell-free DNA (cfDNA) quantity was assessed by TERT quantitative PCR. Recovery efficiency was investigated by quantitative PCR analysis of spiked-in synthetic plant DNA. In addition, a β-actin fragmentation assay was performed to determine the amount of contamination by genomic DNA from lysed leukocytes. ctDNA quality was assessed by digital PCR for somatic variant detection. cfDNA quantity and recovery efficiency were lowest using the MX platform, whereas QA and QS showed a comparable performance. All platforms preferentially isolated small (136 bp) DNA fragments over large (420 and 2000 bp) DNA fragments. Detection of the number variant and wild-type molecules was most comparable between QA and QS. However, there was no significant difference in variant allele frequency comparing QS and MX to QA. In summary, we show that the QS platform has comparable performance to QA, the 'gold standard', and outperformed the MX platform depending on the readout used. We conclude that the QS can replace the more laborious QA platform, especially when high-throughput cfDNA isolation is needed.
Collapse
Affiliation(s)
- Lisanne F van Dessel
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands.,Workgroup Cancer Genomics Netherlands, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Silvia R Vitale
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands.,Workgroup Cancer Genomics Netherlands, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands.,Department of Clinical and Experimental Medicine, Center for Experimental Oncology and Hematology, University of Catania, Italy
| | - Jean C A Helmijr
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands.,Workgroup Cancer Genomics Netherlands, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Michelle van der Vlugt-Daane
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands.,Workgroup Cancer Genomics Netherlands, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Esther Oomen-de Hoop
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands.,Workgroup Cancer Genomics Netherlands, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands.,Workgroup Cancer Genomics Netherlands, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| |
Collapse
|
84
|
Rohanizadegan M. Analysis of circulating tumor DNA in breast cancer as a diagnostic and prognostic biomarker. Cancer Genet 2018; 228-229:159-168. [PMID: 29572011 PMCID: PMC6108954 DOI: 10.1016/j.cancergen.2018.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 01/15/2018] [Accepted: 02/16/2018] [Indexed: 12/17/2022]
Abstract
Despite all the advances in diagnosis and treatment of breast cancer, a large number of patients suffer from late diagnosis or recurrence of their disease. Current available imaging modalities do not reveal micrometastasis and tumor biopsy is an invasive method to detect early stage or recurrent cancer, signifying the need for an inexpensive, non-invasive diagnostic modality. Cell-free tumor DNA (ctDNA) has been tried for early detection and targeted therapy of breast cancer, but its diagnostic and prognostic utility is still under investigation. This review summarizes the existing evidence on the use of ctDNA specifically in breast cancer, including detection methods, diagnostic accuracy, role in genetics and epigenetics evaluation of the tumor, and comparison with other biomarkers. Current evidence suggests that increasing levels of ctDNA in breast cancer can be of significant diagnostic value for early detection of breast cancer although the sensitivity and specificity of the methods is still suboptimal. Additionally, ctDNA allows for characterizing the tumor in a non-invasive way and monitor the response to therapy, although discordance of ctDNA results with direct biopsy (i.e. due to tumor heterogeneity) is still considered a notable limitation.
