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Gao L, Medford A, Spring L, Bar Y, Hu B, Jimenez R, Isakoff SJ, Bardia A, Peppercorn J. Searching for the "Holy Grail" of breast cancer recurrence risk: a narrative review of the hunt for a better biomarker and the promise of circulating tumor DNA (ctDNA). Breast Cancer Res Treat 2024; 205:211-226. [PMID: 38355821 DOI: 10.1007/s10549-024-07253-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND This paper is a narrative review of a major clinical challenge at the heart of breast cancer care: determining which patients are at risk of recurrence, which require systemic therapy, and which remain at risk in the survivorship phase of care despite initial therapy. METHODS We review the literature on prognostic and predictive biomarkers in breast cancer with a focus on detection of minimal residual disease. RESULTS While we have many tools to estimate and refine risk that are used to individualize local and systemic therapy, we know that we continue to over treat many patients and undertreat others. Many patients also experience what is, at least in hindsight, needless fear of recurrence. In this review, we frame this dilemma for the practicing breast oncologist and discuss the search for what we term the "holy grail" of breast cancer evaluation: the ideal biomarker of residual distant disease. We review the history of attempts to address this problem and the up-to-date science on biomarkers, circulating tumor cells and circulating tumor DNA (ctDNA). CONCLUSION This review suggests that the emerging promise of ctDNA may help resolve a crticical dilemma at the heart of breast cancer care, and improve prognostication, treatment selection, and outcomes for patients with breast cancer.
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Affiliation(s)
- Lucy Gao
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Arielle Medford
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Laura Spring
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yael Bar
- Massachusetts General Hospital, Boston, MA, USA
| | - Bonnie Hu
- Massachusetts General Hospital, Boston, MA, USA
| | - Rachel Jimenez
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Steven J Isakoff
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Aditya Bardia
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jeffrey Peppercorn
- Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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2
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Sannachi L, Osapoetra LO, DiCenzo D, Halstead S, Wright F, Look-Hong N, Slodkowska E, Gandhi S, Curpen B, Kolios MC, Oelze M, Czarnota GJ. A priori prediction of breast cancer response to neoadjuvant chemotherapy using quantitative ultrasound, texture derivative and molecular subtype. Sci Rep 2023; 13:22687. [PMID: 38114526 PMCID: PMC10730572 DOI: 10.1038/s41598-023-49478-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023] Open
Abstract
The purpose of this study was to investigate the performances of the tumor response prediction prior to neoadjuvant chemotherapy based on quantitative ultrasound, tumour core-margin, texture derivative analyses, and molecular parameters in a large cohort of patients (n = 208) with locally advanced and earlier-stage breast cancer and combined them to best determine tumour responses with machine learning approach. Two multi-features response prediction algorithms using a k-nearest neighbour and support vector machine were developed with leave-one-out and hold-out cross-validation methods to evaluate the performance of the response prediction models. In a leave-one-out approach, the quantitative ultrasound-texture analysis based model attained good classification performance with 80% of accuracy and AUC of 0.83. Including molecular subtype in the model improved the performance to 83% of accuracy and 0.87 of AUC. Due to limited number of samples in the training process, a model developed with a hold-out approach exhibited a slightly higher bias error in classification performance. The most relevant features selected in predicting the response groups are core-to-margin, texture-derivative, and molecular subtype. These results imply that that baseline tumour-margin, texture derivative analysis methods combined with molecular subtype can potentially be used for the prediction of ultimate treatment response in patients prior to neoadjuvant chemotherapy.
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Affiliation(s)
- Lakshmanan Sannachi
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, 2075, Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Laurentius O Osapoetra
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, 2075, Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Daniel DiCenzo
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, 2075, Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Schontal Halstead
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, 2075, Bayview Avenue, Toronto, ON, M4N 3M5, Canada
- Department of Surgery, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Frances Wright
- Department of Surgery, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Nicole Look-Hong
- Department of Surgery, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Elzbieta Slodkowska
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Sonal Gandhi
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Belinda Curpen
- Department of Medical Imaging, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Michael C Kolios
- Department of Physics, Toronto Metropolitan University, Toronto, ON, Canada
| | - Michael Oelze
- Department of Electrical and Computer Engineering, Univerity of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Gregory J Czarnota
- Physical Sciences Platform, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, 2075, Bayview Avenue, Toronto, ON, M4N 3M5, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada.
