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Sultana GNN, Akter F, Israfil SMH, Ray UC, Jahan RA, Ali MS, Din SA, Rahman S, Halim R, Alam MS. Quantitative analysis of serum cell-free DNA as a predictive and prognostic marker in breast cancer patients. Front Oncol 2023; 13:1171412. [PMID: 37427131 PMCID: PMC10324030 DOI: 10.3389/fonc.2023.1171412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/23/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction According to the GLOBOCAN (Global Cancer Observatory) 2020 report, 13,028 new cases of breast cancer (19%) were diagnosed in the United States, and 6,783 of them succumbed to the disease, making it the most common cancer among women. The clinical stage at the time of diagnosis is one of the most significant survival predictors in breast cancer. With delayed illness detection comes a lower survival rate. The prognosis of breast cancer may be predicted using circulating cell-free DNA (cfDNA), a non-invasive diagnosis technique. Objective This study aimed to determine the most sensitive and effective method for detecting changes in cfDNA levels and for using cfDNA as a diagnostic and prognostic marker of breast cancer. Methods The potential function of serum cfDNA levels as a marker for early breast cancer diagnosis was investigated using UV spectrophotometric, fluorometric, and real-time qPCR assays. Results This research suggests that the most successful way to measure the amount of cfDNA described decades ago could be used as a "liquid biopsy" to track cancer in real time. The RT-qPCR (ALU115) method produced the most statistically significant results (p=0.000). At the threshold concentration of 395.65 ng/ml of cfDNA, the ROC curve reflects the maximum AUC= 0.7607, with a sensitivity of 0.65 and specificity of 0.80. Conclusion For a preliminary assessment of total circulating cfDNA, a combination of all of the above techniques will be most efficacious. Based on our results, we conclude that the RT-qPCR technique combined with fluorometric measurement can identify a statistically significant difference in cfDNA levels between cohorts of breast cancer patients and healthy controls.
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Affiliation(s)
| | - Ferdowsi Akter
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - S. M. Hasan Israfil
- Department of Pharmaceutical Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Utpal Chandra Ray
- Genetic and Cytology Laboratory, Invent Technologies, Banani, Dhaka, Bangladesh
| | - Rumana Akther Jahan
- Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Mohammad Shawkat Ali
- Department of Clinical Pharmacy and Pharmacology, University of Dhaka, Dhaka, Bangladesh
| | - Salim Al Din
- Genetic and Cytology Laboratory, Invent Technologies, Banani, Dhaka, Bangladesh
| | - Shafiqur Rahman
- Institute of Statistical Research and Training, University of Dhaka, Dhaka, Bangladesh
| | - Rezaul Halim
- Genetic and Cytology Laboratory, Invent Technologies, Banani, Dhaka, Bangladesh
| | - Mohammad Sahajadul Alam
- Department of Surgical Oncology, National Institute of Cancer Research and Hospital, Dhaka, Bangladesh
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Papatheodoridi A, Karakousis N, Lembessis P, Chatzigeorgiou A, Papatheodoridis GV. The Significance of Circulating Cell-Free DNA Markers in Chronic Hepatitis B Patients with Hepatocellular Carcinoma. Pathogens 2021; 10:1524. [PMID: 34832679 PMCID: PMC8618100 DOI: 10.3390/pathogens10111524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
(1) Background: Hepatocellular carcinoma (HCC) is the most serious complication of chronic hepatitis B (CHB). Recently, the detection of circulating cell-free (cf) DNA and nucleosomes has found numerous applications in oncology. This study aimed to examine the levels of serum cfDNA markers and nucleosomes in CHB patients with and without HCC and assess their potential association with HCC patients' survival. (2) Methods: Nineteen patients with CHB and HCC and 38 matched patients with CHB without cancer development during 5 years of antiviral therapy were included. Stored serum samples were analyzed for cfDNA species, including the cfDNA concentration and levels of Alu115, Alu247, and nucleosomes. DNA integrity was expressed as the Alu247/Alu115 ratio. (3) Results: Compared to controls, HCC patients had higher median Alu247 levels (64.2 vs. 23.2 genomic equivalent, p = 0.004) and DNA integrity (1.0 vs. 0.7, p < 0.001) and a trend for a higher median cfDNA concentration (36.0 vs. 19.5 ng/mL, p = 0.064). Increased DNA integrity (Alu247/Alu115 > 1) was associated with an increased risk of death during the first year after HCC diagnosis (p = 0.016). (4) Conclusions: Levels of Alu247 and DNA integrity in serum cfDNA are elevated in CHB patients with HCC, whereas increased DNA integrity seems to be associated with a worse short-term prognosis in this setting.
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Affiliation(s)
- Alkistis Papatheodoridi
- Department of Clinical Therapeutics, “Alexandra” General Hospital of Athens, Medical School of National, Kapodistrian University of Athens, 11528 Athens, Greece;
- Department of Physiology, Medical School of National, Kapodistrian University of Athens, 11527 Athens, Greece; (N.K.); (P.L.)
| | - Nikolaos Karakousis
- Department of Physiology, Medical School of National, Kapodistrian University of Athens, 11527 Athens, Greece; (N.K.); (P.L.)