Collapse
Affiliation(s)
- Mersedeh Rohanizadegan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
85
|
Zhai LY, Li MX, Pan WL, Chen Y, Li MM, Pang JX, Zheng L, Chen JX, Duan WJ. In Situ Detection of Plasma Exosomal MicroRNA-1246 for Breast Cancer Diagnostics by a Au Nanoflare Probe. ACS APPLIED MATERIALS & INTERFACES 2018; 10:39478-39486. [PMID: 30350935 DOI: 10.1021/acsami.8b12725] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Breast cancer is the second cause of cancer mortality in women globally. Early detection, treatment, and metastasis monitoring are of great importance to favorable prognosis. Although conventional diagnostic methods, such as breast X-ray mammography and image positioning biopsy, are accurate, they could cause radioactive or invasive damage to patients. Liquid biopsy as a noninvasive method is convenient for repeated sampling in clinical cancer prognostic, metastatic evaluation, and relapse monitoring. MicroRNAs encased in exosomes circulating in biofluids are promising candidate cancer biomarkers because of their cancer-specific expression profiles. Here, we report an in situ detection of microRNA-1246 (miR-1246) in human plasma exosomes as breast cancer biomarker by a nucleic acid functionalized Au nanoflare probe. Needing neither time-consuming and costly isolation of exosomes from the plasma sample nor transfection means, the Au nanoflare probe can directly enter the plasma exosomes to generate fluorescent signal quantitatively by specifically targeting miR-1246. Only 40 μL of plasma is needed to incubate 4 h with the probe, giving signal sensitive enough to distinguish samples of breast cancer to normal control. Using plasma miR-1246 level detected by our assay as a marker, we differentiated 46 breast cancer patients from 28 healthy controls with 100% sensitivity and 92.9% specificity at the best cutoff. This simple, accurate, sensitive, and cost-effective liquid biopsy by the Au nanoflare probe is potent to be developed as a noninvasive breast cancer diagnostic assay for clinical adaption.
Collapse
Affiliation(s)
| | | | | | | | - Min-Min Li
- Center of Clinical Laboratory , The First Affiliated Hospital of Jinan University , Guangzhou 510630 , People's Republic of China
| | | | | | | | | |
Collapse
|
86
|
Choudhury AD, Werner L, Francini E, Wei XX, Ha G, Freeman SS, Rhoades J, Reed SC, Gydush G, Rotem D, Lo C, Taplin ME, Harshman LC, Zhang Z, O'Connor EP, Stover DG, Parsons HA, Getz G, Meyerson M, Love JC, Hahn WC, Adalsteinsson VA. Tumor fraction in cell-free DNA as a biomarker in prostate cancer. JCI Insight 2018; 3:122109. [PMID: 30385733 DOI: 10.1172/jci.insight.122109] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/02/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Tumor content in circulating cell-free DNA (cfDNA) is a promising biomarker, but longitudinal dynamics of tumor-derived and non-tumor-derived cfDNA through multiple courses of therapy have not been well described. METHODS CfDNA from 663 plasma samples from 140 patients with castration-resistant prostate cancer (CRPC) was subject to sparse whole genome sequencing. Tumor fraction (TFx) estimated using the computational tool ichorCNA was correlated with clinical features and responses to therapy. RESULTS TFx associated with the number of bone metastases (median TFx = 0.014 with no bone metastases, 0.047 with 1-3 bone metastases, 0.190 for 4+ bone metastases; P < 0.0001) and with visceral metastases (P < 0.0001). In multivariable analysis, TFx remained associated with metastasis location (P = 0.042); TFx was positively correlated with alkaline phosphatase (P = 0.0227) and negatively correlated with hemoglobin (Hgb) (P < 0.001), but it was not correlated with prostate specific antigen (PSA) (P = 0.75). Tumor-derived and non-tumor-derived cfDNA track together and do not increase with generalized tissue damage from chemotherapy or radiation at the time scales examined. All new treatments that led to ≥30% PSA decline at 6 weeks were associated with TFx decline when baseline TFx was >7%; however, TFx in patients being subsequently maintained on secondary hormonal therapy was quite dynamic. CONCLUSION TFx correlates with clinical features associated with overall survival in CRPC, and TFx decline is a promising biomarker for initial therapeutic response. TRIAL REGISTRATION Dana-Farber/Harvard Cancer Center (DF/HCC) protocol no. 18-135. FUNDING Wong Family Award in Translational Oncology, Dana Farber Cancer Institute Medical Oncology grant, Gerstner Family Foundation, Janssen Pharmaceuticals Inc., and Koch Institute Support (core) grant P30-CA14051 from the National Cancer Institute (NCI).