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Dao J, Conway PJ, Subramani B, Meyyappan D, Russell S, Mahadevan D. Using cfDNA and ctDNA as Oncologic Markers: A Path to Clinical Validation. Int J Mol Sci 2023; 24:13219. [PMID: 37686024 PMCID: PMC10487653 DOI: 10.3390/ijms241713219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The detection of circulating tumor DNA (ctDNA) in liquid biopsy samples as an oncological marker is being used in clinical trials at every step of clinical management. As ctDNA-based liquid biopsy kits are developed and used in clinics, companies work towards increased convenience, accuracy, and cost over solid biopsies and other oncological markers. The technology used to differentiate ctDNA and cell-free DNA (cfDNA) continues to improve with new tests and methodologies being able to detect down to mutant allele frequencies of 0.001% or 1/100,000 copies. Recognizing this development in technology, the FDA has recently given pre-market approval and breakthrough device designations to multiple companies. The purpose of this review is to look at the utility of measuring total cfDNA, techniques used to differentiate ctDNA from cfDNA, and the utility of different ctDNA-based liquid biopsy kits using relevant articles from PubMed, clinicaltrials.gov, FDA approvals, and company newsletters. Measuring total cfDNA could be a cost-effective, viable prognostic marker, but various factors do not favor it as a monitoring tool during chemotherapy. While there may be a place in the clinic for measuring total cfDNA in the future, the lack of standardization means that it is difficult to move forward with large-scale clinical validation studies currently. While the detection of ctDNA has promising standardized liquid biopsy kits from various companies with large clinical trials ongoing, their applications in screening and minimal residual disease can suffer from lower sensitivity. However, researchers are working towards solutions to these issues with innovations in technology, multi-omics, and sampling. With great promise, further research is needed before liquid biopsies can be recommended for everyday clinical management.
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Affiliation(s)
- Jonathan Dao
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Patrick J. Conway
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Baskaran Subramani
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Devi Meyyappan
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
| | - Sammy Russell
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Daruka Mahadevan
- Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Mays Cancer Center, University of Texas Health, San Antonio, TX 78229, USA
- Graduate School of Biomedical Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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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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5
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Huang Q, Ji M, Li F, Li Y, Zhou X, Hsueh CY, Zhou L. Diagnostic and prognostic value of plasma cell-free DNA combined with VEGF-C in laryngeal squamous cell carcinoma. Mol Cell Probes 2023; 67:101895. [PMID: 36682577 DOI: 10.1016/j.mcp.2023.101895] [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: 09/12/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) and vascular endothelial growth factor-C (VEGF-C) can be utilized to detect cancer and predict its prognosis. However, their potential application in laryngeal squamous cell carcinoma (LSCC) is unclear. PURPOSE This study aimed to identify the diagnostic and prognostic value of cfDNA and VEGF-C in LSCC patients. METHODS The plasma cfDNA of 148 LSCC patients and 43 non-tumor patients were isolated. Quantitative real-time PCR (qRT-PCR) was performed to assess long and short DNA fragments in plasma by amplifying the ALU repeats. ALU-qPCR results (ALU247/ALU115) were used to calculate cfDNA integrity index. Vascular endothelial growth factor-C (VEGF-C) level was detected by ELISA assay. Correlation between cfDNA and clinical features was analyzed. For detecting the sensitivity and specificity of cfDNA and VEGF-C alone or in combination for diagnosing LSCC, receiver operator characteristic (ROC) was established. For evaluating the overall survival (OS) of LSCC, Kaplan-Meier curves were established. RESULTS LSCC patients had significantly higher levels of plasma cfDNA (ALU115, ALU247, and cfDNA integrity index) and VEGF-C than those without cancer (p < 0.05), showing area under the curve (AUC) values of 0.79, 0.74, 0.62 and 0.80, when cutoff value was correspondingly defined at 2.14 ng/mL, 1.39 ng/mL, 0.73 and 412.90 pg/mL, respectively. The AUC for distinguishing LSCC patients from non-tumor patients by plasma cfDNA combined with VEGF-C was 0.89 (95% CI: 0.83-0.94). A significant correlation was found between plasma cfDNA levels and Ki-67, tumor size, pT stage, and smoking history (p < 0.05). Based on survival analysis, low VEGF-C concentration groups had longer OS than those with high VEGF-C concentration (p = 0.02). CONCLUSION Indicators such as plasma cfDNA and VEGF-C may be used to diagnose and monitor LSCC for its noninvasiveness and rapid accessibility.
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Affiliation(s)
- Qiang Huang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Mengyou Ji
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Feiran Li
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Yufeng Li
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Xuehua Zhou
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Chi-Yao Hsueh
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
| | - Liang Zhou
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
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Gianni C, Palleschi M, Merloni F, Bleve S, Casadei C, Sirico M, Di Menna G, Sarti S, Cecconetto L, Mariotti M, De Giorgi U. Potential Impact of Preoperative Circulating Biomarkers on Individual Escalating/de-Escalating Strategies in Early Breast Cancer. Cancers (Basel) 2022; 15:96. [PMID: 36612091 PMCID: PMC9817806 DOI: 10.3390/cancers15010096] [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: 11/30/2022] [Revised: 12/18/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The research on non-invasive circulating biomarkers to guide clinical decision is in wide expansion, including the earliest disease settings. Several new intensification/de-intensification strategies are approaching clinical practice, personalizing the treatment for each patient. Moreover, liquid biopsy is revealing its potential with multiple techniques and studies available on circulating biomarkers in the preoperative phase. Inflammatory circulating cells, circulating tumor cells (CTCs), cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), and other biological biomarkers are improving the armamentarium for treatment selection. Defining the escalation and de-escalation of treatments is a mainstay of personalized medicine in early breast cancer. In this review, we delineate the studies investigating the possible application of these non-invasive tools to give a more enlightened approach to escalating/de-escalating strategies in early breast cancer.