- Department of Gastroenterology, General Hospital of Athens “Laiko”, Medical School of National, Kapodistrian University of Athens, 11527 Athens, Greece
| | - Panagiotis Lembessis
- Department of Physiology, Medical School of National, Kapodistrian University of Athens, 11527 Athens, Greece; (N.K.); (P.L.)
| | - Antonios Chatzigeorgiou
- Department of Physiology, Medical School of National, Kapodistrian University of Athens, 11527 Athens, Greece; (N.K.); (P.L.)
- Institute for Clinical Chemistry and Laboratory Medicine, University Clinic Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - George V. Papatheodoridis
- Department of Gastroenterology, General Hospital of Athens “Laiko”, Medical School of National, Kapodistrian University of Athens, 11527 Athens, Greece
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3
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Rykov SV, Filippova EA, Loginov VI, Braga EA. Gene Methylation in Circulating Cell-Free DNA from the Blood Plasma as Prognostic and Predictive Factor in Breast Cancer. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421110120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Davidson BA, Croessmann S, Park BH. The breast is yet to come: current and future utility of circulating tumour DNA in breast cancer. Br J Cancer 2021; 125:780-788. [PMID: 34040179 PMCID: PMC8438047 DOI: 10.1038/s41416-021-01422-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 04/02/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023] Open
Abstract
Advances in genomic strategies and the development of targeted therapies have enabled precision medicine to revolutionise the field of oncology. Precision medicine uses patient-specific genetic and molecular information, traditionally obtained from tumour biopsy samples, to classify tumours and treat them accordingly. However, biopsy samples often fail to provide complete tumour profiling, and the technique is expensive and, of course, relatively invasive. Advances in genomic techniques have led to improvements in the isolation and detection of circulating tumour DNA (ctDNA), a component of a peripheral blood draw/liquid biopsy. Liquid biopsy offers a minimally invasive method to gather genetic information that is representative of a global snapshot of both primary and metastatic sites and can thereby provide invaluable information for potential targeted therapies and methods for tumour surveillance. However, a lack of prospective clinical trials showing direct patient benefit has limited the implementation of liquid biopsies in standard clinical applications. Here, we review the potential of ctDNA obtained by liquid biopsy to revolutionise personalised medicine and discuss current applications of ctDNA both at the benchtop and bedside.
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Affiliation(s)
- Brad A. Davidson
- grid.412807.80000 0004 1936 9916The Vanderbilt-Ingram Cancer Center, Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Sarah Croessmann
- grid.412807.80000 0004 1936 9916The Vanderbilt-Ingram Cancer Center, Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Ben H. Park
- grid.412807.80000 0004 1936 9916The Vanderbilt-Ingram Cancer Center, Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
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5
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Zhu A, Yuan P, Hu N, Li M, Wang W, Wang X, Yue J, Wang J, Luo Y, Ma F, Zhang P, Li Q, Xu B, Cao S, Lippi G, Naito Y, Osman MA, Marta GN, Franceschini G, Orlandi A. Phase II study of apatinib in combination with oral vinorelbine in heavily pretreated HER2-negative metastatic breast cancer and clinical implications of monitoring ctDNA. Cancer Biol Med 2021; 18:j.issn.2095-3941.2020.0418. [PMID: 34037346 PMCID: PMC8330536 DOI: 10.20892/j.issn.2095-3941.2020.0418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Apatinib is an oral TKI targeting VEGFR-2. Single-agent apatinib treatment has been shown to produce an objective response in patients with pretreated mBC. Oral vinorelbine also holds promise as a treatment of choice in patients with mBC. This study aimed to investigate the efficacy and safety of the oral vinorelbine-apatinib combination in patients with pretreated mBC. In addition, we detected gene variants in ctDNA to explore the therapeutic implications. METHODS This study enrolled patients with HER2-negative mBC who were pretreated with anthracycline/taxanes. Patients were treated with apatinib at 500 mg/425 mg daily plus oral vinorelbine 60 mg/m2 on days 1, 8, and 15 of every cycle (3 weeks). The primary endpoint was PFS. The secondary endpoints were ORR, CBR, OS, and safety. Patients eligible for ctDNA detection were evaluated before and during treatment. RESULTS Forty patients were enrolled. The median PFS was 5.2 months (95% CI, 3.4-7.0 months), and the median OS was 17.4 months (95% CI, 8.0-27.0 months). The ORR was 17.1% (6/35), and the CBR was 45.7% (16/35). The most common AEs included gastrointestinal reaction, myelosuppression, and hypertension. In 20 patients, ctDNA was detected at baseline and during treatment. A significant difference was found in PFS for undetected vs. detected baseline ctDNA (13.9 months vs. 3.6 months, P = 0.018). CONCLUSIONS All-oral therapy with apatinib plus vinorelbine displayed objective efficacy in patients with heavily pretreated HER2-negative mBC, with acceptable and manageable toxicity profiles. Patients with no gene variant detected and lower variant allele frequencies in ctDNA at baseline showed longer PFS.
