1
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Sun Y, Yu H, Han S, Ran R, Yang Y, Tang Y, Wang Y, Zhang W, Tang H, Fu B, Fu B, Weng X, Liu SM, Deng H, Peng S, Zhou X. Method for the extraction of circulating nucleic acids based on MOF reveals cell-free RNA signatures in liver cancer. Natl Sci Rev 2024; 11:nwae022. [PMID: 38348130 PMCID: PMC10860518 DOI: 10.1093/nsr/nwae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/24/2023] [Accepted: 09/24/2023] [Indexed: 02/15/2024] Open
Abstract
Cell-free RNA (cfRNA) allows assessment of health, status, and phenotype of a variety of human organs and is a potential biomarker to non-invasively diagnose numerous diseases. Nevertheless, there is a lack of highly efficient and bias-free cfRNA isolation technologies due to the low abundance and instability of cfRNA. Here, we developed a reproducible and high-efficiency isolation technology for different types of cell-free nucleic acids (containing cfRNA and viral RNA) in serum/plasma based on the inclusion of nucleic acids by metal-organic framework (MOF) materials, which greatly improved the isolation efficiency and was able to preserve RNA integrity compared with the most widely used research kit method. Importantly, the quality of cfRNA extracted by the MOF method is about 10-fold that of the kit method, and the MOF method isolates more than three times as many different RNA types as the kit method. The whole transcriptome mapping characteristics of cfRNA in serum from patients with liver cancer was described and a cfRNA signature with six cfRNAs was identified to diagnose liver cancer with high diagnostic efficiency (area under curve = 0.905 in the independent validation cohort) using this MOF method. Thus, this new MOF isolation technique will advance the field of liquid biopsy, with the potential to diagnose liver cancer.
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Affiliation(s)
- Yuqing Sun
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Haixin Yu
- Department of Digestive Surgical Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shaoqing Han
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Ruoxi Ran
- Department of Clinical Laboratory, Center for Gene Diagnosis and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Ying Yang
- Department of Clinical Laboratory, Center for Gene Diagnosis and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yongling Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Yuhao Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Wenhao Zhang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Heng Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Boqiao Fu
- College of Chemistry and Materials Science, Hubei Engineering University, Xiaogan 432000, China
| | - Boshi Fu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Song-Mei Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Hexiang Deng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Shuang Peng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
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2
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Chauhan US, Kohale MG, Jaiswal N, Wankhade R. Emerging Applications of Liquid Biopsies in Ovarian Cancer. Cureus 2023; 15:e49880. [PMID: 38174205 PMCID: PMC10762500 DOI: 10.7759/cureus.49880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
Liquid biopsy is a new diagnostic tool in precision oncology that can be used as a complementary or alternative method to surgical biopsies. It is a cutting-edge sampling technique that examines distinct cancer components, such as exosomes and circulating tumor cells discharged into the peripheral circulation, to identify tumor biomarkers through various methods, including polymerase chain reaction (PCR). Liquid biopsy has several benefits, including its non-invasiveness and practicality, which permit serial sampling and long-term monitoring of dynamic tumor changes. Ovarian cancer (OC), the most lethal gynecologic malignancy in the world, is typically diagnosed at stages II and III, which makes recovery and treatment extremely difficult. Relapsed OC and chemotherapy resistance of ovarian tumor cells are other clinical challenges. Although liquid biopsy is not a routinely used diagnostic test, it should be utilized in the diagnosis and prognosis of OC for early detection and treatment. It is less intrusive than conventional tissue biopsies, allowing for the continuous collection of serial blood samples to track cancer development in real time. Before therapeutic application, more investigation is required to pinpoint the particular release processes, the source tissue, and the biological significance of the bulk of liquid biopsy contents.
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Affiliation(s)
- Urvi S Chauhan
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Mangesh G Kohale
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Neha Jaiswal
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
| | - Rashmi Wankhade
- Pathology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education & Research (Deemed to be University), Wardha, IND
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3
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Anilkumar KV, Rema LP, John MC, Vanesa John T, George A. miRNAs in the prognosis of triple-negative breast cancer: A review. Life Sci 2023; 333:122183. [PMID: 37858714 DOI: 10.1016/j.lfs.2023.122183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/09/2023] [Accepted: 10/14/2023] [Indexed: 10/21/2023]
Abstract
Triple-Negative Breast Cancer (TNBC) is a highly aggressive and invasive type of breast cancer (BC) with high mortality rate wherein effective target medicaments are lacking. It is a very heterogeneous group with several subtypes that account for 10-20% of cancer among women globally, being negative for three most important receptors (estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2)), with an early and high recurrence resulting in poor survival rate. Therefore, a more thorough knowledge on carcinogenesis of TNBC is required for the development of personalized treatment options. miRNAs can either promote or suppress tumorigenesis and have been linked to a number of features of cancer progression, including proliferation, metastasis, apoptosis, and epithelial-mesenchymal transition (EMT). Recent miRNA research shows that there is great potential for the development of novel biomarkers as they have emerged as drivers of tumorigenesis and provide opportunities to target various components involved in TNBC, thus helping to solve this difficult-to-treat disease. In this review, we summarize the most relevant miRNAs that play an essential role in TNBC biology. Their role with regard to molecular mechanisms underlying TNBC progression has been discussed, and their potential use as therapeutic or prognostic markers to unravel the intricacy of TNBC based on the pieces of evidence obtained from various works of literature has been briefly addressed.
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Affiliation(s)
- Kavya V Anilkumar
- PG and Research Department of Zoology, Maharaja's College, Ernakulam, 682011, India; Cell and Molecular Biology Facility, Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur 680005, Kerala, India
| | - L P Rema
- PG and Research Department of Zoology, Maharaja's College, Ernakulam, 682011, India
| | - Mithun Chacko John
- Department of Medical Oncology, Jubilee Mission Medical College and Research Institute, Thrissur, Kerala 680005, India
| | - T Vanesa John
- Department of Pathology, Jubilee Mission Medical College and Research Institute, Thrissur 680005, Kerala, India
| | - Alex George
- Cell and Molecular Biology Facility, Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur 680005, Kerala, India.
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4
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Zhu JW, Charkhchi P, Akbari MR. Potential clinical utility of liquid biopsies in ovarian cancer. Mol Cancer 2022; 21:114. [PMID: 35545786 PMCID: PMC9092780 DOI: 10.1186/s12943-022-01588-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/27/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Ovarian cancer (OC) is the most lethal gynecologic malignancy worldwide. One of the main challenges in the management of OC is the late clinical presentation of disease that results in poor survival. Conventional tissue biopsy methods and serological biomarkers such as CA-125 have limited clinical applications. Liquid biopsy is a novel sampling method that analyzes distinctive tumour components released into the peripheral circulation, including circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), cell-free RNA (cfRNA), tumour-educated platelets (TEPs) and exosomes. Increasing evidence suggests that liquid biopsy could enhance the clinical management of OC by improving early diagnosis, predicting prognosis, detecting recurrence, and monitoring response to treatment. Capturing the unique tumour genetic landscape can also guide treatment decisions and the selection of appropriate targeted therapies. Key advantages of liquid biopsy include its non-invasive nature and feasibility, which allow for serial sampling and longitudinal monitoring of dynamic tumour changes over time. In this review, we outline the evidence for the clinical utility of each liquid biopsy component and review the advantages and current limitations of applying liquid biopsy in managing ovarian cancer. We also highlight future directions considering the current challenges and explore areas where more studies are warranted to elucidate its emerging clinical potential.
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Affiliation(s)
- Jie Wei Zhu
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Parsa Charkhchi
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada.
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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5
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Quantification of Circulating Cell Free Mitochondrial DNA in Extracellular Vesicles with PicoGreen™ in Liquid Biopsies: Fast Assessment of Disease/Trauma Severity. Cells 2021; 10:cells10040819. [PMID: 33917426 PMCID: PMC8067453 DOI: 10.3390/cells10040819] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/25/2022] Open
Abstract
The analysis of circulating cell free DNA (ccf-DNA) is an emerging diagnostic tool for the detection and monitoring of tissue injury, disease progression, and potential treatment effects. Currently, most of ccf-DNA in tissue and liquid biopsies is analysed with real-time quantitative PCR (qPCR) that is primer- and template-specific, labour intensive and cost-inefficient. In this report we directly compare the amounts of ccf-DNA in serum of healthy volunteers, and subjects presenting with various stages of lung adenocarcinoma, and survivors of traumatic brain injury using qPCR and quantitative PicoGreen™ fluorescence assay. A significant increase of ccf-DNA in lung adenocarcinoma and traumatic brain injury patients, in comparison to the group of healthy human subjects, was found using both analytical methods. However, the direct correlation between PicoGreen™ fluorescence and qPCR was found only when mitochondrial DNA (mtDNA)-specific primers were used. Further analysis of the location of ccf-DNA indicated that the majority of DNA is located within lumen of extracellular vesicles (EVs) and is easily detected with mtDNA-specific primers. We have concluded that due to the presence of active DNases in the blood, the analysis of DNA within EVs has the potential of providing rapid diagnostic outcomes. Moreover, we speculate that accurate and rapid quantification of ccf-DNA with PicoGreen™ fluorescent probe used as a point of care approach could facilitate immediate assessment and treatment of critically ill patients.
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6
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Decazes P, Camus V, Bohers E, Viailly PJ, Tilly H, Ruminy P, Viennot M, Hapdey S, Gardin I, Becker S, Vera P, Jardin F. Correlations between baseline 18F-FDG PET tumour parameters and circulating DNA in diffuse large B cell lymphoma and Hodgkin lymphoma. EJNMMI Res 2020; 10:120. [PMID: 33029662 PMCID: PMC7541805 DOI: 10.1186/s13550-020-00717-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
Background 18F-FDG PET/CT is a standard for many B cell malignancies, while blood DNA measurements are emerging tools. Our objective was to evaluate the correlations between baseline PET parameters and circulating DNA in diffuse large B cell lymphoma (DLBCL) and classical Hodgkin lymphoma (cHL).