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Affiliation(s)
- Caterina Gianni
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
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7
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Cell-Free DNA Fragmentomics: A Promising Biomarker for Diagnosis, Prognosis and Prediction of Response in Breast Cancer. Int J Mol Sci 2022; 23:ijms232214197. [PMID: 36430675 PMCID: PMC9695769 DOI: 10.3390/ijms232214197] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022] Open
Abstract
Identifying novel circulating biomarkers predictive of response and informative about the mechanisms of resistance, is the new challenge for breast cancer (BC) management. The integration of omics information will gradually revolutionize the clinical approach. Liquid biopsy is being incorporated into the diagnostic and decision-making process for the treatment of BC, in particular with the analysis of circulating tumor DNA, although with some relevant limitations, including costs. Circulating cell-free DNA (cfDNA) fragmentomics and its integrity index may become a cheaper, noninvasive biomarker that could provide significant additional information for monitoring response to systemic treatments in BC. The purpose of our review is to focus on the available research on cfDNA integrity and its features as a biomarker of diagnosis, prognosis and response to treatments in BC, highlighting new perspectives and critical issues for future applications.
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The Utility of Repetitive Cell-Free DNA in Cancer Liquid Biopsies. Diagnostics (Basel) 2022; 12:diagnostics12061363. [PMID: 35741173 PMCID: PMC9221655 DOI: 10.3390/diagnostics12061363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
Liquid biopsy is a broad term that refers to the testing of body fluids for biomarkers that correlate with a pathological condition. While a variety of body-fluid components (e.g., circulating tumor cells, extracellular vesicles, RNA, proteins, and metabolites) are studied as potential liquid biopsy biomarkers, cell-free DNA (cfDNA) has attracted the most attention in recent years. The total cfDNA population in a typical biospecimen represents an immensely rich source of biological and pathological information and has demonstrated significant potential as a versatile biomarker in oncology, non-invasive prenatal testing, and transplant monitoring. As a significant portion of cfDNA is composed of repeat DNA sequences and some families (e.g., pericentric satellites) were recently shown to be overrepresented in cfDNA populations vs their genomic abundance, it holds great potential for developing liquid biopsy-based biomarkers for the early detection and management of patients with cancer. By outlining research that employed cell-free repeat DNA sequences, in particular the ALU and LINE-1 elements, we highlight the clinical potential of the repeat-element content of cfDNA as an underappreciated marker in the cancer liquid biopsy repertoire.
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Shaban S, Al‑Rahim A, Suleiman A. ALU repeat as potential molecular marker in the detection and prognosis of different cancer types: A systematic review. Mol Clin Oncol 2022; 16:86. [PMID: 35251637 PMCID: PMC8892463 DOI: 10.3892/mco.2022.2519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/13/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer is a major health issue worldwide. cfDNA integrity has been reported as a potential diagnostic molecular marker for different types of cancer, identifying the importance of liquid biopsy. The aim of this review was to evaluate the prognostic and diagnostic performance of Arthrobacter luteus (ALU) repeat in tumor. Following a thorough review of the literature published from January, 2000 to September 2021, 36 studies were included. All of the study descriptions were analyzed. According to several studies, there were increased concentrations of ALU repetitive elements in cancer patients, while these concentrations were decreased in control, benign, different cancer stage, and other diseases. The total ALU (115 and 247) sequence levels are potential biomarkers for the purpose of investigations and cancer prognosis.
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Affiliation(s)
- Semaa Shaban
- Department of Biology, College of Sciences, Tikrit University, Tikrit, Saladin 34001, Iraq
| | - Aya Al‑Rahim
- Department of Molecular and Medical Biotechnology, College of Biotechnology, Al‑Nahrain University, Baghdad 64074, Iraq
| | - Ahmed Suleiman
- Department of Biotechnology, Science College, University of Anbar, Ramadi, Anbar 46006, Iraq
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Alekseeva L, Mironova N. Role of Cell-Free DNA and Deoxyribonucleases in Tumor Progression. Int J Mol Sci 2021; 22:12246. [PMID: 34830126 PMCID: PMC8625144 DOI: 10.3390/ijms222212246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Many studies have reported an increase in the level of circulating cell-free DNA (cfDNA) in the blood of patients with cancer. cfDNA mainly comes from tumor cells and, therefore, carries features of its genomic profile. Moreover, tumor-derived cfDNA can act like oncoviruses, entering the cells of vulnerable organs, transforming them and forming metastatic nodes. Another source of cfDNA is immune cells, including neutrophils that generate neutrophil extracellular traps (NETs). Despite the potential eliminative effect of NETs on tumors, in some cases, their excessive generation provokes tumor growth as well as invasion. Considering both possible pathological contributions of cfDNA, as an agent of oncotransformation and the main component of NETs, the study of deoxyribonucleases (DNases) as anticancer and antimetastatic agents is important and promising. This review considers the pathological role of cfDNA in cancer development and the role of DNases as agents to prevent and/or prohibit tumor progression and the development of metastases.