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Affiliation(s)
- Anjie Zhu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Nanlin Hu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Mingzhou Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wenmiao Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xue Wang
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jian Yue
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jiayu Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yang Luo
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Pin Zhang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qing Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shanbo Cao
- AcornMed Biotechnology Co., Ltd., Beijing 101102, China
| | - Giuseppe Lippi
- Section of Clinical Biochemistry, University Hospital of Verona, Verona 37100, Italy
| | - Yoichi Naito
- Department of Breast and Medical Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Mohammed A. Osman
- Clinical Oncology, General Organization for Teaching Hospitals, Cairo 11435, Egypt
| | - Gustavo N. Marta
- Department of Radiation Oncology, Hospital Sírio-Libanês, Sao Paulo 01308-050, Brazil
| | - Gianluca Franceschini
- Multidisciplinary Breast Center, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome 00176, Italy
| | - Armando Orlandi
- Unit of Medical Oncology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma 00176, Italy
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Guo Q, Hua Y. The assessment of circulating cell-free DNA as a diagnostic tool for breast cancer: an updated systematic review and meta-analysis of quantitative and qualitative ssays. Clin Chem Lab Med 2021; 59:1479-1500. [PMID: 33951758 DOI: 10.1515/cclm-2021-0193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES This updated meta-analysis aimed to assess the diagnostic accuracy of circulating cell-free DNA (cfDNA) in breast cancer (BC). CONTENT An extensive systematic search was performed in PubMed, Scopus, Embase, and Science Direct databases to retrieve all related literature. Various diagnostic estimates, including sensitivity (SE), specificity (SP), likelihood ratios (LRs), diagnostic odds ratio (DOR), and area under the curve (AUC) of summary receiver operating characteristic (sROC) curve, were also calculated using bivariate linear mixed models. SUMMARY In this meta-analysis, 57 unique articles (130 assays) on 4246 BC patients and 2,952 controls, were enrolled. For quantitative approaches, pooled SE, SP, PLR, NLR, DOR, and AUC were obtained as 0.80, 0.88, 6.7, 0.23, 29, and 0.91, respectively. Moreover, for qualitative approaches, pooled SE and SP for diagnostic performance were obtained as 0.36 and 0.98, respectively. In addition, PLR was 14.9 and NLR was 0.66. As well, the combined DOR was 23, and the AUC was 0.79. OUTLOOK Regardless of promising SE and SP, analysis of LRs suggested that quantitative assays are not robust enough neither for BC confirmation nor for its exclusion. On the other hand, qualitative assays showed satisfying performance only for confirming the diagnosis of BC, but not for its exclusion. Furthermore, qualitative cfDNA assays showed a better diagnostic performance in patients at the advanced stage of cancer, which represented no remarkable clinical significance as a biomarker for early detection.
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Affiliation(s)
- Qingfeng Guo
- Department of General Surgery, Affiliated Hospital of Jiangnan University (Original Area of Wuxi No. 3 People's Hospital), Wuxi, P.R. China
| | - Yuming Hua
- Department of General Surgery, Affiliated Hospital of Jiangnan University (Original Area of Wuxi No. 3 People's Hospital), Wuxi, P.R. China
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Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13040728. [PMID: 33578793 PMCID: PMC7916622 DOI: 10.3390/cancers13040728] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed. Abstract Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.
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Salimi M, Sedaghati Burkhani S. Integrity and Quantity Evaluation of Plasma Cell-Free DNA in Triple Negative Breast Cancer. Avicenna J Med Biotechnol 2019; 11:334-338. [PMID: 31908742 PMCID: PMC6925404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/03/2018] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Triple-Negative Breast Cancer (TNBC) is a subtype of breast cancer that lacks expression of the estrogen and progesterone receptor and does not overex-press human epidermal growth factor 2 receptor protein. TNBC is associated with special characteristics, including aggressiveness, poor prognosis, and treatment response. Non-invasive blood-based molecular markers such as cell-free DNA (cfDNA) variables have been shown to be putative markers in breast cancer prognosis. METHODS The cfDNA quantity and integrity were assessed in a case-control study of 96 breast cancer patients including 46 triple negative and 50 non-triple negative compared with 50 unaffected controls. A quantitative real-time PCR approach based on the quantification of two amplicons of the β-actin gene with different lengths (99 and 394 bp) was used to evaluate the integrity index 394/99. RESULTS Both cfDNA integrity index and quality were significantly elevated in breast cancer patients but integrity index can be considered as the more reliable diagnostic marker. The statistically significant increase of cfDNA quantity and integrity was observed in TNBC patients, somehow associated with nodal metastasis (p<0.001). CONCLUSION Elevated cfDNA concentration and integrity index in breast cancer patients compared with normal control and significant difference observed between TNBC and non-TNBC may be considered as a possible effective non-invasive diagnostic and prognostic molecular marker in breast cancer.