Collapse
Affiliation(s)
- Atish D Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lillian Werner
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Edoardo Francini
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Sapienza University of Rome, Rome, Italy
| | - Xiao X Wei
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Gavin Ha
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samuel S Freeman
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Justin Rhoades
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Sarah C Reed
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gregory Gydush
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Denisse Rotem
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christopher Lo
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Lauren C Harshman
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Zhenwei Zhang
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | | | - Heather A Parsons
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gad Getz
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - J Christopher Love
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Viktor A Adalsteinsson
- Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
87
|
Malbec R, Cacheux J, Cordelier P, Leichlé T, Joseph P, Bancaud A. Microfluidics for minute DNA sample analysis: open challenges for genetic testing of cell-free circulating DNA in blood plasma. MICRO AND NANO ENGINEERING 2018. [DOI: 10.1016/j.mne.2018.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
88
|
Li Q, Wang X, Li X, He X, Wan Q, Yin J, Sun J, Yang X, Chen Q, Miao X. Obtaining High-Quality Blood Specimens for Downstream Applications: A Review of Current Knowledge and Best Practices. Biopreserv Biobank 2018; 16:411-418. [PMID: 30383403 DOI: 10.1089/bio.2018.0052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Blood is a biological fluid that contains multiple blood fraction and cellular components. High-quality blood specimens are essential prerequisites for various downstream applications such as molecular epidemiology studies, genomics, and proteomics studies. Currently, protocols and research publications concerning the collection, handling, preservation, and stability of blood or blood fractions are constantly emerging. Moreover, standardized guidelines are a requirement for biorepositories to tightly control preanalytical variables originating from these procedures and obtain high-quality blood specimen for downstream analyses. In this review article, we summarize the best practices and fit-for-purpose protocols regarding blood collection, processing, storage, and stability. In addition, we present some typical quality biomarkers, which could be used to evaluate the integrity of blood specimens.
Collapse
Affiliation(s)
- Qiyuan Li
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xian Wang
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xue Li
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xuheng He
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Qian Wan
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jiefang Yin
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jianbo Sun
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xiaoping Yang
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Qiaohong Chen
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xinyuan Miao
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| |
Collapse
|
89
|
Leão R, Ahmad AE, Hamilton RJ. Testicular Cancer Biomarkers: A Role for Precision Medicine in Testicular Cancer. Clin Genitourin Cancer 2018; 17:e176-e183. [PMID: 30497810 DOI: 10.1016/j.clgc.2018.10.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/11/2018] [Accepted: 10/14/2018] [Indexed: 12/16/2022]
Abstract
Testicular germ cell tumors (TGCTs) represent the most common solid tumors among men aged 15 to 34 years. Fortunately, recent advances have made testicular cancer a highly curable disease. Despite the high cure rates, there are still several areas in testis cancer care where treatment decisions are controversial and guided only with clinical factors and historic serum tumor markers. Unfortunately, unlike other genitourinary malignancies, modern research techniques have not been widely tested or applied to germ cell tumors, perhaps as a result of excellent prognosis in this cohort of young men. Despite this, there remain numerous challenges and pitfalls in testis cancer care that need to be addressed. A reliable set of biomarkers could be extremely useful in helping risk-stratify patients, detect relapse early, guide surgical decision-making, and tailor follow-up. Current tumor markers (Alpha-fetoprotein, human chorionic gonadotrophin, and lactate dehydrogenase) have low accuracy and low sensitivity when used not only as diagnostic but also as prognostic and predictive markers. In twenty-first century medicine, there is a role for further prognostic stratification and the development of novel biomarkers that offer greater sensitivity and specificity for TGCTs. Despite the initial promising results, the majority of preclinical biomarkers do not, as yet have a proven validated role in clinical practice, and future prospective trials are needed to support and confirm the results of cohort studies. In this narrative review, we aimed to highlight the recent innovations in the development and implementation of novel testicular tumor markers and discuss their clinical applications and limitations in the management of this disease.