Methods Twenty-seven DLBCL and forty-eight cHL were prospectively included. Twelve PET parameters were analysed. Spearman’s correlations were used to compare PET parameters each other and to circulating cell-free DNA ([cfDNA]) and circulating tumour DNA ([ctDNA]). p values were controlled by Benjamini–Hochberg correction. Results Among the PET parameters, three different clusters for tumour burden, fragmentation/massiveness and dispersion parameters were observed. Some PET parameters were significantly correlated with blood DNA parameters, including the total metabolic tumour surface (TMTS) describing the tumour–host interface (e.g. ρ = 0.81 p < 0.001 for [ctDNA] of DLBLC), the tumour median distance between the periphery and the centroid (medPCD) describing the tumour’s massiveness (e.g. ρ = 0.81 p < 0.001 for [ctDNA] of DLBLC) and the volume of the bounding box including tumours (TumBB) describing the disease’s dispersion (e.g. ρ = 0.83 p < 0.001 for [ctDNA] of DLBLC). Conclusions Some PET parameters describing tumour burden, fragmentation/massiveness and dispersion are significantly correlated with circulating DNA parameters of DLBCL and cHL patients. These results could help to understand the pathophysiology of B cell malignancies.
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Affiliation(s)
- Pierre Decazes
- Department of Nuclear Medicine, Henri Becquerel Cancer Centre, Rouen, France. .,QuantIF-LITIS-EA4108, University of Rouen, Rouen, France.
| | - Vincent Camus
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Elodie Bohers
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Pierre-Julien Viailly
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Hervé Tilly
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Philippe Ruminy
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Mathieu Viennot
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
| | - Sébastien Hapdey
- Department of Nuclear Medicine, Henri Becquerel Cancer Centre, Rouen, France.,QuantIF-LITIS-EA4108, University of Rouen, Rouen, France
| | - Isabelle Gardin
- Department of Nuclear Medicine, Henri Becquerel Cancer Centre, Rouen, France.,QuantIF-LITIS-EA4108, University of Rouen, Rouen, France
| | - Stéphanie Becker
- Department of Nuclear Medicine, Henri Becquerel Cancer Centre, Rouen, France.,QuantIF-LITIS-EA4108, University of Rouen, Rouen, France
| | - Pierre Vera
- Department of Nuclear Medicine, Henri Becquerel Cancer Centre, Rouen, France.,QuantIF-LITIS-EA4108, University of Rouen, Rouen, France
| | - Fabrice Jardin
- Department of Haematology, Henri Becquerel Cancer Centre, Rouen, France.,INSERM U1245, Henri Becquerel Cancer Centre and Rouen University, Rouen, France
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7
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Abstract
Pancreatic cancer is the fourth leading cause of cancer death in the United States. Pancreatic cancer presents dismal clinical outcomes in patients, and the incidence of pancreatic cancer has continuously increased to likely become the second most common cause of cancer-related deaths by as early as 2030. One of main reasons for the high mortality rate of pancreatic cancer is the lack of tools for early-stage detection. Current practice in detecting and monitoring therapeutic response in pancreatic cancer relies on imaging analysis and invasive endoscopic examination. Liquid biopsy-based analysis of genetic alterations in biofluids has become a fundamental component in the diagnosis and management of cancers. There is an urgent need for scientific and technological advancement to detect pancreatic cancer early and to develop effective therapies. The development of a highly sensitive and specific liquid biopsy tool will require extensive understanding on the characteristics of circulating tumor DNA in biofluids. Here, we have reviewed the current status of liquid biopsy in detecting and monitoring pancreatic cancers and our understanding of circulating tumor DNA that should be considered for the development of a liquid biopsy tool, which will greatly aid in the diagnosis and healthcare of people at risk.
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8
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The future of cell-free DNA testing to guide therapeutic decisions in B-cell lymphomas. Curr Opin Hematol 2020; 26:281-287. [PMID: 31082825 DOI: 10.1097/moh.0000000000000516] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW Tissue biopsy is the current gold standard technique for diagnosis and molecular profiling of lymphomas, but it carries several disadvantages in terms of procedural risks (infectious and haemorrhagic complications, anaesthesiologic risks) and analytic aspects (heterogeneity of tumors, low representation of tumor cells in the tissue). Noninvasive genotyping of B-cell lymphomas through circulating tumor DNA (ctDNA) is emerging as a practical tool to monitor the genetics and course of the disease from diagnosis to eventual relapse.This review will explore recent advances in the field of liquid biopsy in lymphomas, highlighting their clinical implications. RECENT FINDINGS ctDNA has been recently proposed an alternative source of tumor DNA for genotyping purposes, especially for those samples having low tumor representation or when longitudinal genetic monitoring is limited by the inaccessibility of relapsed tumor tissues. Also, ctDNA has been recently proposed radiation-free tool for the early identification of chemorefractory lymphoma patients. SUMMARY The detection of ctDNA circulating in the bloodstream of lymphoma patients can inform about the genetics of the disease at diagnosis identifying druggable alterations, detect the onset of mutation of resistance during treatment, anticipate about relapse earlier than standard methods [e.g. PET associated with computed tomography (PET/CT)] during follow-up.
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9
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Plasma Cell-Free Human Papillomavirus Oncogene E6 and E7 DNA Predicts Outcome in Oropharyngeal Squamous Cell Carcinoma. J Mol Diagn 2020; 22:1333-1343. [PMID: 32822851 DOI: 10.1016/j.jmoldx.2020.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/24/2022] Open
Abstract
Persistent human papillomavirus (HPV) infection is associated with the development of oropharyngeal squamous cell carcinoma (OPSCC), and increasing incidences of OPSCC are reported. The generally favorable treatment outcome in patients with HPV-driven OPSCC has brought de-escalation of treatment into discussion. Nevertheless, 13% to 25% develop a relapse within two years after current standard treatment. New biomarkers are urgently required to monitor therapy response, tumor burden, and minimal residual disease during follow-up. This observational study examined 50 patients with OPSCC to investigate plasma cell-free (cf) HPV-DNA derived from tumor cells before therapy and during follow-up. Real-time PCR was applied to quantify the DNA concentration of HPV oncogenes E6 and E7. A total of 85.7% of pretreatment samples from patients with HPV-driven OPSCC (n = 28) were positive for at least one marker, and cfHPV-DNA concentration increased with tumor size. Virtually no signals were detected in HPV-negative OPSCC patients (n = 20; P ≤ 0.001). Patients without clinical evidence of recurrence had significantly reduced cfHPV-DNA concentrations after therapy (P ≤ 0.001). Conversely, cfHPV-DNA levels increased or remained above threshold in five patients who had residual disease or developed recurrence. In conclusion, plasma cfHPV-DNA detection correlates with the clinical course of disease in patients with HPV-driven OPSCC. Consequently, extensive clinical investigation should be considered if cfHPV-DNA is detected during follow-up of patients with HPV-driven OPSCC.
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10
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Manoharan A, Sambandam R, Bhat V. Recent technologies enhancing the clinical utility of circulating tumor DNA. Clin Chim Acta 2020; 510:498-506. [PMID: 32795543 DOI: 10.1016/j.cca.2020.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022]
Abstract
Circulating tumor DNA (ctDNA) is a promising blood based biomarker that is set to revolutionize cancer management. Non-invasive biopsy takes precedence over tissue biopsy for enabling longitudinal monitoring, providing a comprehensive profile of tumor heterogeneity and the ease of repeated sampling. Advanced genomic technologies enable real-time disease monitoring, detect minimal residual disease and recurrence at the earliest stages, the potential time points when treatment significantly reduces morbidity and mortality and enable tailored and personalized therapy. The review highlights evidence from literature that make ctDNA a potential liquid biopsy marker and the clinical utility of the recent techniques that leverage up on ctDNA.
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Affiliation(s)
- Aarthi Manoharan
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India
| | - Ravikumar Sambandam
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India.
| | - Vishnu Bhat
- Multi-Disciplinary Center for Biomedical Research, Vinayaka Mission's Research Foundation, Aarupadai Veedu Medical College and Hospital (Deemed-to-be-University), Kirumampakkam, Puducherry 607402, India
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11
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Hufnagl C, Leisch M, Weiss L, Melchardt T, Moik M, Asslaber D, Roland G, Steininger P, Meissnitzer T, Neureiter D, Greil R, Egle A. Evaluation of circulating cell-free DNA as a molecular monitoring tool in patients with metastatic cancer. Oncol Lett 2019; 19:1551-1558. [PMID: 31966080 DOI: 10.3892/ol.2019.11192] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/06/2019] [Indexed: 01/16/2023] Open
Abstract
The clinical decisions made when treating patients with metastatic cancer require knowledge of the current tumor extent and response to therapy. For the majority of solid tumors, a response assessment, which is based on imaging, is used to guide these decisions. However, measuring serum protein biomarkers (i.e. tumor markers) may be of additional use. Furthermore, tumor markers exhibit variable specificity and sensitivity and cannot therefore be solely relied upon when making decisions regarding cancer treatment. Therefore, there is a clinical requirement for the identification of specific, sensitive and quantitative biomarkers. In recent years, circulating cell-free DNA (cfDNA) and mutation-specific circulating cell-free tumor DNA (cftDNA) have been identified as novel potential biomarkers. In the current study, cfDNA and cftDNA were compared using imaging-based staging and current tumor markers in 15 patients with metastatic colorectal, pancreatic or breast cancer. These patients were treated at the Third Medical Department of Paracelsus Medical University Salzburg (Austria). The results of the current study demonstrated a statistically significant correlation between the concentration changes of cfDNA and cftDNA and response to treatment, which was assessed by imaging. A correlation was not indicated with current clinically used tumor markers, including carcinoembryonic antigen, carcinoma antigen 15-3 and carcinoma antigen 19-9. The present study also indicated a correlation between cfDNA and cftDNA and the tumor volume of metastatic lesions, which was not observed with the current clinically used tumor markers. In conclusion, cfDNA and cftDNA exhibit the potential to become novel biomarkers for the response assessment following cancer treatment, and may serve as a tool for the estimation of tumor volume. The current study further supports the increasingly important role of cfDNA and cftDNA as new monitoring tools for use during cancer therapy.