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Affiliation(s)
- Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Somayeh Sedaghati Burkhani
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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9
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Yu D, Tong Y, Guo X, Feng L, Jiang Z, Ying S, Jia J, Fang Y, Yu M, Xia H, Shi L, Lou J. Diagnostic Value of Concentration of Circulating Cell-Free DNA in Breast Cancer: A Meta-Analysis. Front Oncol 2019; 9:95. [PMID: 30881916 PMCID: PMC6405437 DOI: 10.3389/fonc.2019.00095] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/01/2019] [Indexed: 12/30/2022] Open
Abstract
The diagnostic value of the concentration of circulating cell-free DNA (cfDNA) for breast cancer has generated inconsistent results. The aim of this study was to evaluate the first diagnostic value of the concentration of cfDNA for breast cancer by meta-analysis. Studies were retrieved by searching PubMed, Cochrane Library, and Web of Science before June 2018. Sensitivity, specificity, diagnostic odds ratio (DOR), the summary receiver operating characteristic (SROC) curve, and the area under curve (AUC) were used to summarize overall diagnostic performance. The random-effects model was used to calculate the pooled statistics. Subgroup analysis and meta-regression analysis were carried out to detect the source of heterogeneity. A total of 13 studies were identified with 1,087 breast cancer patients and 720 healthy controls. Overall, the pooled sensitivity and specificity of concentration of cfDNA for breast cancer were 87% (95% CI, 73–94%) and 87% (95% CI, 79–93%), respectively. The pooled DOR was 32.93 (95% CI, 13.52–80.19) and the SROC curve revealed an AUC of 0.93 (95% CI, 0.91–0.95). Meta-regression analysis showed that no covariate had a significant correlation with relative DOR (RDOR). Publication bias was not detected in this meta-analysis. This meta-analysis indicates that the concentration of cfDNA has potential first diagnostic value for breast cancer and plasma may be a better source of cfDNA for detection of breast cancer.
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Affiliation(s)
- Dandan Yu
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Yan Tong
- Department of Outpatient Office, Affiliated Hangzhou First People's Hospiital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinnian Guo
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Lingfang Feng
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Zhaoqiang Jiang
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Shibo Ying
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Junlin Jia
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Yuan Fang
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Min Yu
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Hailing Xia
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Li Shi
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
| | - Jianlin Lou
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences (ZJAMS), Hangzhou, China
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10
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Rohanizadegan M. Analysis of circulating tumor DNA in breast cancer as a diagnostic and prognostic biomarker. Cancer Genet 2018; 228-229:159-168. [PMID: 29572011 PMCID: PMC6108954 DOI: 10.1016/j.cancergen.2018.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 01/15/2018] [Accepted: 02/16/2018] [Indexed: 12/17/2022]
Abstract
Despite all the advances in diagnosis and treatment of breast cancer, a large number of patients suffer from late diagnosis or recurrence of their disease. Current available imaging modalities do not reveal micrometastasis and tumor biopsy is an invasive method to detect early stage or recurrent cancer, signifying the need for an inexpensive, non-invasive diagnostic modality. Cell-free tumor DNA (ctDNA) has been tried for early detection and targeted therapy of breast cancer, but its diagnostic and prognostic utility is still under investigation. This review summarizes the existing evidence on the use of ctDNA specifically in breast cancer, including detection methods, diagnostic accuracy, role in genetics and epigenetics evaluation of the tumor, and comparison with other biomarkers. Current evidence suggests that increasing levels of ctDNA in breast cancer can be of significant diagnostic value for early detection of breast cancer although the sensitivity and specificity of the methods is still suboptimal. Additionally, ctDNA allows for characterizing the tumor in a non-invasive way and monitor the response to therapy, although discordance of ctDNA results with direct biopsy (i.e. due to tumor heterogeneity) is still considered a notable limitation.