Collapse
Affiliation(s)
- Ricardo Leão
- Division of Urology, Department of Surgery, University of Toronto, Toronto, Ontario, Canada; Faculty of Medicine, University of Coimbra, Coimbra, Portugal; CUF Department of Urology, Lisbon, Portugal
| | - Ardalan E Ahmad
- Division of Urology, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Robert J Hamilton
- Division of Urology, Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
90
|
Mojtabanezhad Shariatpanahi A, Rokni P, Shahabi E, Varshoee Tabrizi F, Kerachian MA. Simple and cost-effective laboratory methods to evaluate and validate cell-free DNA isolation. BMC Res Notes 2018; 11:757. [PMID: 30352614 PMCID: PMC6199704 DOI: 10.1186/s13104-018-3866-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/17/2018] [Indexed: 01/26/2023] Open
Abstract
Objective In the present study, we investigated different simple and cost effective methods to evaluate and validate cell free DNA (cfDNA) isolation. The ability of the QIAamp DNA Blood Mini Kit method to extract cfDNA was assessed by several approaches, including purification of endogenous cfDNA and exogenous spike-in control material, prior to plasma extraction, and followed by quantitative-PCR. Results Using QIAamp DNA Blood Mini kit, nearly 27% (380 bp) to 35% (173 bp) cfDNA was recovered with a higher recovery of smaller size cfDNA (173 bp) in comparison to larger ones (380 bp). These simple laboratory methods can be used to assess the efficiency of any cfDNA isolation method. Electronic supplementary material The online version of this article (10.1186/s13104-018-3866-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Parisa Rokni
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.,Department of Medical Genetic, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elaheh Shahabi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.,Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | | | - Mohammad Amin Kerachian
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran. .,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran. .,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
91
|
Somatic alterations in circulating cell-free DNA of oesophageal carcinoma patients during primary staging are indicative for post-surgical tumour recurrence. Sci Rep 2018; 8:14941. [PMID: 30297788 PMCID: PMC6175817 DOI: 10.1038/s41598-018-33027-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 09/20/2018] [Indexed: 12/18/2022] Open
Abstract
Oesophageal cancer (OC) has high mortality. This study aims at determining the feasibility of liquid biopsies for genomic profiling in early stage OC, comparing two different technologies for mutational analysis in circulating cell -free DNA (ccfDNA) and evaluating the clinical impact of these somatic alterations during primary staging. In 25 patients with locally advanced OC, endoscopic tumour biopsies and simultaneous blood samples were taken during primary staging. Genomic DNA from biopsies and ccfDNA were analysed for mutations using a 12 gene panel next-generation sequencing (NGS) assay as well as digital droplet PCR (ddPCR). Genetic data was correlated with patients' outcome. In 21 of the tested biopsies (84%) at least one somatic mutation was detected by NGS. Mutations detected by NGS were detectable by ddPCR with similar allele frequencies. In three out of the 21 patients with proven mutations, the same mutations were also detectable in ccfDNA using NGS (14%). In contrast, ddPCR detected mutations in ccfDNA of five additional patients (8/21, 38%). Post-surgical outcome analysis was performed for those patients who had received complete tumour resection (n = 16). Five of them suffered from an early relapse within the first year after surgery, including four with detectable somatic mutations in ccfDNA during primary staging. Taken together, we showed a higher sensitivity for ddPCR compared to NGS in detecting mutated ccfDNA in OC. Detection of somatically altered ccfDNA during primary staging seems to be indicative for post-surgical tumour recurrence.