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Affiliation(s)
- Clemens Hufnagl
- Institute of Pathology, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria
| | - Michael Leisch
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Lukas Weiss
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Thomas Melchardt
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Martin Moik
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Daniela Asslaber
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Geisberger Roland
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Philipp Steininger
- Institute for Research and Development on Advanced Radiation Technologies, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria
| | - Thomas Meissnitzer
- Institute of Radiology, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria
| | - Daniel Neureiter
- Institute of Pathology, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria
| | - Richard Greil
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
| | - Alexander Egle
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University Salzburg, A-5020 Salzburg, Austria.,Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, A-5020 Salzburg, Austria.,Cancer Cluster Salzburg, A-5020 Salzburg, Austria
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12
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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.
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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
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13
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Jain S, Lin SY, Song W, Su YH. Urine-Based Liquid Biopsy for Nonurological Cancers. Genet Test Mol Biomarkers 2019; 23:277-283. [PMID: 30986103 DOI: 10.1089/gtmb.2018.0189] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
AIMS The use of circulating cell-free DNA for detection of cancer genetics has been studied extensively. Liquid biopsy often refers to the use of blood as a minimally invasive source of body fluid for detecting circulating tumor DNA (ctDNA). However, urine collection, which is completely noninvasive, has been shown to also have great promise to serve as an alternate body fluid source for ctDNA. In this review article, we focus on the clinical utility of urine for genetic liquid biopsy of nonurological cancers. CONCLUSION Although still in early stages as compared with blood-based liquid biopsy, recent studies have demonstrated the value of urine-based liquid biopsies for: nonurological cancer screening; early detection; monitoring for recurrence and metastasis; and therapeutic efficacy. Overall, the completely noninvasive and patient-friendly nature of the urine-based biopsy warrants further development and offers a promising alternative to blood-based biopsies.
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Affiliation(s)
- Surbhi Jain
- 1 JBS Science, Inc., Doylestown, Pennsylvania
| | | | - Wei Song
- 1 JBS Science, Inc., Doylestown, Pennsylvania
| | - Ying-Hsiu Su
- 2 Department of Translational Medical Science, The Baruch S. Blumberg Institute, Doylestown, Pennsylvania
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14
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Tamkovich S, Laktionov P. Cell-surface-bound circulating DNA in the blood: Biology and clinical application. IUBMB Life 2019; 71:1201-1210. [PMID: 31091350 DOI: 10.1002/iub.2070] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/17/2019] [Indexed: 01/04/2023]
Abstract
Cell-surface-bound extracellular DNA (csbDNA) is present on the outer membrane of blood cells, including both red blood cells and leukocytes. Although less well characterized than cell-free DNA (cfDNA) in plasma and serum, leukocyte and red blood cell csbDNA form a considerable fraction of the blood extracellular nucleic acids pool, with typically at least comparable amount of DNA occurring bound to the outer surface of cells as compared with circulating free DNA in plasma. The cellular origin of csbDNA is not clear; however, as with cfDNA, in patients with cancer a proportion is derived from the tumor, thus making it potentially a useful source of DNA for cancer diagnosis, prognosis, and monitoring. © 2019 IUBMB Life, 71(9):1201-1210, 2019.
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Affiliation(s)
- Svetlana Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk National Research State University, Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia
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15
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Alimirzaie S, Bagherzadeh M, Akbari MR. Liquid biopsy in breast cancer: A comprehensive review. Clin Genet 2019; 95:643-660. [PMID: 30671931 DOI: 10.1111/cge.13514] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/04/2019] [Accepted: 01/11/2019] [Indexed: 12/11/2022]
Abstract
Breast cancer is the most common cancer among women worldwide. Due to its complexity in nature, effective breast cancer treatment can encounter many challenges. Traditional methods of cancer detection such as tissue biopsy are not comprehensive enough to capture the entire genomic landscape of breast tumors. However, with the introduction of novel techniques, the application of liquid biopsy has been enhanced, enabling the improvement of various aspects of breast cancer management including early diagnosis and screening, prediction of prognosis, early detection of relapse, serial sampling and efficient longitudinal monitoring of disease progress and response to treatment. Various components of tumor cells released into the blood circulation can be analyzed in liquid biopsy sampling, some of which include circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), cell-free RNA, tumor-educated platelets and exosomes. These components can be utilized for different purposes. As an example, ctDNA can be sequenced for genetic profiling of the tumors to enhance individualized treatment and longitudinal screening. CTC plasma count analysis or ctDNA detection after curative tumor resection surgery could facilitate early detection of minimal residual disease, aiding in the initiation of adjuvant therapy to prevent recurrence. Furthermore, CTC plasma count can be assessed to determine the stage and prognosis of breast cancer. In this review, we discuss the advantages and limitations of the various components of liquid biopsy used in breast cancer diagnosis and will expand on aspects that require further focus in future research.
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Affiliation(s)
- Sahar Alimirzaie
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, Ontario, Canada.,Faculty of Arts and Science, University of Toronto, Toronto, Ontario, Canada
| | - Maryam Bagherzadeh
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, Ontario, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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16
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Buono G, Gerratana L, Bulfoni M, Provinciali N, Basile D, Giuliano M, Corvaja C, Arpino G, Del Mastro L, De Placido S, De Laurentiis M, Cristofanilli M, Puglisi F. Circulating tumor DNA analysis in breast cancer: Is it ready for prime-time? Cancer Treat Rev 2019; 73:73-83. [PMID: 30682661 DOI: 10.1016/j.ctrv.2019.01.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/06/2023]
Abstract
Precision Medicine is becoming the new paradigm in healthcare as it enables better resources allocation, treatment optimization with a potential side-effects reduction and consequent impact on quality of life and survival. This revolution is being catalyzed by liquid biopsy technologies, which provide prognostic and predictive information for advanced cancer patients, without the analytical and procedural drawbacks of tissue-biopsy. In particular, circulating tumor DNA (ctDNA) is gaining momentum as a clinically feasible option capable to capture both spatial and temporal tumor heterogeneity. Several techniques are currently available for ctDNA extraction and analysis, each with its preferential case scenarios and preanalytical implications which must be taken into consideration to effectively support clinical decision-making and to better highlight its clinical utility. Aim of this review is to summarize both analytical developments and clinical evidences to offer a comprehensive update on the deployment of ctDNA in breast cancer's (BC) characterization and treatment.
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Affiliation(s)
- Giuseppe Buono
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Lorenzo Gerratana
- Department of Medicine (DAME), University of Udine, Italy; Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Michela Bulfoni
- Department of Pathology, ASUIUD University Hospital, Udine, Italy
| | | | - Debora Basile
- Department of Medicine (DAME), University of Udine, Italy
| | - Mario Giuliano
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy; Lester and Sue Smith Breast Center at Baylor College of Medicine, Houston, TX, USA
| | - Carla Corvaja
- Department of Medicine (DAME), University of Udine, Italy
| | - Grazia Arpino
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Lucia Del Mastro
- Department of Medical Oncology, IRCCS AOU San Martino-IST, National Cancer Institute, Genova, Italy
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | | | - Massimo Cristofanilli
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano, PN, Italy
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17
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Bohers E, Viailly PJ, Becker S, Marchand V, Ruminy P, Maingonnat C, Bertrand P, Etancelin P, Picquenot JM, Camus V, Menard AL, Lemasle E, Contentin N, Leprêtre S, Lenain P, Stamatoullas A, Lanic H, Libraire J, Vaudaux S, Pepin LF, Vera P, Tilly H, Jardin F. Non-invasive monitoring of diffuse large B-cell lymphoma by cell-free DNA high-throughput targeted sequencing: analysis of a prospective cohort. Blood Cancer J 2018; 8:74. [PMID: 30069017 PMCID: PMC6070497 DOI: 10.1038/s41408-018-0111-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/28/2018] [Accepted: 06/08/2018] [Indexed: 12/15/2022] Open
Abstract
From a liquid biopsy, cell-free DNA (cfDNA) can provide information regarding basal tumoral genetic patterns and changes upon treatment. In a prospective cohort of 30 diffuse large B-cell lymphomas (DLBCL), we determined the clinical relevance of cfDNA using targeted next-generation sequencing and its correlation with PET scan imaging at the time of diagnosis and during treatment. Using a dedicated DLBCL panel, mutations were identified at baseline for 19 cfDNAs and profiles were consistent with expected DLBCL patterns. Tumor burden-related clinical and PET scan features (LDH, IPI, and metabolic tumor volume) were significantly correlated with the quantity of tumoral cfDNA. Among the four patients presenting additional mutations in their cfDNAs, three had high metabolic tumor volumes, suggesting that cfDNA more accurately reflects tumor heterogeneity than tissues biopsy itself. Mid-treatment, four patients still had basal mutations in their cfDNAs, including three in partial response according to their Deauville scores. Our study highlights the major interests in liquid biopsy, in particular in the context of bulky tumors where cfDNA allows capturing the entire tumoral mutation profile. Therefore, cfDNA analysis in DLBCL represents a complementary approach to PET scan imaging.
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Affiliation(s)
- Elodie Bohers
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | - Stéphanie Becker
- Department of Nuclear Medicine, Centre Henri Becquerel, University of Rouen, Rouen, France
- QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - Vinciane Marchand
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | - Philippe Bertrand
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | | | - Vincent Camus
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Anne-Lise Menard
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Emilie Lemasle
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Nathalie Contentin
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Stéphane Leprêtre
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Pascal Lenain
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | | | - Hélène Lanic
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Julie Libraire
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | | | | | - Pierre Vera
- Department of Nuclear Medicine, Centre Henri Becquerel, University of Rouen, Rouen, France
- QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - Hervé Tilly
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France.
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France.
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France.
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18
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Ge YF, Guan X, Jiang XJ. Clinical significance of Helicobacter pylori in the grouth of ulcerative colitis. Shijie Huaren Xiaohua Zazhi 2018; 26:1071-1076. [DOI: 10.11569/wcjd.v26.i17.1071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the relationship between Helicobacter pylori (H. pylori) infection and ulcerative colitis (UC).