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Affiliation(s)
- Mersedeh Rohanizadegan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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11
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Campos CDM, Gamage SST, Jackson JM, Witek MA, Park DS, Murphy MC, Godwin AK, Soper SA. Microfluidic-based solid phase extraction of cell free DNA. LAB ON A CHIP 2018; 18:3459-3470. [PMID: 30339164 PMCID: PMC6391159 DOI: 10.1039/c8lc00716k] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cell-free DNA (cfDNA) is a liquid biopsy marker that can carry signatures (i.e., mutations) associated with certain pathological conditions. Therefore, the extraction of cfDNA from a variety of clinical samples can be an effective and minimally invasive source of markers for disease detection and subsequent management. In the oncological diseases, circulating tumor DNA (ctDNA), a cfDNA sub-class, can carry clinically actionable mutations and coupled with next generation sequencing or other mutation detection methods provide a venue for effective in vitro diagnostics. However, cfDNA mutational analyses require high quality inputs. This necessitates extraction platforms that provide high recovery over the entire ctDNA size range (50 → 150 bp) with minimal interferences (i.e., co-extraction of genomic DNA), and high reproducibility with a simple workflow. Herein, we present a novel microfluidic solid-phase extraction device (μSPE) consisting of a plastic chip that is activated with UV/O3 to generate surface-confined carboxylic acid functionalities for the μSPE of cfDNA. The μSPE uses an immobilization buffer (IB) consisting of polyethylene glycol and salts that induce cfDNA condensation onto the activated plastic microfluidic surface. The μSPE consists of an array of micropillars to increase extraction bed load (scalable to loads >700 ng of cfDNA) and can be produced at low-cost using replication-based techniques. The entire μSPE can be fabricated in a single molding step negating the need for adding additional extraction supports to the device simplifying production and keeping device and assay cost low. The μSPE allowed for recoveries >90% of model cfDNA fragments across a range of sizes (100-700 bp) and even the ability to extract efficiently short cfDNA fragments (50 bp, >70%). In addition, the composition of the IB allowed for reducing the interference of co-extracted genomic DNA. We demonstrated the clinical utility of the μSPE by quantifying the levels of cfDNA in healthy donors and patients with non-small-cell lung and colorectal cancers. μSPE extracted cfDNA from plasma samples was also subjected to a ligase detection reaction (LDR) for determining the presence of mutations in the KRAS gene for colorectal and non-small cell lung cancer patients.
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Affiliation(s)
- Camila D. M. Campos
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
| | - Sachindra S. T. Gamage
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
| | - Joshua M. Jackson
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
| | - Malgorzata A. Witek
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
- Department of Biomedical Engineering, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel S. Park
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Michael C. Murphy
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Andrew K. Godwin
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Steven A. Soper
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Center of Biomodular Multi-scale Systems for Precision Medicine, USA
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
- BioEngineering Program, The University of Kansas, Lawrence, KS 66047, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66047, USA
- Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
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12
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Value of circulating cell-free DNA analysis as a diagnostic tool for breast cancer: a meta-analysis. Oncotarget 2018; 8:26625-26636. [PMID: 28460452 PMCID: PMC5432284 DOI: 10.18632/oncotarget.15775] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/15/2017] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES The aim of this study was to systematically evaluate the diagnostic value of cell free DNA (cfDNA) for breast cancer. RESULTS Among 308 candidate articles, 25 with relevant diagnostic screening qualified for final analysis. The mean sensitivity, specificity and area under the curve (AUC) of SROC plots for 24 studies that distinguished breast cancer patients from healthy controls were 0.70, 0.87, and 0.9314, yielding a DOR of 32.31. When analyzed in subgroups, the 14 quantitative studies produced sensitivity, specificity, AUC, and a DOR of 0.78, 0.83, 0.9116, and 24.40. The 10 qualitative studies produced 0.50, 0.98, 0.9919, and 68.45. For 8 studies that distinguished malignant breast cancer from benign diseases, the specificity, sensitivity, AUC and DOR were 0.75, 0.79, 0.8213, and 9.49. No covariate factors had a significant correlation with relative DOR. Deek's funnel plots indicated an absence of publication bias. MATERIALS AND METHODS Databases were searched for studies involving the use of cfDNA to diagnose breast cancer. The studies were analyzed to determine sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio (DOR), and the summary receiver operating characteristic (SROC). Covariates were evaluated for effect on relative DOR. Deek's Funnel plots were generated to measure publication bias. CONCLUSIONS Our analysis suggests a promising diagnostic potential of using cfDNA for breast cancer screening, but this diagnostic method is not yet independently sufficient. Further work refining qualitative cfDNA assays will improve the correct diagnosis of breast cancers.
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Wang H, Liu Z, Xie J, Wang Z, Zhou X, Fang Y, Pan H, Han W. Quantitation of cell-free DNA in blood is a potential screening and diagnostic maker of breast cancer: a meta-analysis. Oncotarget 2017; 8:102336-102345. [PMID: 29254249 PMCID: PMC5731959 DOI: 10.18632/oncotarget.21827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 09/22/2017] [Indexed: 12/25/2022] Open
Abstract
INTRODUCTION Increased cell-free DNA (cfDNA) levels in circulating blood have been associated with higher possibility of breast cancer, however, researchers have not reached an agreement on its analysis. MATERIALS AND METHODS We conducted a meta-analysis of 12 retrospective studies to clarify the value of cfDNA quantification in screening and diagnosis of breast cancer. PubMed, EMBASE, Web of Science and Cochrane library were searched from January, 2000 to October, 2016. Pooled analyses were estimated using a random effects model. RESULTS In total, 1003 primary breast cancer patients, 283 cases with benign breast disease and 575 healthy individuals were included. Pooled diagnostic odds ratio (DOR) was 27.63 (95% confidence interval [CI]: 10.96~69.61, I2 = 86.2%, P < 0.001) in discriminating between breast cancer and healthy controls; the area under the summary receiver operating characteristic (SROC) curve measured 0.91 (95% CI: 0.17~1.00). Analysis of available data in distinguishing breast cancer and benign breast disease showed a pooled DOR of 35.30 (95% CI: 7.58~164.39, I2 = 79.9%, P = 0.002) with an area under SROC of 0.91 (95% CI: 0.89~0.93). Ethnic group distribution based geographical factors suggested by meta-regression and subgroup analyses explained most of the heterogeneity. CONCLUSIONS Quantification of cfDNA is a promising test in screening and diagnostic of breast cancer, but population-based standardization of test methods require completion prior to clinical use.