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Affiliation(s)
| | - Nadezhda Mironova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia;
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11
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Udomruk S, Orrapin S, Pruksakorn D, Chaiyawat P. Size distribution of cell-free DNA in oncology. Crit Rev Oncol Hematol 2021; 166:103455. [PMID: 34464717 DOI: 10.1016/j.critrevonc.2021.103455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022] Open
Abstract
Tumor-specific, circulating cell-free DNA (cfDNA) in liquid biopsy test is a novel promising biomarker in the advancement of cancer management, including early diagnosis, screening, prognosis, identification of actionable targets, and serial tumor monitoring. The specific size pattern of DNA fragments derived from cancer cells is observed to differ from that of cfDNA fragments shed by non-cancer cells. Research into the physiological and biological properties of cfDNA reveals the molecular signature carried by each cfDNA fragments, which can reflect their tissue origins, as well as the mutational profiles with significant genetic alterations. Understanding the fragmentation and size distribution of cfDNA might be a valuable hotspot in liquid biopsy research, with the potential to drive innovation in oncology.
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Affiliation(s)
- Sasimol Udomruk
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Santhasiri Orrapin
- Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Dumnoensun Pruksakorn
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Department of Orthopedics, Faculty of Medicine, Chiang Mai University, 110 Intawaroros, Sriphoom, Muang, Chiang Mai 50200, Thailand.
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand.
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12
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Plasma DNA Integrity as a Prognostic Biomarker for Colorectal Cancer Chemotherapy. JOURNAL OF ONCOLOGY 2021; 2021:5569783. [PMID: 34135960 PMCID: PMC8175143 DOI: 10.1155/2021/5569783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022]
Abstract
Objectives To verify whether the concentrations and integrity index of circulating cell-free DNA (cfDNA) in serum may be clinically useful for the progression monitoring of colorectal cancer (CRC) patients. Methods Serum samples were collected from 76 primary CRC patients who underwent surgery, including 60 with chemotherapy and 43 with follow-up. Long (247 bp) and short (115 bp) DNA fragments in serum were detected by real-time quantitative PCR by amplifying the ALU repeats. Ten serum traditional biomarkers levels were detected by chemiluminescence immunoassay assay. Results The median DNA integrity index (ALU247/ALU115) of serum DNA in the preoperative group was significantly higher than those in the postchemotherapy and the follow-up groups, while cfDNA concentration (ALU115) was significantly lower in the preoperative group compared with the postchemotherapy and the follow-up groups. CEA and CA242 were significantly lower in the postoperative group than in the preoperative group. Conclusions Serum DNA integrity index (ALU247/115) may prove to be a promising candidate biomarker for prognostic prediction of CRC who underwent chemotherapy and during short-term follow-up.
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Zhou Y, Xu Y, Wang C, Gong Y, Zhang Y, Yao R, Li P, Zhu X, Bai J, Guan Y, Xia X, Yang L, Yi X, Sun Q. Serial circulating tumor DNA identification associated with the efficacy and prognosis of neoadjuvant chemotherapy in breast cancer. Breast Cancer Res Treat 2021; 188:661-673. [PMID: 34003409 DOI: 10.1007/s10549-021-06247-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/27/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) provides a promising noninvasive alternative to evaluate the efficacy of neoadjuvant chemotherapy (NCT) in breast cancer. METHODS Herein, we collected 63 tissue (aspiration biopsies and resected tissues) and 206 blood samples (baseline, during chemotherapy (Chemo), after chemotherapy (Post-Chemo), after operation (Post-Op), during follow-up) from 32 patients, and preformed targeted deep sequencing with a customed 1021-gene panel. RESULTS As the results, TP53 (43.8%) and PIK3CA (40.6%) were the most common mutant genes in the primary tumors. At least one tumor-derived mutation was detected in the following number of blood samples: 21, baseline; 3, Chemo; 9, Post-Chemo; and 5, Post-Op. Four patients with pathologic complete response had no tissue mutation in Chemo and Post-Chemo blood. Compared to patients with mutation-positive Chemo or Post-Chemo blood, the counterparts showed a superior primary tumor decrease (median, 86.5% versus 54.6%) and lymph involvement (median, 1 versus 3.5). All five patients with mutation-positive Post-Op developed distant metastases during follow-up, and the sensitivity of detecting clinically relapsed patients was 71.4% (5/7). The median DFS was 9.8 months for patients with mutation-positive Post-Op but not reached for the others (HR 23.53; 95% CI, 1.904-290.9; p < 0.0001). CONCLUSIONS Our study shows that sequential monitoring of blood ctDNA was an effective method for evaluating NCT efficacy and patient recurrence. Integrating ctDNA profiling into the management of LABC patients might improve clinical outcome. TRIAL REGISTRATION This prospective study recruited LABC patients at Peking Union Medical College Hospital (ClinicalTrials.gov Identifier: NCT02797652).