METHODS One hundred and forty-six patients with UC diagnosed by colonoscopy and pathological examination were selected as a UC group. In addition, 150 volunteers who had no obvious colonic lesions as detected by electronic colonoscopy were collected as a control group. Rapid urease test and histopathological biopsy were used to detect H. pylori infection.
RESULTS In UC Group, 146 cases, 27 positive, H. pylori infection positive rate of 18.49%, control group of 150 cases, 64 positive, H. pylori infection positive rate 42.67%, UC group is significantly lower than the control group, the difference is statistically significant (P < 0.05). According to lesion Range: Rectal Group 27 cases, 7 positive, H. pylori positive rate is 21.88%, left half colon group 48 cases, 9 cases positive, H. pylori positive rate is 18.75%, extensive colon group 66 cases, 11 cases positive, H. pylori positive rate is 16.67%. There was no statistically significant difference among the three groups (P > 0.05). Active period of UC patients in 117 cases (80.14%), remission period of UC patients in 29 cases. The positive rate of H. pylori infection was the highest in remission period (37.93%), the lowest rate of severe activity was (6.25%), the difference was obvious (P < 0.05).
CONCLUSION H. pylori infection may have a preventive effect on the grouth of UC, with the severity of the disease increasing, the H. pylori positive rate decreased. In addition, it will be very important to strengthen the follow-up compliance of UC patients.
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Affiliation(s)
- Yong-Fang Ge
- Department of Gastroenterology (Division II), Qingdao Municipal Hospital, Qingdao University Medical College, Qingdao 266000, Shandong Province, China
| | - Xin Guan
- Department of Gastroenterology (Division II), Qingdao Municipal Hospital, Qingdao University Medical College, Qingdao 266000, Shandong Province, China
| | - Xiang-Jun Jiang
- Department of Gastroenterology (Division II), Qingdao Municipal Hospital, Qingdao University Medical College, Qingdao 266000, Shandong Province, China
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19
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Murray MJ, Watson HL, Ward D, Bailey S, Ferraresso M, Nicholson JC, Gnanapragasam VJ, Thomas B, Scarpini CG, Coleman N. "Future-Proofing" Blood Processing for Measurement of Circulating miRNAs in Samples from Biobanks and Prospective Clinical Trials. Cancer Epidemiol Biomarkers Prev 2017; 27:208-218. [PMID: 29254935 DOI: 10.1158/1055-9965.epi-17-0657] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/16/2017] [Accepted: 11/22/2017] [Indexed: 12/12/2022] Open
Abstract
Background: Quantifying circulating nucleic acids is an important new approach to cancer diagnosis/monitoring.Methods: We compared the suitability of serum versus plasma for measuring miRNAs using qRT-PCR and assessed how preanalytic variables that can affect circulating tumor DNA (ctDNA) quantification in plasma also influence miRNA levels.Results: Across 62 blood-derived specimens, plasma samples in EDTA, Streck-DNA, and Streck-RNA tubes showed significantly higher Ct values for multiple housekeeping miRNAs, compared with serum samples. For the EDTA-plasma tubes, this difference was only seen when including the high-speed centrifugation protocol used to optimize ctDNA extraction. In plasma samples derived from blood stored at room temperature for up to 14 days (conditions that typically apply to samples processed for biobanking), levels of endogenous housekeeping miRNAs gradually increased, in parallel with the hemolysis marker hsa-miR-451a, consistent with release from blood cells/platelets. It was necessary to normalize levels of the housekeeping miRNAs to those of hsa-miR-451a, to obtain the stable values needed for referencing test miRNA levels.Conclusions: Our data indicate that plasma samples prepared for ctDNA extraction are suboptimal for miRNA quantification and require the incorporation of multiple data normalization steps. For prospective studies designed to measure both miRNAs and ctDNA, the most suitable approach would be to obtain both serum (for miRNAs) and plasma (for ctDNA). If only plasma can be collected, we recommend an initial low-speed centrifugation step, followed by aliquoting the supernatant into parallel samples, one for direct miRNA quantification, and the other for a further high-speed centrifugation step to optimize ctDNA retrieval.Impact: These recommendations will help "future-proof" clinical studies in which quantification of circulating miRNAs is a component. Cancer Epidemiol Biomarkers Prev; 27(2); 208-18. ©2017 AACR.
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Affiliation(s)
- Matthew J Murray
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom. .,Department of Paediatric Haematology and Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Hannah L Watson
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
| | - Dawn Ward
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
| | - Shivani Bailey
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
| | - Marta Ferraresso
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
| | - James C Nicholson
- Department of Paediatric Haematology and Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | | | - Benjamin Thomas
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Cinzia G Scarpini
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
| | - Nicholas Coleman
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom. .,Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
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20
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Camus V, Bohers E, Dubois S, Tilly H, Jardin F. Circulating tumor DNA: an important tool in precision medicine for lymphoma. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2017. [DOI: 10.1080/23808993.2018.1412798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Vincent Camus
- UMR INSERM U1245 and Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Elodie Bohers
- UMR INSERM U1245 and Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Sydney Dubois
- UMR INSERM U1245 and Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Hervé Tilly
- UMR INSERM U1245 and Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- UMR INSERM U1245 and Department of Clinical Hematology, Centre Henri Becquerel, Rouen, France
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21
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Strotman LN, Millner LM, Valdes R, Linder MW. Liquid Biopsies in Oncology and the Current Regulatory Landscape. Mol Diagn Ther 2017; 20:429-36. [PMID: 27324559 DOI: 10.1007/s40291-016-0220-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is a profound need in oncology to detect cancer earlier, guide individualized therapies, and better monitor progress during treatment. Currently, some of this information can be achieved through solid tissue biopsy and imaging. However, these techniques are limited because of the invasiveness of the procedure and the size of the tumor. A liquid biopsy can overcome these barriers as its non-invasive nature allows samples to be collected over time. Liquid biopsies may also allow earlier detection than traditional imaging. Liquid biopsies include the analysis of circulating tumor cells (CTCs), cell-free nucleic acid (cfNA), or extracellular vesicles obtained from a variety of biofluids, such as peripheral blood. In this review, we discuss different liquid biopsy types and how they fit into the current regulatory landscape.
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Affiliation(s)
- Lindsay N Strotman
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Louisville, 511 South Floyd Street, MDR 221, Louisville, KY, 40202, USA
- PGXL Technologies, 201 E. Floyd St., Suite 306, Louisville, KY, USA
| | - Lori M Millner
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Louisville, 511 South Floyd Street, MDR 221, Louisville, KY, 40202, USA
- PGXL Technologies, 201 E. Floyd St., Suite 306, Louisville, KY, USA
| | - Roland Valdes
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Louisville, 511 South Floyd Street, MDR 221, Louisville, KY, 40202, USA
- PGXL Technologies, 201 E. Floyd St., Suite 306, Louisville, KY, USA
| | - Mark W Linder
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Louisville, 511 South Floyd Street, MDR 221, Louisville, KY, 40202, USA.
- PGXL Technologies, 201 E. Floyd St., Suite 306, Louisville, KY, USA.
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22
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Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management. Int J Mol Sci 2017; 18:ijms18020264. [PMID: 28146051 PMCID: PMC5343800 DOI: 10.3390/ijms18020264] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/10/2017] [Accepted: 01/18/2017] [Indexed: 02/06/2023] Open
Abstract
Circulating tumoral DNA (ctDNA), commonly named “liquid biopsy”, has emerged as a new promising noninvasive tool to detect biomarker in several cancers including lung cancer. Applications involving molecular analysis of ctDNA in lung cancer have increased and encompass diagnosis, response to treatment, acquired resistance and prognosis prediction, while bypassing the problem of tumor heterogeneity. ctDNA may then help perform dynamic genetic surveillance in the era of precision medicine through indirect tumoral genomic information determination. The aims of this review were to examine the recent technical developments that allowed the detection of genetic alterations of ctDNA in lung cancer. Furthermore, we explored clinical applications in patients with lung cancer including treatment efficiency monitoring, acquired therapy resistance mechanisms and prognosis value.
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23
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Zhang J, Zhu X, Li Y, Zhu L, Li S, Zheng G, Ren Q, Xiao Y, Feng F. Correlation of CpG Island Methylation of the Cytochrome P450 2E1/2D6 Genes with Liver Injury Induced by Anti-Tuberculosis Drugs: A Nested Case-Control Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13080776. [PMID: 27490558 PMCID: PMC4997462 DOI: 10.3390/ijerph13080776] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 07/18/2016] [Accepted: 07/27/2016] [Indexed: 12/21/2022]
Abstract
This study investigated the role of CpG island methylation of the CYP2E1 and CYP2D6 genes in liver injury induced by anti-TB drugs from an epigenetic perspective in a Chinese cohort. A 1:1 matched nested case-control study design was applied. Pulmonary tuberculosis (TB) patients, who underwent standard anti-TB therapy and developed liver injury were defined as cases, while those who did not develop liver injury were defined as control. The two groups were matched in terms of sex, treatment regimen, and age. In 114 pairs of cases, CpG island methylation levels of the CYP2E1 and CYP2D6 genes in plasma cell-free DNA were found to be significantly correlated with the occurrence of anti-TB drug-induced liver injury (ADLI), with odds ratio (OR) values of 2.429 and 3.500, respectively (p < 0.01). Moreover, through multivariate logistic regression analysis, CpG island methylation of the CYP2E1 and CYP2D6 genes in plasma cell-free DNA were found to be significantly correlated with the occurrence of ADLI, with adjusted OR values of 4.390 (95% confidence interval (CI): 1.982–9.724) and 9.193 (95% CI: 3.624–25.888), respectively (p < 0.001). These results suggest that aberrantly elevated methylation of CpG islands of the CYP2E1 and CYP2D6 genes in plasma cell-free DNA may increase the risk of ADLI in Chinese TB patients.