Collapse
|
92
|
Syedmoradi L, Esmaeili F, Norton ML. Towards DNA methylation detection using biosensors. Analyst 2018; 141:5922-5943. [PMID: 27704092 DOI: 10.1039/c6an01649a] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methylation, a stable and heritable covalent modification which mostly occurs in the context of a CpG dinucleotide, has great potential as a biomarker to detect disease, provide prognoses and predict therapeutic responses. It can be detected in a quantitative manner by many different approaches both genome-wide and at specific gene loci, in various biological fluids such as urine, plasma, and serum, which can be obtained without invasive procedures. The current, classical methods are effective in studying DNA methylation patterns, however, for the most part; they have major drawbacks such as expensive instruments, complicated and time consuming protocols as well as relatively low sensitivity, and high false positive rates. To overcome these obstacles, great efforts have been made toward the development of reliable sensor devices to solve these limitations, providing sensitive, fast and cost-effective measurements. The use of biosensors for DNA methylation biomarkers has increased in recent years, because they are portable, simple, rapid, and inexpensive which offers a straightforward way to detect methylated biomarkers. In this review, we give an overview of the conventional techniques for the detection of DNA methylation and then will focus on recent advances in biosensor based methylation detection that eliminate bisulfite conversion and PCR amplification.
Collapse
Affiliation(s)
- Leila Syedmoradi
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fariba Esmaeili
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Michael L Norton
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, WV 25755, USA.
| |
Collapse
|
93
|
Utility of circulating tumor DNA in cancer diagnostics with emphasis on early detection. BMC Med 2018; 16:166. [PMID: 30285732 PMCID: PMC6167864 DOI: 10.1186/s12916-018-1157-9] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/17/2018] [Indexed: 02/06/2023] Open
Abstract
Various recent studies have focused on analyzing tumor genetic material released into the blood stream, known as circulating tumor DNA (ctDNA). Herein, we describe current research on the application of ctDNA to cancer management, including prognosis determination, monitoring for treatment efficacy/relapse, treatment selection, and quantification of tumor size and disease burden. Specifically, we examine the utility of ctDNA for early cancer diagnostics focusing on the development of a blood test to detect cancer in asymptomatic individuals by sequencing and analyzing mutations in ctDNA. Next, we discuss the prospect of using ctDNA to test for cancer, and present our calculations based on previously published empirical findings in cancer and prenatal diagnostics. We show that very early stage (asymptomatic) tumors are not likely to release enough ctDNA to be detectable in a typical blood draw of 10 mL. Data are also presented showing that mutations in circulating free DNA can be found in healthy individuals and will likely be very difficult to distinguish from those associated with cancer.We conclude that the ctDNA test, in addition to its high cost and complexity, will likely suffer from the same issues of low sensitivity and specificity as traditional biomarkers when applied to population screening and early (asymptomatic) cancer diagnosis.
Collapse
|
94
|
Niu Z, Tang W, Liu T, Xu P, Zhu D, Ji M, Huang W, Ren L, Wei Y, Xu J. Cell-free DNA derived from cancer cells facilitates tumor malignancy through Toll-like receptor 9 signaling-triggered interleukin-8 secretion in colorectal cancer. Acta Biochim Biophys Sin (Shanghai) 2018; 50:1007-1017. [PMID: 30239551 DOI: 10.1093/abbs/gmy104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Indexed: 12/20/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) has become a potential diagnostic and prognostic biomarker for colorectal cancer (CRC). In non-cancerous diseases, it has been confirmed that cfDNA can be recognized by Toll-like receptor 9 (TLR9), leading to a significant biological change. Nevertheless, the biological significance of cfDNA and its relationship with TLR9 in tumor malignancy is still unclear. Therefore, the purpose of this study is to explore the biological role of cfDNA in colorectal cancer (CRC). The expression of TLR9 was measured in different CRC cell lines and cancerous samples by RT-PCR or immunohistochemistry, which showed that high expression of TLR9 was significantly correlated with the tumor metastasis, advanced TNM stage and poor prognosis of patients. Then, cfDNA was obtained from fluorouracil (5FU)-induced apoptotic cancer cells in vitro and transfection techniques were used to transfect siRNA and cDNA plasmid for TLR9. Cancer cells were stimulated using isolated cfDNA fragments, and results showed that cfDNA could promote colorectal cancer cell proliferation via TLR9. Meanwhile, we demonstrated that the cfDNA binding to TLR9 could facilitate cell migration and invasion. Finally, we demonstrated that cfDNA initiated downstream TLR9-MyD88 signaling and induced robust release of chemokine interleukin 8 (IL-8), which helped to elucidate the mechanisms underlying these phenomena. Our data suggest that cancer cell-derived cfDNA contributes to cancer progression through activation of TLR9-MyD88 signaling and IL-8 secretion in CRC. These findings provide a novel perspective for understanding of tumor progression and provoke a potential therapeutic target for CRC treatment.