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Affiliation(s)
- Yidong Zhou
- Department of Breast Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, No.1 Shuaifu Garden, Dongcheng District, Beijing, 100010, China.
| | - Yaping Xu
- Geneplus-Beijing, Beijing, 102206, China
| | - Changjun Wang
- Department of Breast Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, No.1 Shuaifu Garden, Dongcheng District, Beijing, 100010, China
| | - Yuhua Gong
- Geneplus-Beijing, Beijing, 102206, China
| | | | - Ru Yao
- Department of Breast Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, No.1 Shuaifu Garden, Dongcheng District, Beijing, 100010, China
| | - Peng Li
- Department of Breast Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, No.1 Shuaifu Garden, Dongcheng District, Beijing, 100010, China
| | - Xiuli Zhu
- Geneplus-Beijing, Beijing, 102206, China
| | - Jing Bai
- Geneplus-Beijing, Beijing, 102206, China
| | | | | | - Ling Yang
- Geneplus-Beijing, Beijing, 102206, China
| | - Xin Yi
- Geneplus-Beijing, Beijing, 102206, China
| | - Qiang Sun
- Department of Breast Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, No.1 Shuaifu Garden, Dongcheng District, Beijing, 100010, China.
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14
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Darrigues L, Pierga JY, Bernard-Tessier A, Bièche I, Silveira AB, Michel M, Loirat D, Cottu P, Cabel L, Dubot C, Geiss R, Ricci F, Vincent-Salomon A, Proudhon C, Bidard FC. Circulating tumor DNA as a dynamic biomarker of response to palbociclib and fulvestrant in metastatic breast cancer patients. Breast Cancer Res 2021; 23:31. [PMID: 33676547 PMCID: PMC7937332 DOI: 10.1186/s13058-021-01411-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/22/2021] [Indexed: 12/21/2022] Open
Abstract
Background Following the PALOMA-3 study results, the combination of palbociclib, a CDK4/6 inhibitor, with fulvestrant, a selective estrogen receptor degrader, has become a standard therapy in women with estrogen receptor-positive (ER+) HER2-negative (HER2−) metastatic breast cancer (MBC). Palbociclib has been shown to increase the progression-free survival (PFS) overall but no predictive biomarker of palbociclib efficacy has been validated so far. We thus evaluated whether early changes of circulating tumor DNA (ctDNA) levels are associated with palbociclib plus fulvestrant efficiency. Methods ER+ HER2− MBC patients were included in a prospective observational cohort before treatment initiation. Tumor response was assessed by radiological evaluation (RECIST v1.1) every 3 months. Plasma samples were collected before treatment (baseline), at day 15 (D15), at day 30 (D30), and at disease progression. We searched for somatic mutations from archived tumor tissues by targeted deep sequencing. For patients with somatic mutations identified, circulating tumor DNA (ctDNA) was tracked using digital droplet PCR. Ratios of ctDNA levels ([D15/baseline] and [D30/baseline]) were then correlated with prospectively registered patient characteristics and outcomes. Results Twenty-five of the 61 patients enrolled had a somatic mutation testable in plasma (NPIK3CA = 21, NTP53 = 2, NAKT1 = 2). At baseline, 84% of patients had detectable ctDNA levels but ctDNA levels had no prognostic impact on PFS (p = 0.10). Among those patients, ctDNA was still detected in 82% at D15 and 68% at D30. ctDNA clearance observed at day 30 was associated with longer PFS (HR = 7.2, 95% CI = 1.5–32.6, p = 0.004). On the contrary, a [D30/baseline] ctDNA ratio > 1 was associated with a shorter PFS (HR = 5.1, 95% CI = 1.4–18.3, p = 0.02) and all 5 patients with increased ctDNA levels at D30 showed disease progression after 3 months under palbociclib-fulvestrant. Finally, at the time of radiological tumor progression, ctDNA was detected in all patients tested. Conclusion Our study demonstrates that the efficiency of palbociclib and fulvestrant can be monitored by serial analyses of ctDNA before radiological evaluation and that early ctDNA variation is a prognostic factor of PFS. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-021-01411-0.
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Affiliation(s)
- Lauren Darrigues
- Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT 1428, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France.,Department of Surgical Oncology, Institut Curie, Paris, France.,Université de Paris, Paris, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT 1428, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France.,Université de Paris, Paris, France.,Department of Medical Oncology, Institut Curie, 35 rue Dailly, 92210, Saint Cloud, France
| | - Alice Bernard-Tessier
- Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT 1428, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Ivan Bièche
- Université de Paris, Paris, France.,Department of Biopathology, Institut Curie, Paris, France
| | - Amanda Bartolini Silveira
- Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT 1428, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Marc Michel
- Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT 1428, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Delphine Loirat
- Department of Medical Oncology, Institut Curie, 35 rue Dailly, 92210, Saint Cloud, France
| | - Paul Cottu
- Department of Medical Oncology, Institut Curie, 35 rue Dailly, 92210, Saint Cloud, France
| | - Luc Cabel
- Department of Medical Oncology, Institut Curie, 35 rue Dailly, 92210, Saint Cloud, France.,INSERM U934 CNRS UMR3215, Paris, France
| | - Coraline Dubot
- Department of Medical Oncology, Institut Curie, 35 rue Dailly, 92210, Saint Cloud, France
| | - Romain Geiss
- Department of Medical Oncology, Institut Curie, 35 rue Dailly, 92210, Saint Cloud, France
| | - Francesco Ricci
- Department of Medical Oncology, Institut Curie, 35 rue Dailly, 92210, Saint Cloud, France
| | | | - Charlotte Proudhon
- Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT 1428, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France. .,INSERM U934 CNRS UMR3215, Paris, France.
| | - François-Clément Bidard
- Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT 1428, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France. .,Department of Medical Oncology, Institut Curie, 35 rue Dailly, 92210, Saint Cloud, France. .,UVSQ Paris-Saclay University, Saint Cloud, France.