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Affiliation(s)
- Jinling Zhang
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, No.57 Jianshe Road, Tangshan 063000, China.
| | - Xuebin Zhu
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, No.57 Jianshe Road, Tangshan 063000, China.
| | - Yuhong Li
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, No.57 Jianshe Road, Tangshan 063000, China.
| | - Lingyan Zhu
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, No.57 Jianshe Road, Tangshan 063000, China.
| | - Shiming Li
- Department of Clinical Laboratories, Tangshan Tuberculosis Hospital, Tangshan 063000, China.
| | - Guoying Zheng
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, No.57 Jianshe Road, Tangshan 063000, China.
| | - Qi Ren
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, No.57 Jianshe Road, Tangshan 063000, China.
| | - Yonghong Xiao
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, No.57 Jianshe Road, Tangshan 063000, China.
| | - Fumin Feng
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, No.57 Jianshe Road, Tangshan 063000, China.
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24
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Vietsch EE, van Eijck CHJ, Wellstein A. Circulating DNA and Micro-RNA in Patients with Pancreatic Cancer. PANCREATIC DISORDERS & THERAPY 2015; 5:156. [PMID: 26161297 PMCID: PMC4494744 DOI: 10.4172/2165-7092.1000156] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Collecting repeat samples of blood ("liquid biopsies") is a broadly used clinical approach for serial monitoring of disease or response to treatments. In patients with cancer the most distinct molecular feature are somatic mutations acquired by cancer cells present in the diseased tissue. Indeed, mutant DNA derived from dying or lysed cancer cells can be isolated from patient serum samples, subjected to DNA sequencing and to analysis of abundance as a measure of tumor burden. Also, changes in the DNA mutation patterns in serum samples collected over time can indicate altered pathways or clonal evolution of the disease and altered abundance of mutant DNA suggests an altered disease burden. In addition, during the course of treatment, changes in circulating DNA mutation patterns can indicate the emergence of resistant clones and prompt changes in treatment. In contrast to mutant DNA, microRNAs (miR) are transcribed, processed, packaged and released from cells in normal and in diseased tissues as part of the extracellular crosstalk between cells. Interestingly, released miR can function in cell-to-cell communication and as hormone-like signals that operate at a distance through their release into the circulation and subsequent uptake into cells in distant tissues. Circulating miR expression patterns can be established from serial serum samples and monitored for alterations over time. Circulating miR provide a readout of the organism's steady state and serial analyses will indicate changes in the response to therapy or an altered physiologic or disease state. Furthermore, changes in circulating miR patterns can indicate treatment efficacy or resistance as well as adverse effects associated with the respective intervention. Thus, the combined serial analysis of mutant DNA and miR in the circulation has the potential to provide a molecular footprint of pancreatic cancer and can be used to monitor treatment responses or resistance to treatment in real time with a minimally invasive procedure.
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Affiliation(s)
- Eveline E Vietsch
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA
| | | | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington DC, USA
- Corresponding author: Anton Wellstein, Georgetown University Medical School, Lombardi, Comprehensive Cancer Center, Research Building; Room E311, 3970 Reservoir Road, Washington DC, Tel: +1202687-3672,
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Sikora K, Bedin C, Vicentini C, Malpeli G, D'Angelo E, Sperandio N, Lawlor RT, Bassi C, Tortora G, Nitti D, Agostini M, Fassan M, Scarpa A. Evaluation of cell-free DNA as a biomarker for pancreatic malignancies. Int J Biol Markers 2015; 30:e136-e141. [PMID: 24832178 DOI: 10.5301/jbm.5000088] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2014] [Indexed: 01/05/2023]
Abstract
BACKGROUND Currently, no reliable blood-based assay for early detection of pancreatic ductal adenocarcinoma (PDAC) is available. Cell-free DNA (cfDNA) quantitation in patients' plasma has been recently applied in monitoring several cancer types. This study evaluates the diagnostic potential of cfDNA in PDAC patients. METHODS Plasma cfDNA levels and integrity ratio were assayed using quantitative real-time PCR of Alu-repeat amplicons in patients with pancreatic ductal adenocarcinoma (n=50), pancreatic neuroendocrine tumor (n=23), and chronic pancreatitis (n=20), as well as in healthy volunteers without evidence of pancreatic disease (n=23). RESULTS The total load of cfDNA, obtained by Alu83 quantitation, was the highest in PDAC patients than in any of the other patient groups (Welch t test; p<0.001) and was an average predictor of PDAC disease (AUC=0.664; CI, 0.56-0.77). A nonlinear association between Alu83 levels and subjects' age was detected (Spearman's rho=0.35; p<0.001) in the overall population, as well as within the PDAC patients' group (Spearman's rho=0.47; p<0.001). Necrosis-derived cfDNA fragments, quantitated with the Alu244 amplicon, were barely detectable in any of the samples and, in that respect, comparable between the different subject groups. CfDNA integrity estimation (Alu244/Alu83 ratio) was significantly affected by the limited detectability of plasma Alu244 levels. CONCLUSION The lack of detectable levels of necrosis-derived cfDNA in pancreatic pathologies considerably affects the clinical use of such biomarker in PDAC patients. Different methods of analysis should be applied in the evaluation of the cfDNA diagnostic value in pancreas pathology.
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Zane M, Agostini M, Enzo MV, Casal Ide E, Del Bianco P, Torresan F, Merante Boschin I, Pennelli G, Saccani A, Rubello D, Nitti D, Pelizzo MR. Circulating cell-free DNA, SLC5A8 and SLC26A4 hypermethylation, BRAF(V600E): A non-invasive tool panel for early detection of thyroid cancer. Biomed Pharmacother 2013; 67:723-30. [PMID: 23931930 DOI: 10.1016/j.biopha.2013.06.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/24/2013] [Indexed: 01/05/2023] Open
Abstract
PURPOSE In the latest years, high levels of circulating cell-free DNA (cf-DNA) have been found to be associated with cancer diagnosis and progression, and cf-DNA has become a potential candidate as biomarker for tumor detection. cf-DNA has been investigated in plasma or serum of many tumor patients affected by different malignancies, but not yet in thyroid cancer (TC). Furthermore, in TC cells the capability to metabolize iodine is frequently lost. SLC5A8 and SLC26A4 genes are both involved in the iodine metabolism, and SLC5A8 hypermethylation status is associated with the BRAF(V600E) mutation, which is the most frequent genetic event underlying the development of papillary TC. The aim of our study is the development of a new non-invasive tool for the diagnosis and prognosis of TC based on cf-DNA, SLC5A8 and SLC26A4 hypermethylation, and BRAF(V600E) analysis. METHODS cf-DNA was measured by quantitative real-time PCR in nine cases of anaplastic thyroid cancer (ATC), 58 medullary thyroid cancers (MTC), five of synchronous medullary and follicular thyroid cancers (SMFC), 23 follicular adenomas (FA), 86 papillary thyroid cancers (PTC). A control group of 19 healthy subjects was taken. Moreover, in the PTC group we analyze the state of hypermethylation of SLC5A8 and SLC26A4, BRAF(V600E) mutation, and their involvement in the loss of function of the thyroid. RESULTS cf-DNA showed a high ability to discriminate healthy individuals from cancer patients. cf-DNAALU83 and cf-DNAALU244 values were significantly correlated with the histological type of TC (P-value < 0.0001). A significant increase in the amount of cf-DNAALU83 and cf-DNAALU244 when methylation occurs was observed (P-value = 0.02). A correlation between BRAF(V600E) and cf-DNAALU244/ALU83 was also found (P-value = 0.02). CONCLUSIONS According to our experimental results, the panel including cf-DNA, SLC5A8 and SLC26A4 hypermethylation, and BRAF(V600E) analysis appears easy, reproducible, and non-invasive for the diagnosis on TC. Its possible implication in clinical setting remains to be elucidated.
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Affiliation(s)
- Mariangela Zane
- Surgical clinic II, Department of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Padova, Italy
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Guzmán L, Depix MS, Salinas AM, Roldán R, Aguayo F, Silva A, Vinet R. Analysis of aberrant methylation on promoter sequences of tumor suppressor genes and total DNA in sputum samples: a promising tool for early detection of COPD and lung cancer in smokers. Diagn Pathol 2012; 7:87. [PMID: 22818553 PMCID: PMC3424112 DOI: 10.1186/1746-1596-7-87] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 07/20/2012] [Indexed: 01/29/2023] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a disorder associated to cigarette smoke and lung cancer (LC). Since epigenetic changes in oncogenes and tumor suppressor genes (TSGs) are clearly important in the development of LC. In this study, we hypothesize that tobacco smokers are susceptible for methylation in the promoter region of TSGs in airway epithelial cells when compared with non-smoker subjects. The purpose of this study was to investigate the usefulness of detection of genes promoter methylation in sputum specimens, as a complementary tool to identify LC biomarkers among smokers with early COPD. Methods We determined the amount of DNA in induced sputum from patients with COPD (n = 23), LC (n = 26), as well as in healthy subjects (CTR) (n = 33), using a commercial kit for DNA purification, followed by absorbance measurement at 260 nm. The frequency of CDKN2A, CDH1 and MGMT promoter methylation in the same groups was determined by methylation-specific polymerase chain reaction (MSP). The Fisher’s exact test was employed to compare frequency of results between different groups. Results DNA concentration was 7.4 and 5.8 times higher in LC and COPD compared to the (CTR) (p < 0.0001), respectively. Methylation status of CDKN2A and MGMT was significantly higher in COPD and LC patients compared with CTR group (p < 0.0001). Frequency of CDH1 methylation only showed a statistically significant difference between LC patients and CTR group (p < 0.05). Conclusions We provide evidence that aberrant methylation of TSGs in samples of induced sputum is a useful tool for early diagnostic of lung diseases (LC and COPD) in smoker subjects. Virtual slides The abstract MUST finish with the following text: Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1127865005664160
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Affiliation(s)
- Leda Guzmán
- Departamento de Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
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Song BP, Jain S, Lin SY, Chen Q, Block TM, Song W, Brenner DE, Su YH. Detection of hypermethylated vimentin in urine of patients with colorectal cancer. J Mol Diagn 2012; 14:112-9. [PMID: 22251609 DOI: 10.1016/j.jmoldx.2011.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 12/01/2011] [Accepted: 12/07/2011] [Indexed: 02/06/2023] Open
Abstract
We demonstrated previously that urine contains low-molecular-weight (LMW) (<300 bp), circulation-derived DNA that can be used to detect cancer-specific mutations if a tumor is present. The goal of this study was to develop an assay to detect the colorectal cancer (CRC)-associated, circulation-derived, epigenetic DNA marker hypermethylated vimentin gene (mVIM) in the urine of patients with CRC. An artificial 18-nucleotide DNA sequence was tagged at the 5' end of the primers of the first PCR cycle to increase the amplicon size, which was then integrated into the primers of the second PCR cycle. A quantitative MethyLight PCR-based assay targeting a 39-nucleotide template was developed and used to quantify mVIM in CRC tissues and matched urine samples. mVIM was detected in 75% of LMW urine DNA samples from patients with CRC (n = 20) and in 10% of urine samples of control subjects with no known neoplasia (n = 20); 12 of 17 LMW urine DNA samples (71%) but only 2 of 17 high-molecular-weight urine DNA samples (12%) from patients with mVIM-positive tissues contained detectable mVIM, suggesting that the mVIM detected in LMW urine DNA is derived from the circulation. The detection of mVIM in urine was significantly associated with CRC compared with controls (P < 0.0001, by Fisher's exact test). A potential urine test for CRC screening using epigenetic markers is discussed.