Collapse
Affiliation(s)
- Zhengchuan Niu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Wentao Tang
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Tianyu Liu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Pingping Xu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Dexiang Zhu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Meiling Ji
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Wenbai Huang
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Li Ren
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Ye Wei
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| |
Collapse
|
95
|
Hwang MT, Wang Z, Ping J, Ban DK, Shiah ZC, Antonschmidt L, Lee J, Liu Y, Karkisaval AG, Johnson ATC, Fan C, Glinsky G, Lal R. DNA Nanotweezers and Graphene Transistor Enable Label-Free Genotyping. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1802440. [PMID: 29984525 PMCID: PMC6326894 DOI: 10.1002/adma.201802440] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/16/2018] [Indexed: 05/04/2023]
Abstract
Electronic DNA-biosensor with a single nucleotide resolution capability is highly desirable for personalized medicine. However, existing DNA-biosensors, especially single nucleotide polymorphism (SNP) detection systems, have poor sensitivity and specificity and lack real-time wireless data transmission. DNA-tweezers with graphene field effect transistor (FET) are used for SNP detection and data are transmitted wirelessly for analysis. Picomolar sensitivity of quantitative SNP detection is achieved by observing changes in Dirac point shift and resistance change. The use of DNA-tweezers probe with high-quality graphene FET significantly improves analytical characteristics of SNP detection by enhancing the sensitivity more than 1000-fold in comparison to previous work. The electrical signal resulting from resistance changes triggered by DNA strand-displacement and related changes in the DNA geometry is recorded and transmitted remotely to personal electronics. Practical implementation of this enabling technology will provide cheaper, faster, and portable point-of-care molecular health status monitoring and diagnostic devices.
Collapse
Affiliation(s)
- Michael T Hwang
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Zejun Wang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jinglei Ping
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Deependra Kumar Ban
- Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Zi Chao Shiah
- Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Leif Antonschmidt
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Joon Lee
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Yushuang Liu
- School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot, 010018, China
| | - Abhijith G Karkisaval
- Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Alan T Charlie Johnson
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Chunhai Fan
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Gennadi Glinsky
- Institute of Engineering in Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ratnesh Lal
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| |
Collapse
|
96
|
Paraskevaidi M, Morais CLM, Raglan O, Lima KMG, Paraskevaidis E, Martin-Hirsch PL, Kyrgiou M, Martin FL. Aluminium foil as an alternative substrate for the spectroscopic interrogation of endometrial cancer. JOURNAL OF BIOPHOTONICS 2018; 11:e201700372. [PMID: 29512302 DOI: 10.1002/jbio.201700372] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/04/2018] [Indexed: 06/08/2023]
Abstract
Biospectroscopy has the potential to investigate and characterize biological samples and could, therefore, be utilized to diagnose various diseases in a clinical environment. An important consideration in spectrochemical studies is the cost-effectiveness of the substrate used to support the sample, as high expense would limit their translation into clinic. In this paper, the performance of low-cost aluminium (Al) foil substrates was compared with the commonly used low-emissivity (low-E) slides. Attenuated total reflection-Fourier transform infrared spectroscopy was used to analyse blood plasma and serum samples from women with endometrial cancer and healthy controls. The 2 populations were differentiated using principal component analysis with support vector machines with 100% sensitivity in plasma samples (endometrial cancer = 70; healthy controls = 15) using both Al foil and low-E slides as substrates. The same sensitivity results (100%) were achieved for serum samples (endometrial cancer = 60; healthy controls = 15). Specificity was found higher using Al foil (90%) in comparison to low-E slides (85%) and lower using Al foil (70%) in comparison to low-E slides in serum samples. The establishment of Al foil as low-cost and highly performing substrate would pave the way for large-scale, multicentre studies and potentially for routine clinical use.