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15
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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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16
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Hinestrosa JP, Searson DJ, Lewis JM, Kinana A, Perrera O, Dobrovolskaia I, Tran K, Turner R, Balcer HI, Clark I, Bodkin D, Hoon DSB, Krishnan R. Simultaneous Isolation of Circulating Nucleic Acids and EV-Associated Protein Biomarkers From Unprocessed Plasma Using an AC Electrokinetics-Based Platform. Front Bioeng Biotechnol 2020; 8:581157. [PMID: 33224932 PMCID: PMC7674311 DOI: 10.3389/fbioe.2020.581157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/29/2020] [Indexed: 01/04/2023] Open
Abstract
The power of personalized medicine is based on a deep understanding of cellular and molecular processes underlying disease pathogenesis. Accurately characterizing and analyzing connections between these processes is dependent on our ability to access multiple classes of biomarkers (DNA, RNA, and proteins)—ideally, in a minimally processed state. Here, we characterize a biomarker isolation platform that enables simultaneous isolation and on-chip detection of cell-free DNA (cfDNA), extracellular vesicle RNA (EV-RNA), and EV-associated proteins in unprocessed biological fluids using AC Electrokinetics (ACE). Human biofluid samples were flowed over the ACE microelectrode array (ACE chip) on the Verita platform while an electrical signal was applied, inducing a field that reversibly captured biomarkers onto the microelectrode array. Isolated cfDNA, EV-RNA, and EV-associated proteins were visualized directly on the chip using DNA and RNA specific dyes or antigen-specific, directly conjugated antibodies (CD63, TSG101, PD-L1, GPC-1), respectively. Isolated material was also eluted off the chip and analyzed downstream by multiple methods, including PCR, RT-PCR, next-generation sequencing (NGS), capillary electrophoresis, and nanoparticle size characterization. The detection workflow confirmed the capture of cfDNA, EV-RNA, and EV-associated proteins from human biofluids on the ACE chip. Tumor specific variants and the mRNAs of housekeeping gene PGK1 were detected in cfDNA and RNA isolated directly from chips in PCR, NGS, and RT-PCR assays, demonstrating that high-quality material can be isolated from donor samples using the isolation workflow. Detection of the luminal membrane protein TSG101 with antibodies depended on membrane permeabilization, consistent with the presence of vesicles on the chip. Protein, morphological, and size characterization revealed that these vesicles had the characteristics of EVs. The results demonstrated that unprocessed cfDNA, EV-RNA, and EV-associated proteins can be isolated and simultaneously fluorescently analyzed on the ACE chip. The compatibility with established downstream technologies may also allow the use of the platform as a sample preparation method for workflows that could benefit from access to unprocessed exosomal, genomic, and proteomic biomarkers.
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Affiliation(s)
| | | | - Jean M Lewis
- Biological Dynamics, Inc., San Diego, CA, United States
| | - Alfred Kinana
- Biological Dynamics, Inc., San Diego, CA, United States
| | | | | | - Kevin Tran
- Departments of Translational Molecular Medicine and Sequence Center, John Wayne Cancer Institute, Santa Monica, CA, United States
| | - Robert Turner
- Biological Dynamics, Inc., San Diego, CA, United States
| | | | - Iryna Clark
- Biological Dynamics, Inc., San Diego, CA, United States
| | - David Bodkin
- Cancer Center Oncology Medical Group, La Mesa, CA, United States
| | - Dave S B Hoon
- Departments of Translational Molecular Medicine and Sequence Center, John Wayne Cancer Institute, Santa Monica, CA, United States
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17
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Ma G, Wang J, Huang H, Han X, Xu J, Veeramootoo JS, Xia T, Wang S. Identification of the plasma total cfDNA level before and after chemotherapy as an indicator of the neoadjuvant chemotherapy response in locally advanced breast cancer. Cancer Med 2020; 9:2271-2282. [PMID: 32017472 PMCID: PMC7131846 DOI: 10.1002/cam4.2906] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/03/2020] [Accepted: 01/22/2020] [Indexed: 02/06/2023] Open
Abstract
This study aimed to retrospectively evaluate the circulating free DNA (cfDNA) level in patients with locally advanced breast cancer (LABC) having different neoadjuvant chemotherapy (NCT) responses and to investigate whether dynamic changes in cfDNA level could predict the effectiveness of NCT in patients with LABC. Data on 61 patients with LABC were included. NCT responses were evaluated using the response evaluation criteria. Blood samples were collected for cfDNA detection before treatment and after the first and eighth courses of chemotherapy. The Alu 111‐bp and 260‐bp fragment levels were evaluated by polymerase chain reaction, and the predictive value of the cfDNA level in the NCT response was determined. In vitro, the MCF‐7 and MCF‐7/ADR cell lines were applied to simulate the phenomenon of drug resistance and explain the underlying mechanism. The Alu 111‐bp level increased after the first NCT course (P = .014) and then remained high after NCT in the high‐R group (P = .047), but it remained steady in the low‐R group during NCT. A similar tendency in the Alu 260‐bp level was revealed in different groups. The ∆∆Ct value of Alu 260‐bp had good diagnostic efficiency in assessing predictive ability. The area under the curve for the ∆∆Ct1 and ∆∆Ct2 of Alu 260‐bp was 0.697 and 0.647, respectively. The cfDNA level was closely related to epirubicin‐induced apoptosis and changes in the Ki‐67 index in vitro. The elevation of cfDNA after one chemotherapy cycle was mediated by the apoptosis of tumor cells and related to the improved chemotherapy response.