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Affiliation(s)
- Benjamin P Song
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 18901, USA
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Morimura R, Komatsu S, Ichikawa D, Takeshita H, Tsujiura M, Nagata H, Konishi H, Shiozaki A, Ikoma H, Okamoto K, Ochiai T, Taniguchi H, Otsuji E. Novel diagnostic value of circulating miR-18a in plasma of patients with pancreatic cancer. Br J Cancer 2011; 105:1733-40. [PMID: 22045190 PMCID: PMC3242609 DOI: 10.1038/bjc.2011.453] [Citation(s) in RCA: 212] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 09/28/2011] [Accepted: 10/05/2011] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Several recent studies have demonstrated that microRNAs (miRNAs) are stably detectable in the plasma/serum. We hypothesised that miR-18a in the plasma is a potential biomarker in patients with pancreatic cancer. METHODS miR-18a is located in the miR-17-92 cluster and reported to be highly expressed in pancreatic cancer tissues. This study was divided into three parts: (1) Confirmation of higher miR-18a levels in primary pancreatic cancer tissues and cell lines than in normal pancreatic tissues and a human fibroblast cell line. (2) Evaluation of the plasma miR-18a assay using quantitative RT-PCR by comparing plasma results obtained from 36 patients with pancreatic cancer and from 30 healthy volunteers. (3) Evaluation of the assay for monitoring tumour dynamics in patients with pancreatic cancer. RESULTS (1) The expression of miR-18a was significantly higher in pancreatic cancer tissues (P=0.012) and pancreatic cancer cell lines (P=0.015) than in normal tissues and fibroblasts. (2) Plasma concentrations of miR-18a were significantly higher in pancreatic cancer patients than in controls (P<0.0001). The value of the area under the receiver-operating characteristic curve (AUC) was 0.9369. (3) Plasma levels of miR-18a were significantly lower in postoperative samples than in preoperative samples (P=0.0077). CONCLUSION Circulating miR-18a might provide new complementary tumour markers for pancreatic cancer.
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Affiliation(s)
- R Morimura
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - S Komatsu
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - D Ichikawa
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - H Takeshita
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - M Tsujiura
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - H Nagata
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - H Konishi
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - A Shiozaki
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - H Ikoma
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - K Okamoto
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - T Ochiai
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - H Taniguchi
- Department of Surgery, Kyoto Second Red Cross Hospital, 355-5 Kamanzadoori Marutacho Hruobicho, Kamigyo-ku, Kyoto, Japan
| | - E Otsuji
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
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Cao H, Banh A, Kwok S, Shi X, Wu S, Krakow T, Khong B, Bavan B, Bala R, Pinsky BA, Colevas D, Pourmand N, Koong AC, Kong CS, Le QT. Quantitation of human papillomavirus DNA in plasma of oropharyngeal carcinoma patients. Int J Radiat Oncol Biol Phys 2011; 82:e351-8. [PMID: 21985946 DOI: 10.1016/j.ijrobp.2011.05.061] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 05/28/2011] [Indexed: 10/16/2022]
Abstract
PURPOSE To determine whether human papillomavirus (HPV) DNA can be detected in the plasma of patients with HPV-positive oropharyngeal carcinoma (OPC) and to monitor its temporal change during radiotherapy. METHODS AND MATERIALS We used polymerase chain reaction to detect HPV DNA in the culture media of HPV-positive SCC90 and VU147T cells and the plasma of SCC90 and HeLa tumor-bearing mice, non-tumor-bearing controls, and those with HPV-negative tumors. We used real-time quantitative polymerase chain reaction to quantify the plasma HPV DNA in 40 HPV-positive OPC, 24 HPV-negative head-and-neck cancer patients and 10 non-cancer volunteers. The tumor HPV status was confirmed by p16(INK4a) staining and HPV16/18 polymerase chain reaction or HPV in situ hybridization. A total of 14 patients had serial plasma samples for HPV DNA quantification during radiotherapy. RESULTS HPV DNA was detectable in the plasma samples of SCC90- and HeLa-bearing mice but not in the controls. It was detected in 65% of the pretreatment plasma samples from HPV-positive OPC patients using E6/7 quantitative polymerase chain reaction. None of the HPV-negative head-and-neck cancer patients or non-cancer controls had detectable HPV DNA. The pretreatment plasma HPV DNA copy number correlated significantly with the nodal metabolic tumor volume (assessed using (18)F-deoxyglucose positron emission tomography). The serial measurements in 14 patients showed a rapid decline in HPV DNA that had become undetectable at radiotherapy completion. In 3 patients, the HPV DNA level had increased to a discernable level at metastasis. CONCLUSIONS Xenograft studies indicated that plasma HPV DNA is released from HPV-positive tumors. Circulating HPV DNA was detectable in most HPV-positive OPC patients. Thus, plasma HPV DNA might be a valuable tool for identifying relapse.
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Affiliation(s)
- Hongbin Cao
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305-5847, USA
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Evidence of heavy methylation in the galectin 3 promoter in early stages of prostate adenocarcinoma: development and validation of a methylated marker for early diagnosis of prostate cancer. Transl Oncol 2011; 2:146-56. [PMID: 19701499 DOI: 10.1593/tlo.09118] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 03/12/2009] [Accepted: 03/13/2009] [Indexed: 12/31/2022] Open
Abstract
Galectins, soluble intracellular and extracellular beta-galactoside-binding proteins, are known to be involved in the progression and metastasis of various cancers, including prostate adenocarcinoma, but the detailed mechanism of their biological roles remains elusive. In the prostate cancer cell lines PC-3 and DU-145, galectin 3 (gal3) is present at normal levels, whereas in LNCaP, its expression is silenced. In LNCaP, the gal3 promoter was heavily methylated, whereas PC-3 or DU-145 cells showed negligible or no methylation in the gal3 promoter indicating a negative correlation between gal3 promoter methylation and its expression. On immunohistochemical analysis of normal and tumor prostate tissues, gal3 was found expressed both in nucleus and cytoplasm of benign prostatic hyperplasia, high-grade prostatic intraepithelial neoplasia, and stage I. The expression of the gal3 was found drastically downregulated in advanced stages and, interestingly, mostly in the cytoplasm. On methylation analysis, the gal3 promoter in stage II prostate adenocarcinoma (PCa) was found heavily methylated, whereas in stages III and IV, it was only lightly methylated. However, in stage I PCa, both heavy and light methylations were observed in the gal3 promoter. In normal and benign prostatic hyperplasia tissues, the gal3 promoter was almost unmethylated. The differential cytosine methylation in the gal3 promoter in stages I to IV PCa enabled us to develop and validate a methylation-specific polymerase chain reaction-based sensitive assay specific for stages I and II PCa. These stages are considered the critical stages for successful intervention, thus underscoring the significance of this diagnostic assay.
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A locked nucleic acid clamp-mediated PCR assay for detection of a p53 codon 249 hotspot mutation in urine. J Mol Diagn 2011; 13:474-84. [PMID: 21726666 DOI: 10.1016/j.jmoldx.2011.05.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/16/2011] [Accepted: 05/06/2011] [Indexed: 11/22/2022] Open
Abstract
Hepatocellular carcinoma (HCC) has a 5-year survival rate of <10% because it is difficult to diagnose early. Mutations in the TP53 gene are associated with approximately 50% of human cancers. A hotspot mutation, a G:C to T:A transversion at codon 249 (249T), may be a potential DNA marker for HCC screening because of its exclusive presence in HCC and its detection in the circulation of some patients with HCC. A locked nucleic acid clamp-mediated PCR assay, followed by melting curve analysis (using the SimpleProbe), was developed to detect the TP53 249T mutation. In this assay, the locked nucleic acid clamp suppressed 10(7) copies of wild-type templates and permitted detection of 249T-mutated template, with a sensitivity of 0.1% (1:1000) of the mutant/wild-type ratio, assessed by a reconstituted standard within 2 hours. With an amplicon size of 41 bp, it detects target DNA sequences in short fragmented DNA templates. The detected mutations were validated by DNA sequencing analysis. We then tested DNA isolated from urine samples of patients with HCC for p53 mutations and identified positive TP53 mutations in 9 of 17 samples. The possibility of using this novel TP53 249T assay to develop a urine or blood test for HCC screening is discussed.