Collapse
Affiliation(s)
- Maria Paraskevaidi
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, UK
| | - Camilo L M Morais
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, UK
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Olivia Raglan
- Faculty of Medicine, Institute of Reproductive and Developmental Biology, Imperial College, London, UK
| | - Kássio M G Lima
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | - Pierre L Martin-Hirsch
- Department of Obstetrics and Gynaecology, Sharoe Green Unit, Lancashire Teaching Hospitals NHS Foundation, Preston, UK
| | - Maria Kyrgiou
- Faculty of Medicine, Institute of Reproductive and Developmental Biology, Imperial College, London, UK
| | - Francis L Martin
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, UK
| |
Collapse
|
97
|
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.
Collapse
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.
| |
Collapse
|
98
|
Zhong L, Chen J, Huang X, Li Y, Jiang T. Monitoring immunoglobulin heavy chain and T-cell receptor gene rearrangement in cfDNA as minimal residual disease detection for patients with acute myeloid leukemia. Oncol Lett 2018; 16:2279-2288. [PMID: 30008930 PMCID: PMC6036514 DOI: 10.3892/ol.2018.8966] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/31/2018] [Indexed: 12/16/2022] Open
Abstract
The present study aimed to examine whether monoclonal immunoglobulin heavy chain (IGH) or T-cell receptor (TCR) gene rearrangement in cell-free DNA (cfDNA) may be used for minimal residual disease (MRD) monitoring in patients with acute myeloid leukemia (AML). Monoclonal IGH and TCR rearrangement in cfDNA were monitored in patients with AML. A total of 94 (40%) patients had monoclonal IGH or TCR rearrangements in cfDNA at diagnosis; 84% of these patients (79 cases) achieved complete remission following 1–3 courses of induction chemotherapy. Among these cases, 89.9% were negative for monoclonal IGH or TCR rearrangement in cfDNA following consolidation chemotherapies. A total of 8 patients with consistently positive monoclonal IGH or TCR rearrangement in cfDNA relapsed within 6–10 months. During follow up, 39 patients demonstrated positive monoclonal IGH or TCR rearrangement in cfDNA and relapsed. Recurrence of monoclonal IGH or TCR rearrangement in cfDNA was observed 1–3 months earlier than bone marrow relapse and 11 patients with solitary extramedullary relapse demonstrated positive monoclonal IGH or TCR rearrangement recurrence in cfDNA. In conclusion, the detection of monoclonal IGH and TCR rearrangement in cfDNA may represent a useful tool for MRD monitoring in patients with AML.