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Affiliation(s)
- Ge Ma
- Department of Breast Surgery, The Firsft Affiliated Hospital with Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jingyi Wang
- Department of Breast Surgery, The Firsft Affiliated Hospital with Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Huaxing Huang
- The First Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Xu Han
- Department of Breast Surgery, The Firsft Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Jin Xu
- Department of Breast and Thyroid Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | | | - Tiansong Xia
- Department of Breast Surgery, The Firsft Affiliated Hospital with Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shui Wang
- Department of Breast Surgery, The Firsft Affiliated Hospital with Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
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18
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Bronkhorst AJ, Ungerer V, Holdenrieder S. Comparison of methods for the quantification of cell-free DNA isolated from cell culture supernatant. Tumour Biol 2019; 41:1010428319866369. [DOI: 10.1177/1010428319866369] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gaining a better understanding of the biological properties of cell-free DNA constitutes an important step in the development of clinically meaningful cell-free DNA–based tests. Since the in vivo characterization of cell-free DNA is complicated by the immense heterogeneity of blood samples, an increasing number of in vitro cell culture experiments, which offer a greater level of control, are being conducted. However, cell culture studies are currently faced with three notable caveats. First, the concentration of cell-free DNA in vitro is relatively low. Second, the median amount and size of cell-free DNA in culture medium varies greatly between cell types. Third, the amount and size of cell-free DNA in the culture medium of a single cell line fluctuates over time. Although these are interesting findings, it can also be a great source of experimental confusion and emphasizes the importance of method optimization and standardization. Therefore, in this study, we compared five commonly used cell-free DNA quantification methods, including quantitative polymerase chain reaction, Qubit Double-Stranded DNA High Sensitivity assay, Quant-iT PicoGreen Assay, Bioanalyzer High Sensitivity DNA assay, and NanoDrop Onec. Analysis of the resulting data, along with an interpretation of theoretical values (i.e. the theoretical detection and quantification limits of the respective methods), enables the calculation of optimal conditions for several important preanalytical steps pertaining to each quantification method and different cell types, including the (1) time-point at which culture medium should be collected for cell-free DNA extraction, (2) amount of cell culture supernatant from which to isolate cell-free DNA, (3) volume of elution buffer, and (4) volume of cell-free DNA sample to use for quantification.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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19
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Lee J, Park SS, Lee YK, Norton JA, Jeffrey SS. Liquid biopsy in pancreatic ductal adenocarcinoma: current status of circulating tumor cells and circulating tumor DNA. Mol Oncol 2019; 13:1623-1650. [PMID: 31243883 PMCID: PMC6670020 DOI: 10.1002/1878-0261.12537] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 06/07/2019] [Accepted: 06/25/2019] [Indexed: 12/22/2022] Open
Abstract
Reliable biomarkers are required to evaluate and manage pancreatic ductal adenocarcinoma. Circulating tumor cells and circulating tumor DNA are shed into blood and can be relatively easily obtained from minimally invasive liquid biopsies for serial assays and characterization, thereby providing a unique potential for early diagnosis, forecasting disease prognosis, and monitoring of therapeutic response. In this review, we provide an overview of current technologies used to detect circulating tumor cells and circulating tumor DNA and describe recent advances regarding the multiple clinical applications of liquid biopsy in pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Jee‐Soo Lee
- Department of Laboratory MedicineHallym University Sacred Heart HospitalAnyangKorea
- Department of Laboratory MedicineSeoul National University College of MedicineSeoulKorea
| | - Sung Sup Park
- Department of Laboratory MedicineSeoul National University College of MedicineSeoulKorea
| | - Young Kyung Lee
- Department of Laboratory MedicineHallym University Sacred Heart HospitalAnyangKorea
- Department of Laboratory MedicineHallym University College of MedicineAnyangKorea
| | - Jeffrey A. Norton
- Department of SurgeryStanford University School of MedicineStanfordCAUSA
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20
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Wang W, Zhang W, Su L, Sang J, Wang S, Yao Y. Plasma cell-free DNA integrity: a potential biomarker to monitor the response of breast cancer to neoadjuvant chemotherapy. Transl Cancer Res 2019; 8:1531-1539. [PMID: 35116896 PMCID: PMC8799030 DOI: 10.21037/tcr.2019.08.05] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/09/2019] [Indexed: 12/26/2022]
Abstract
Background Although the clinical significance of neoadjuvant chemotherapy (NACT) is widely recognized, there is still no effective means to monitor the therapeutic response in real time. The present study aimed to investigate the significance of the cell-free DNA (cfDNA) concentration and integrity (cfDI) to monitor the response of breast cancer to NACT. Methods Twenty-nine patients with breast cancer receiving NACT were included in this study. Patients’ peripheral blood was drawn before, in the mid-term, and at the end of chemotherapy. The cfDNA concentration and cfDI were assessed using absolute quantitative PCR. Results The results showed that the cfDNA concentration and cfDI pre-NACT were not obviously correlated with the patients’ clinical characteristics. The mean cfDI value increased significantly when the patients received NACT (P<0.05), and an increasing cfDI was associated with tumor shrinkage and reduced Ki67 levels (P<0.05). In addition, the cfDI after NACT was inversely correlated with the number of metastatic lymph nodes, and the cfDI value of patients with a pathologically complete response was significantly higher than that of patients with distant metastasis after surgery. Conclusions This study suggested that cfDI could be used as an indicator to monitor the therapeutic response to NACT; however, more research is needed to confirm this conclusion.