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Komatsu S, Ichikawa D, Takeshita H, Tsujiura M, Morimura R, Nagata H, Kosuga T, Iitaka D, Konishi H, Shiozaki A, Fujiwara H, Okamoto K, Otsuji E. Circulating microRNAs in plasma of patients with oesophageal squamous cell carcinoma. Br J Cancer 2011; 105:104-11. [PMID: 21673684 PMCID: PMC3137413 DOI: 10.1038/bjc.2011.198] [Citation(s) in RCA: 199] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 05/04/2011] [Accepted: 05/11/2011] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Several recent studies demonstrated that microRNAs (miRNAs) are stably detectable in plasma/serum. We hypothesised that plasma miRNAs concentrations contributed to potential biomarkers in patients with oesophageal squamous cell carcinoma (ESCC). METHODS We selected three oncogenic miRNAs (miR-21, miR-184, miR-221) and one tumour suppressive miRNA (miR-375), which are frequently reported in squamous cell carcinoma, as candidate targets for this plasma miRNA assay. This study was divided into three steps: (1) Determination of appropriate plasma miRNAs in preliminary tests. (2) Evaluation of whether the plasma miRNA assays could monitor tumour dynamics. (3) Validation study on the clinical application of plasma miRNA assays in 50 ESCC patients and 20 healthy volunteers. RESULTS (1) In preliminary tests, the plasma level of miR-21 was significantly higher (P=0.0218) and that of miR-375 (P=0.0052) was significantly lower in ESCC patients than controls. (2) The high plasma miR-21 levels reflected tumour levels in all cases (100%). The plasma level of miR-21 was significantly reduced in postoperative samples (P=0.0058). (3) On validation analysis, the plasma level of miR-21 tended to be higher in ESCC patients (P=0.0649), while that of miR-375 was significantly lower (P<0.0001) and the miR-21/miR-375 ratio was significantly higher (P<0.0001) in ESCC patients than in controls. The value of the area under the receiver-operating characteristic curve (AUC) was 0.816 for the miR-21/miR-375 ratio assay. Patients with a high plasma level of miR-21 tended to have greater vascular invasion (P=0.1554) and to show a high correlation with recurrence (P=0.0164). CONCLUSION Detection of circulating miRNAs might provide new complementary tumour markers for ESCC.
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Affiliation(s)
- S Komatsu
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - D Ichikawa
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - H Takeshita
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - M Tsujiura
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - R Morimura
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - H Nagata
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - T Kosuga
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - D Iitaka
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - H Konishi
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - A Shiozaki
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - H Fujiwara
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - K Okamoto
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - E Otsuji
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
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Ortiz-Cuaran S, Hainaut P. Molecular Signatures of Environmental Mutagens in Hepatocellular Carcinoma. Genes Environ 2011. [DOI: 10.3123/jemsge.33.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Abstract
Background: We examined plasma microRNA (miRNA) concentrations from patients with gastric cancers (GCs) to assess their clinical application for diagnosing and monitoring diseases. Methods: We initially investigated the appropriateness of plasma miRNA assay, and then compared plasma miRNA results with the expressions in cancer tissues from eight GC patients, and also compared plasma miRNAs between pre- and post-operative paired samples from 10 GC patients. Then, plasma miRNAs (miR-17-5p, miR-21, miR-106a, miR-106b and let-7a) were analysed in 69 GC patients and 30 healthy volunteers in total. Results: The initial analysis showed that miRNAs were stable and detectable in all plasma samples, and the plasma miRNA levels reflected the tumour miRNAs in most cases. The levels of these miRNAs were significantly reduced in post-operative samples. In large-scale analysis, the plasma concentrations of miRNAs (miR-17-5p, miR-21, miR-106a, miR-106b) were significantly higher in GC patients than controls (P=0.05, 0.006, 0.008 and <0.001 respectively), whereas let-7a was lower in GC patients (P=0.002). The values of the area under the receiver-operating characteristic curve were 0.721 for the miR-106b assay and 0.879 for the miR-106a/let-7a ratio assay. Conclusion: Detection of circulating miRNAs might provide new complementary tumour markers for GC.
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Toyoshima M, Tanaka Y, Matumoto M, Yamazaki M, Nagase S, Sugamura K, Yaegashi N. Generation of a syngeneic mouse model to study the intraperitoneal dissemination of ovarian cancer with in vivo luciferase imaging. LUMINESCENCE 2010; 24:324-31. [PMID: 19711487 DOI: 10.1002/bio.1112] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In order to facilitate the discovery and investigation of anti-cancer therapeutics under physiological conditions, we have engineered the ovarian cancer cell line, HM-1/luc, in mice. This cell stably expresses firefly luciferase and produces light that can be detected using an in vivo imaging system (IVIS). Parental HM-1 cells cause severe carcinomatous peritonitis to B6C3F1 mice, but not to C57BL6 mice. Established HM-1/luc cells showed pathologically similar findings to HM-1 cells. HM-1/luc cells were injected into the peritoneal cavity of B6C3F1 mice and IVIS 2000 was conducted weekly after inoculation to monitor intra-peritoneal tumor growth. The mice were divided into three groups: non-CDDP-treated (control) and CDDP-treated (0.2 and 0.4 mg). A disease-suppressive effect of the CDDP was reflected by the significantly prolonged survival of the CDDP-treated mice (control 23 +/- 1.9 days, CDDP 0.2 mg 29.6 +/- 2.9 days; p < 0.05); the total photon and area of flux were decreased. The optical imaging of intraperitoneal tumors via in vivo bioluminescence is effective for noninvasive monitoring and semi-quantitative analysis. Our syngeneic mouse model has the relevant clinical features of ovarian cancer, which makes it a useful model for developing new ovarian cancer therapies.
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Affiliation(s)
- Masafumi Toyoshima
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan.
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Gnanamony M, Peedicayil A, Subhashini J, Ram TS, Rajasekar A, Gravitt P, Abraham P. Detection and quantitation of HPV 16 and 18 in plasma of Indian women with cervical cancer. Gynecol Oncol 2009; 116:447-51. [PMID: 19922992 DOI: 10.1016/j.ygyno.2009.10.081] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 10/29/2009] [Accepted: 10/30/2009] [Indexed: 10/20/2022]
Abstract
OBJECTIVE HPV infection is a necessary but insufficient cause of cervical cancer. The significance of HPV DNA in blood however is debatable because of variable detection rates due to the differences in the methodology used. The aim of this study was to detect and quantitate HPV 16 and 18 plasma viremia in women with cervical neoplasia. METHODS HPV DNA was detected in cervical tissue using consensus PGMY primers and genotyped using reverse line blot hybridization. HPV 16 and 18 quantitation in tissue and detection and quantitation in plasma was performed using sensitive real time PCRs targeting E6/E7 region of HPV 16/18 genome respectively. Results were correlated with viral loads in corresponding tissue and with clinical disease stage. RESULTS Viremia was detected in 56.4% of HPV 16 positive women and 20% of HPV 18 positive women. The prevalence of HPV 16 DNA in plasma increased with advancing disease stage (p=0.001), although HPV 16 absolute plasma viral load was not significantly associated with advancing disease stage (p=0.281). There was no correlation between absolute plasma viral load and viral load in corresponding cervical tissue (Spearman's rho=0.184, p=0.187). The prevalence of HPV 18 viremia and absolute HPV 18 plasma viral load were not associated with advancing disease stage (p=0.620, p=0.508). CONCLUSION The presence of HPV 16 in plasma is a marker of advancing cervical disease.
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Affiliation(s)
- Manu Gnanamony
- Department of Clinical Virology, Christian Medical College, Tamil Nadu, India
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Gornik I, Wagner J, Gašparović V, Lauc G, Gornik O. Free serum DNA is an early predictor of severity in acute pancreatitis. Clin Biochem 2009; 42:38-43. [DOI: 10.1016/j.clinbiochem.2008.09.121] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2008] [Revised: 09/09/2008] [Accepted: 09/26/2008] [Indexed: 10/21/2022]
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Schmidt B, Weickmann S, Witt C, Fleischhacker M. Integrity of cell-free plasma DNA in patients with lung cancer and nonmalignant lung disease. Ann N Y Acad Sci 2008; 1137:207-13. [PMID: 18837948 DOI: 10.1196/annals.1448.034] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In several papers an increased quantity of cell-free plasma DNA as well as the presence of long DNA fragments in cell-free plasma and serum has been described. We isolated cell-free DNA from plasma, serum, and bronchial lavage supernatants from 33 lung cancer patients and 27 patients with a benign lung disease. The DNA was amplified by real-time PCR, and the quantity as well as the DNA integrity was determined. We did not find significant differences between the patient populations. Our results led us to conclude that this method is not useful in a diagnostic setting and is not able to differentiate between lung cancer patients and patients with a benign lung disease.
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Affiliation(s)
- Bernd Schmidt
- Medizinische Klinik m.S. Infektiologie und Pneumologie, Pneumologie, Charité-Universitätsmedizin, Berlin, Germany
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Tuaeva NO, Abramova ZI, Sofronov VV. The origin of elevated levels of circulating DNA in blood plasma of premature neonates. Ann N Y Acad Sci 2008; 1137:27-30. [PMID: 18837920 DOI: 10.1196/annals.1448.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The relationship between the concentration of cell-free DNA (cfDNA) and the number of proliferating/apoptotic lymphocytes in peripheral blood of premature newborns of different gestation age and full-term newborns was determined. The experiments were performed using fluorescent spectrophotometry (with Hoechst 33342), flow cytometry, and microscopy (Feulgen staining of lymphocytes). It was determined that the lymphocyte population of premature newborns may consist of 4.6% of proliferating and 22.1% apoptotic cells. For full-term newborns, the percentage was 2.5% and 2.9%, respectively. A direct correlation between the concentration of extracellular DNA and the number of proliferating lymphocytes of full-term newborns was ascertained (r= 0.400; P < 0.05). For premature newborns, the concentration of extracellular DNA correlated both with proliferating lymphocytes and apoptotic cells. The results show that premature birth causes the induction in lymphocytes of both apoptosis and proliferation that are accompanied by an increased extracellular DNA concentration in the blood of newborn babies.