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Affiliation(s)
- Huadi Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Liu
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiansheng Xie
- Laboratory of Cancer Biology, Institute of Clinical Science, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhanggui Wang
- Department of Radiotherapy, The Second People's Hospital of Anhui Province, Hefei, Anhui, China
| | - Xiaoyun Zhou
- Department of Medical Oncology, Xiasha Campus, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yong Fang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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14
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Cree IA, Uttley L, Buckley Woods H, Kikuchi H, Reiman A, Harnan S, Whiteman BL, Philips ST, Messenger M, Cox A, Teare D, Sheils O, Shaw J. The evidence base for circulating tumour DNA blood-based biomarkers for the early detection of cancer: a systematic mapping review. BMC Cancer 2017; 17:697. [PMID: 29061138 PMCID: PMC5654013 DOI: 10.1186/s12885-017-3693-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/18/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The presence of circulating cell-free DNA from tumours in blood (ctDNA) is of major importance to those interested in early cancer detection, as well as to those wishing to monitor tumour progression or diagnose the presence of activating mutations to guide treatment. In 2014, the UK Early Cancer Detection Consortium undertook a systematic mapping review of the literature to identify blood-based biomarkers with potential for the development of a non-invasive blood test for cancer screening, and which identified this as a major area of interest. This review builds on the mapping review to expand the ctDNA dataset to examine the best options for the detection of multiple cancer types. METHODS The original mapping review was based on comprehensive searches of the electronic databases Medline, Embase, CINAHL, the Cochrane library, and Biosis to obtain relevant literature on blood-based biomarkers for cancer detection in humans (PROSPERO no. CRD42014010827). The abstracts for each paper were reviewed to determine whether validation data were reported, and then examined in full. Publications concentrating on monitoring of disease burden or mutations were excluded. RESULTS The search identified 94 ctDNA studies meeting the criteria for review. All but 5 studies examined one cancer type, with breast, colorectal and lung cancers representing 60% of studies. The size and design of the studies varied widely. Controls were included in 77% of publications. The largest study included 640 patients, but the median study size was 65 cases and 35 controls, and the bulk of studies (71%) included less than 100 patients. Studies either estimated cfDNA levels non-specifically or tested for cancer-specific mutations or methylation changes (the majority using PCR-based methods). CONCLUSION We have systematically reviewed ctDNA blood biomarkers for the early detection of cancer. Pre-analytical, analytical, and post-analytical considerations were identified which need to be addressed before such biomarkers enter clinical practice. The value of small studies with no comparison between methods, or even the inclusion of controls is highly questionable, and larger validation studies will be required before such methods can be considered for early cancer detection.
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Affiliation(s)
- Ian A. Cree
- WHO Classification of Tumours Group, International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372 Lyon, CEDEX 08 France
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
- Institute of Ophthalmology, University College London, EC1V 9EL, London, UK
| | - Lesley Uttley
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Helen Buckley Woods
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Hugh Kikuchi
- Department of Pathology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX UK
| | - Anne Reiman
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
| | - Susan Harnan
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Becky L. Whiteman
- London North West Healthcare NHS Trust, Northwick Park Hospital, Watford Road, Harrow, HA1 3UJ UK
| | | | - Michael Messenger
- Leeds Centre for Personalised Medicine and Health, University of Leeds and NIHR Diagnostic Evidence Co-Operative Leeds, Leeds Teaching Hospitals NHS Trust, Leeds, LS9 7TF UK
| | - Angela Cox
- Sheffield Institute for Nucleic Acids, Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield, S10 2RX UK
| | - Dawn Teare
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Orla Sheils
- Sir Patrick Dun Research Laboratory, Central Pathology Laboratory, St James’s Hospital & Trinity College Dublin, Dublin 8, Ireland
| | - Jacqui Shaw
- University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX UK
| | - For the UK Early Cancer Detection Consortium
- WHO Classification of Tumours Group, International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372 Lyon, CEDEX 08 France