Collapse
Affiliation(s)
- Ling Zhong
- Department of Clinical Laboratory, Sichuan Academy of Medical Science, Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, P.R. China
| | - Jiao Chen
- Department of Hematology, Sichuan Academy of Medical Science, Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, P.R. China
| | - Xiaobing Huang
- Department of Hematology, Sichuan Academy of Medical Science, Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, P.R. China
| | - Yanxing Li
- Department of Clinical Laboratory, Sichuan Academy of Medical Science, Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, P.R. China
| | - Tao Jiang
- Department of Hematology, Sichuan Academy of Medical Science, Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, P.R. China
| |
Collapse
|
99
|
Yadav DK, Bai X, Yadav RK, Singh A, Li G, Ma T, Chen W, Liang T. Liquid biopsy in pancreatic cancer: the beginning of a new era. Oncotarget 2018; 9:26900-26933. [PMID: 29928492 PMCID: PMC6003564 DOI: 10.18632/oncotarget.24809] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/25/2018] [Indexed: 12/21/2022] Open
Abstract
With dismal survival rate pancreatic cancer remains one of the most aggressive and devastating malignancy. Predominantly, due to the absence of a dependable methodology for early identification and limited therapeutic options for advanced disease. However, it takes over 17 years to develop pancreatic cancer from initiation of mutation to metastatic cancer; therefore, if diagnosed early; it may increase overall survival dramatically, thus, providing a window of opportunity for early detection. Recently, genomic expression analysis defined 4 subtypes of pancreatic cancer based on mutated genes. Hence, we need simple and standard, minimally invasive test that can monitor those altered genes or their associated pathways in time for the success of precision medicine, and liquid biopsy seems to be one answer to all these questions. Again, liquid biopsy has an ability to pair with genomic tests. Additionally, liquid biopsy based development of circulating tumor cells derived xenografts, 3D organoids system, real-time monitoring of genetic mutations by circulating tumor DNA and exosome as the targeted drug delivery vehicle holds lots of potential for the treatment and cure of pancreatic cancer. At present, diagnosis of pancreatic cancer is frantically done on the premise of CA19-9 and radiological features only, which doesn't give a picture of genetic mutations and epigenetic alteration involved. In this manner, the current diagnostic paradigm for pancreatic cancer diagnosis experiences low diagnostic accuracy. This review article discusses the current state of liquid biopsy in pancreatic cancer as diagnostic and therapeutic tools and future perspectives of research in the light of circulating tumor cells, circulating tumor DNA and exosomes.
Collapse
Affiliation(s)
- Dipesh Kumar Yadav
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Rajesh Kumar Yadav
- Department of Pharmacology, Gandaki Medical College, Tribhuwan University, Institute of Medicine, Pokhara 33700, Nepal
| | - Alina Singh
- Department of Surgery, Bir Hospital, National Academy of Medical Science, Kanti Path, Kathmandu 44600, Nepal
| | - Guogang Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Tao Ma
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Wei Chen
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| |
Collapse
|
100
|
Xie J, Yang J, Hu P. Correlations of Circulating Cell-Free DNA With Clinical Manifestations in Acute Myocardial Infarction. Am J Med Sci 2018; 356:121-129. [PMID: 30219153 DOI: 10.1016/j.amjms.2018.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND The objective of the study was to examine the potential use of circulating cell free DNA (cfDNA) in acute myocardial infarction (AMI) patients and correlate it with clinical features. Serial monitoring was conducted to assess any associations to disease. METHODS Quantification of cfDNA was performed on 130 cardiovascular disease (CVD) patients as well as 30 healthy volunteers. Serial samplings were conducted using PicoGreen dsDNA assay. Of the 130 patients with CVD, 100 had an AMI and measurements were taken during treatment. Short and medium intervals serial sampling of patients' blood were undertaken. RESULTS The results were highly correlative of CVD disease status. The mean concentration of cfDNA in patients with AMI was 5 folds higher during the onset of disease compared with healthy volunteers. The cfDNA content was also higher than other patients with CVD. Interestingly, short term monitoring of patients with AMI showed distinct trends that highlighted the severity of the disease and linked to complication events. Medium term monitoring showed 2 distinctive groups with 1 that had their cfDNA returned to basal levels and the other with persistently elevated cfDNA levels. CONCLUSIONS Measuring cfDNA in patients with CVD offers an alternative approach to monitor the disease and has potential clinical applications to identify high-risk individuals.
Collapse
Affiliation(s)
- Jin Xie
- Department of Cardiology, Jingzhou Central Hospital, the Second Clinical Medical College, Yangtze University, Jingzhou, Hubei Sheng, China
| | - Jiawei Yang
- Department of Cardiology, Jingzhou Central Hospital, the Second Clinical Medical College, Yangtze University, Jingzhou, Hubei Sheng, China
| | - Pei Hu
- Department of Cardiology, Jingzhou Central Hospital, the Second Clinical Medical College, Yangtze University, Jingzhou, Hubei Sheng, China.
| |
Collapse
|