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Liedl T, Dietz H, Yurke B, Simmel F. Controlled trapping and release of quantum dots in a DNA-switchable hydrogel. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2007; 3:1688-93. [PMID: 17786918 DOI: 10.1002/smll.200700366] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- Tim Liedl
- Department of Physics and Center for Nanoscience, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539 München, Germany
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Suzuki N, Kamataki A, Yamaki J, Homma Y. Characterization of circulating DNA in healthy human plasma. Clin Chim Acta 2007; 387:55-8. [PMID: 17916343 DOI: 10.1016/j.cca.2007.09.001] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 09/02/2007] [Accepted: 09/03/2007] [Indexed: 12/16/2022]
Abstract
BACKGROUND The importance of circulating DNA has been recognized since the detection of mutated oncogene products in cancer patients; however, there is little information about circulating DNA in normal human plasma. We characterized circulating DNA in normal human plasma to obtain basic information. METHODS Circulating DNA was purified from plasma samples obtained from 10 healthy donors and examined. Purified DNA was cloned and their sequence determined and analyzed. The terminal structure was examined by a labeling method. RESULTS The DNA levels in normal plasma samples were quite low (3.6-5.0 ng/ml). All 556 clones analyzed were independent, and obtained from various chromosomes and various regions of the gene. The mean values of their length and GC content were 176 bp and 53.7%, respectively. Their 5' and 3' ends were rich in C and G, respectively, and they presented as 5' protruding forms of double-stranded DNA in plasma. CONCLUSION Circulating DNA in normal human plasma is derived from apoptotic cells but not from necrotic cells. Structural characteristics of the circulating DNA might be associated with their stability in plasma.
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Affiliation(s)
- Nobuyasu Suzuki
- Department of Biomolecular Science, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
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Abstract
DNA methylation is a common mechanism of inactivation of tumour-suppressor and other cancer genes in neoplastic cells. The advantages of gene methylation as a target for the detection and diagnosis of cancer in biopsy specimens and non-invasive body fluids such as urine or blood has led to many studies of application in genitourinary cancer. Here, we consider the background, promise and status, challenges and future directions of gene methylation and its clinical utility for the early detection of genitourinary cancer. The challenges of, and strategies for, advancing gene-methylation-based detection are relevant to all types of cancer.
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Affiliation(s)
- Paul Cairns
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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Peltonen J, Welsh JA, Vähäkangas KH. Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Hum Exp Toxicol 2007; 26:9-18. [PMID: 17334176 DOI: 10.1177/0960327107071918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mutation analysis methods have increased in variety during the past years. High-throughput microarray methods have especially increased in popularity. However, new methods require reference points, and not all of the methods are equal in sensitivity and specificity. Furthermore, the detection of unknown missense mutations, such as unknown TP53 mutations in human tumors, for clinical purposes requires great accuracy, which may be difficult to acquire with the current high-throughput methods. For these reasons, the classical methods, such as PCR-manual sequencing and PCR-SSCP, are still valuable and necessary.
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Affiliation(s)
- J Peltonen
- Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
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Cummings J, Ranson M, Butt F, Moore D, Dive C. Qualification of M30 and M65 ELISAs as surrogate biomarkers of cell death: long term antigen stability in cancer patient plasma. Cancer Chemother Pharmacol 2007; 60:921-4. [PMID: 17333190 DOI: 10.1007/s00280-007-0437-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 02/02/2007] [Indexed: 12/30/2022]
Abstract
PURPOSE M30 and M65 ELISAs are proposed as surrogate biomarkers of tumour cell death in patients and are being applied increasingly in the pharmacodynamic (PD) evaluation of anticancer drugs during clinical trials. In the absence of such data, we have studied the long-term stability of the antigens of both assays in plasma of cancer patients stored at -80 degrees C over 2 years. RESULTS No evidence was detected of degradation in the M65 antigen. However, in a proportion of patients significant increases in levels of M30 antigen were detected CONCLUSION Plasma samples for M65 analysis can be stored at -80 degrees C for 2 years; however, caution is recommended when considering long-term storage of samples for the M30 assay.
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Affiliation(s)
- J Cummings
- Clinical and Experimental Pharmacology Group, Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester, M20 4BX, England.
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Tangkijvanich P, Hourpai N, Rattanatanyong P, Wisedopas N, Mahachai V, Mutirangura A. Serum LINE-1 hypomethylation as a potential prognostic marker for hepatocellular carcinoma. Clin Chim Acta 2007; 379:127-33. [PMID: 17303099 DOI: 10.1016/j.cca.2006.12.029] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 12/26/2006] [Accepted: 12/28/2006] [Indexed: 12/24/2022]
Abstract
BACKGROUND We investigated the clinical implications of global hypomethylation, one of the most consistent epigenetic changes in cancer, in the sera of patients with hepatocellular carcinoma (HCC). METHODS Combined bisulfite restriction analysis PCR was used to assess the methylation status of LINE-1 repetitive sequences in genomic DNA derived from sera of 85 patients with HCC, 73 patients with cirrhosis, 20 healthy carriers of hepatitis B virus (HBV) and 30 healthy controls. RESULTS Serum genome hypomethylation, the percentage of unmethylated LINE-1, was significantly increased in patients with HCC (P<0.001). The levels of serum LINE-1 hypomethylation at initial presentation correlated significantly with the presence of HBsAg, large tumor sizes, and advanced tumor stages classified by the CLIP score. Multivariate analyses showed that serum LINE-1 hypomethylation was a significant and independent prognostic factor of overall survival. CONCLUSION Serum LINE-1 hypomethylation may serve as a prognostic marker for patients with HCC.
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Affiliation(s)
- Pisit Tangkijvanich
- Department of Bichemistry, Faculty of Medicine, Chulalongkorn University, Thailand
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Man YG, Nieburgs HE. A subset of cell clusters with malignant features in morphologically normal-appearing and hyperplastic tissues. ACTA ACUST UNITED AC 2006; 30:239-47. [PMID: 16872754 DOI: 10.1016/j.cdp.2006.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2006] [Indexed: 11/29/2022]
Abstract
BACKGROUND The development of human breast cancer may be a multistep process, sequentially undergoing normal, hyperplastic, in situ, invasive, and metastatic stages. METHODS Our previous and current studies have revealed that a subset of morphologically normal-appearing and hyperplastic breast tissues adjacent to or distant from malignant breast lesions contained cell clusters that showed malignancy-associated immunohistochemical and cytological alterations. RESULTS Compared to their morphologically similar counterparts within the same lesion, these cell clusters exhibited several unique features: (1) a significantly increased frequency of focal disruptions in surrounding myoepithelial cell layers and the loss of estrogen receptor expression, (2) signs of stromal and vascular invasion, (3) distinct alterations in the cytoplasmic-nuclear ratio and nuclear shape, size, and polarity, (4) the expression of multiple malignancy-associated biomarkers, and (5) malignancy-associated nuclear changes in benign-appearing cells. CONCLUSIONS These changes are likely to reflect DNA structural abnormalities resulting from the disposition of DNA and RNA structural defects or cancer susceptibility genes that facilitate progression and invasion, or to suggest that breast tumor progression and invasion may not always follow the hypothesized sequences. Thus, an integrated immunohistochemical and cytological assessment might facilitate the differential diagnosis, early detection and prevention of malignant breast lesions.
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Affiliation(s)
- Yan-gao Man
- Department of Gynecologic and Breast Pathology, Armed Forces Institute of Pathology and American Registry of Pathology, NW, Washington, DC 20306-6000, USA.
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Weaver KD, Grossman SA, Herman JG. Methylated tumor-specific DNA as a plasma biomarker in patients with glioma. Cancer Invest 2006; 24:35-40. [PMID: 16466990 DOI: 10.1080/07357900500449546] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
OBJECTIVE Patients with systemic malignancies have substantial quantities of tumor-specific DNA in their plasma which may serve as a potential biomarker for tumor burden. This approach has not been studied in gliomas. METHODS Methylation specific polymerase chain reaction (MSP) was used to determine the methylation status the promoters for p16/(INK4a), MGMT, p73, and RARbeta within glioma tissue and plasma. Blood was collected prior to craniotomy in 10 patients with glioma. DNA was extracted from tumor and plasma samples and assayed with MSP. Total plasma DNA also was quantified. Tumor-specific plasma DNA was defined as identification of the same methylated promoter (MP) in both tumor and plasma. RESULTS Total plasma DNA concentration was markedly elevated (mean 6,503 ng/ml, SEM 1,400 ng/ml). Glioma tissue contained methylation of at least one promoter in 9 out of 10 (90 percent) of patients studied. Of these patients, 6 out of 9 (67 percent) demonstrated methylation of at least one of the same promoters in plasma. Five of these had one MP identified in the plasma and one had 2 MP. Overall, glioma-specific plasma DNA was present in plasma of 6 out of 10 (60 percent) of patients. Each MP DNA marker found in the plasma also was present in the intracranial tumor. CONCLUSIONS Patients with high grade gliomas have large amounts of DNA in the plasma. Of these primary brain tumors, 90 percent contained methylated gene promoters, and in over 60 percent of these patients the same methylated promoters present in the tumor also were found in the plasma. This represents the first step to developing a quantitative plasma biomarker that could be used to monitor glioma status.
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Affiliation(s)
- Kyle D Weaver
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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Kondratova VN, Serd'uk OI, Shelepov VP, Lichtenstein AV. Concentration and isolation of DNA from biological fluids by agarose gel isotachophoresis. Biotechniques 2006; 39:695-9. [PMID: 16312218 DOI: 10.2144/000112020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Isotachophoresis is an electrophoretic method of separation of charged substances. The method is characterized by a discontinuous buffer system, constant velocity of separated molecules, and the distribution of separated components in the form of narrow concentrated bands located one right after another. As a rule, isotachophoresis is not used for the separation of nucleic acids because the mobility of polynucleotides in this system does not depend on their size. However, this circumstance proved to be very useful for the quantitative isolation of heterogeneous DNA fragments from biological fluids, for gene diagnostics of cancer in particular. The proposed method of agarose gel isotachophoresis of DNA has been used for the isolation of blood DNA and its successful PCR analysis.
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