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
- Institute of Ophthalmology, University College London, EC1V 9EL, London, UK
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
- Department of Pathology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX UK
- London North West Healthcare NHS Trust, Northwick Park Hospital, Watford Road, Harrow, HA1 3UJ UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
- Leeds Centre for Personalised Medicine and Health, University of Leeds and NIHR Diagnostic Evidence Co-Operative Leeds, Leeds Teaching Hospitals NHS Trust, Leeds, LS9 7TF UK
- Sheffield Institute for Nucleic Acids, Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield, S10 2RX UK
- Sir Patrick Dun Research Laboratory, Central Pathology Laboratory, St James’s Hospital & Trinity College Dublin, Dublin 8, Ireland
- University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX UK
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15
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Polivka J, Pesta M, Janku F. Testing for oncogenic molecular aberrations in cell-free DNA-based liquid biopsies in the clinic: are we there yet? Expert Rev Mol Diagn 2015; 15:1631-44. [PMID: 26559503 DOI: 10.1586/14737159.2015.1110021] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The optimal choice of cancer therapy depends upon analysis of the tumor genome for druggable molecular alterations. The spatial and temporal intratumor heterogeneity of cancers creates substantial challenges, as molecular profile depends on time and site of tumor tissue collection. To capture the entire molecular profile, multiple biopsies from primary and metastatic sites at different time points would be required, which is not feasible for ethical or economic reasons. Molecular analysis of circulating cell-free DNA offers a novel, minimally invasive method that can be performed at multiple time-points and plausibly better represents the prevailing molecular profile of the cancer. Molecular analysis of this cell-free DNA offers multiple clinically useful applications, such as identification of molecular targets for cancer therapy, monitoring of tumor molecular profile in real time, detection of emerging molecular aberrations associated with resistance to particular therapy, determination of cancer prognosis and diagnosis of cancer recurrence or progression.
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Affiliation(s)
- Jiri Polivka
- a Department of Histology and Embryology and Biomedical Centre, Faculty of Medicine in Plzen , Charles University in Prague , Plzen , Czech Republic.,b Department of Neurology , Faculty Hospital Plzen , Plzen , Czech Republic
| | - Martin Pesta
- c Department of Biology, Faculty of Medicine in Plzen , Charles University in Prague , Plzen , Czech Republic
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16
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Buas MF, Rho JH, Chai X, Zhang Y, Lampe PD, Li CI. Candidate early detection protein biomarkers for ER+/PR+ invasive ductal breast carcinoma identified using pre-clinical plasma from the WHI observational study. Breast Cancer Res Treat 2015; 153:445-54. [PMID: 26319120 DOI: 10.1007/s10549-015-3554-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 08/21/2015] [Indexed: 01/08/2023]
Abstract
Estrogen receptor (ER)-positive/progesterone receptor (PR)-positive invasive ductal carcinoma accounts for ~45 % of invasive breast cancer (BC) diagnoses in the U.S. Despite reductions in BC mortality attributable to mammography screening and adjuvant hormonal therapy, an important challenge remains the development of clinically useful blood-based biomarkers for risk assessment and early detection. The objective of this study was to identify novel protein markers for ER+/PR+ ductal BC. A nested case-control study was conducted within the Women's Health Initiative observational study. Pre-clinical plasma specimens, collected up to 12.5 months before diagnosis from 121 cases and 121 matched controls, were equally divided into training and testing sets and interrogated using a customized antibody array targeting >2000 proteins. Statistically significant differences (P < 0.05) in matched case versus control signals were observed for 39 candidates in both training and testing sets, and four markers (CSF2, RYBP, TFRC, ITGB4) remained significant after Bonferroni correction (P < 2.03 × 10(-5)). A multivariate modeling procedure based on elastic net regression with Monte Carlo cross-validation achieved an estimated AUC of 0.75 (SD 0.06). Most candidates did not overlap with those described previously for triple-negative BC, suggesting sub-type specificity. Gene set enrichment analyses identified two GO gene sets as upregulated in cases-microtubule cytoskeleton and response to hormone stimulus (P < 0.05, q < 0.25). This study has identified a pool of novel candidate plasma protein biomarkers for ER+/PR+ ductal BC using pre-diagnostic biospecimens. Further validation studies are needed to confirm these candidates and assess their potential clinical utility for BC risk assessment/early detection.
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MESH Headings
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/blood
- Breast Neoplasms/diagnosis
- Breast Neoplasms/metabolism
- Carcinoma, Ductal, Breast/blood
- Carcinoma, Ductal, Breast/diagnosis
- Carcinoma, Ductal, Breast/metabolism
- Case-Control Studies
- Computational Biology/methods
- Early Detection of Cancer
- Female
- Humans
- Middle Aged
- Neoplasm Invasiveness
- Neoplasm Staging
- Proteome
- Proteomics/methods
- ROC Curve
- Receptors, Estrogen/metabolism
- Receptors, Progesterone/metabolism
- Risk Factors
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Affiliation(s)
- Matthew F Buas
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,
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17
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An exposure to the oxidized DNA enhances both instability of genome and survival in cancer cells. PLoS One 2013; 8:e77469. [PMID: 24147001 PMCID: PMC3798467 DOI: 10.1371/journal.pone.0077469] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 09/03/2013] [Indexed: 11/19/2022] Open
Abstract
Background Cell free DNA (cfDNA) circulates throughout the bloodstream of both healthy people and patients with various diseases and acts upon the cells. Response to cfDNA depends on concentrations and levels of the damage within cfDNA. Oxidized extracellular DNA acts as a stress signal and elicits an adaptive response. Principal Findings Here we show that oxidized extracellular DNA stimulates the survival of MCF-7 tumor cells. Importantly, in cells exposed to oxidized DNA, the suppression of cell death is accompanied by an increase in the markers of genome instability. Short-term exposure to oxidized DNA results in both single- and double strand DNA breaks. Longer treatments evoke a compensatory response that leads to a decrease in the levels of chromatin fragmentations across cell populations. Exposure to oxidized DNA leads to a decrease in the activity of NRF2 and an increase in the activity of NF-kB and STAT3. A model that describes the role of oxidized DNA released from apoptotic cells in tumor biology is proposed. Conclusions/Significance Survival of cells with an unstable genome may substantially augment progression of malignancy. Further studies of the effects of extracellular DNA on malignant and normal cells are warranted.
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18
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Plasma HER2 amplification in cell-free DNA during neoadjuvant chemotherapy in breast cancer. J Cancer Res Clin Oncol 2013. [PMID: 23479212 DOI: 10.1007/s00432‐013‐1413‐5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE Measurement of human epidermal growth factor receptor 2 (HER2) gene amplification in cell-free DNA (cfDNA) is an evolving technique in breast cancer, enabling liquid biopsies and treatment monitoring. The present study investigated the dynamics of plasma HER2 gene copy number and amplification in cfDNA during neoadjuvant chemotherapy. PATIENTS AND METHODS The study included 50 patients from a prospective cohort analyzed during neoadjuvant chemotherapy. Fifty healthy women with no history of cancer served as control group and 15 patients with metastatic breast cancer were used to validate the assay. Total cfDNA and HER2 gene amplification were measured by quantitative real-time polymerase chain reaction. RESULTS Plasma HER2 gene copy number (p = 0.794), HER2 gene amplification (p = 0.127) and total cfDNA (p = 0.440) did not differ significantly from the levels in the control group. Eighteen patients (36 %) obtained pathological complete response (pCR). HER2 gene copy number before the operation was significantly higher than the baseline level (p < 0.0001), but there was no difference between patients with and without pCR (p = 0.569). Likewise, there was no difference in plasma HER2 gene amplification between tissue HER2-positive and -negative patients (p = 0.754). CONCLUSIONS The results indicate that neither total cfDNA nor HER2 gene copy number is elevated in primary breast cancer patients compared to healthy controls. The level of both parameters increased during neoadjuvant chemotherapy, but without any relation to treatment effect. There was no indication of plasma HER2 gene amplification in the HER2-positive patients in the neoadjuvant setting.
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19
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Bechmann T, Andersen RF, Pallisgaard N, Madsen JS, Maae E, Jakobsen EH, Bak Jylling AM, Steffensen KD, Jakobsen A. Plasma HER2 amplification in cell-free DNA during neoadjuvant chemotherapy in breast cancer. J Cancer Res Clin Oncol 2013; 139:995-1003. [PMID: 23479212 DOI: 10.1007/s00432-013-1413-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 02/28/2013] [Indexed: 12/14/2022]
Abstract
PURPOSE Measurement of human epidermal growth factor receptor 2 (HER2) gene amplification in cell-free DNA (cfDNA) is an evolving technique in breast cancer, enabling liquid biopsies and treatment monitoring. The present study investigated the dynamics of plasma HER2 gene copy number and amplification in cfDNA during neoadjuvant chemotherapy. PATIENTS AND METHODS The study included 50 patients from a prospective cohort analyzed during neoadjuvant chemotherapy. Fifty healthy women with no history of cancer served as control group and 15 patients with metastatic breast cancer were used to validate the assay. Total cfDNA and HER2 gene amplification were measured by quantitative real-time polymerase chain reaction. RESULTS Plasma HER2 gene copy number (p = 0.794), HER2 gene amplification (p = 0.127) and total cfDNA (p = 0.440) did not differ significantly from the levels in the control group. Eighteen patients (36 %) obtained pathological complete response (pCR). HER2 gene copy number before the operation was significantly higher than the baseline level (p < 0.0001), but there was no difference between patients with and without pCR (p = 0.569). Likewise, there was no difference in plasma HER2 gene amplification between tissue HER2-positive and -negative patients (p = 0.754). CONCLUSIONS The results indicate that neither total cfDNA nor HER2 gene copy number is elevated in primary breast cancer patients compared to healthy controls. The level of both parameters increased during neoadjuvant chemotherapy, but without any relation to treatment effect. There was no indication of plasma HER2 gene amplification in the HER2-positive patients in the neoadjuvant setting.
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Affiliation(s)
- Troels Bechmann
- The Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.
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