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Affiliation(s)
- Wei Wang
- Department of Breast Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Weijie Zhang
- Department of Breast Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Lei Su
- Department of Breast Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Jianfeng Sang
- Department of Breast Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Shui Wang
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Yongzhong Yao
- Department of Breast Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
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21
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Tadayyon H, Gangeh M, Sannachi L, Trudeau M, Pritchard K, Ghandi S, Eisen A, Look-Hong N, Holloway C, Wright F, Rakovitch E, Vesprini D, Tran WT, Curpen B, Czarnota G. A priori prediction of breast tumour response to chemotherapy using quantitative ultrasound imaging and artificial neural networks. Oncotarget 2019; 10:3910-3923. [PMID: 31231468 PMCID: PMC6570472 DOI: 10.18632/oncotarget.26996] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/13/2019] [Indexed: 11/25/2022] Open
Abstract
We demonstrate the clinical utility of combining quantitative ultrasound (QUS) imaging of the breast with an artificial neural network (ANN) classifier to predict the response of breast cancer patients to neoadjuvant chemotherapy (NAC) administration prior to the start of treatment. Using a 6 MHz ultrasound system, radiofrequency (RF) ultrasound data were acquired from 100 patients with biopsy-confirmed locally advanced breast cancer prior to the start of NAC. Quantitative ultrasound mean parameter intensity and texture features were computed from the tumour core and margin, and were compared to the clinical/pathological response and 5-year recurrence-free survival (RFS) of patients. A multi-parametric QUS model in conjunction with an ANN classifier predicted patient response with 96 ± 6% accuracy, and a 0.96 ± 0.08 area under the receiver operating characteristic curve (AUC), compared to 65 ± 10 % accuracy and 0.67 ± 0.14 AUC achieved using a K-Nearest Neighbour (KNN) algorithm. A separate ANN model predicted patient RFS with 85 ± 7% accuracy, and a 0.89 ± 0.11 AUC, whereas the KNN methodology achieved a 58 ± 6 % accuracy and a 0.64 ± 0.09 AUC. The application of ANN for classifying patient response based on tumour QUS features performs well in terms of predicting response to chemotherapy. The findings here provide a framework for developing personalized a priori chemotherapy selection for patients that are candidates for NAC, potentially resulting in improved patient treatment outcomes and prognosis.
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Affiliation(s)
- Hadi Tadayyon
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mehrdad Gangeh
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Lakshmanan Sannachi
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Maureen Trudeau
- Division of Medical Oncology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Kathleen Pritchard
- Division of Medical Oncology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Sonal Ghandi
- Division of Medical Oncology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Andrea Eisen
- Division of Medical Oncology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Nicole Look-Hong
- Surgical Oncology, Department of Surgery, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Claire Holloway
- Surgical Oncology, Department of Surgery, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Frances Wright
- Surgical Oncology, Department of Surgery, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Eileen Rakovitch
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Danny Vesprini
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - William Tyler Tran
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Belinda Curpen
- Department of Medical Imaging, Sunnybrook Health Sciences Centre, and Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Gregory Czarnota
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Division of Medical Oncology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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22
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Abstract
Cell-free DNA integrity (cfDNAi) could be a valuable biomarker for solid tumors, to define prognosis and response to therapy. Several elements have been studied for cfDNAi, such as specific genes involved in cancer progression or repetitive DNA sequences as surrogate markers for the whole circulating DNA.However, the lack of a standardized method for cfDNAi evaluation remains one of its main critical issues. Apoptotic index (AI) and integrity index (II) of cfDNA could be useful biomarkers to identify the patients likely to recur, progress, or relapse, which is an urgent need in translational research in oncology.Here it is provided an adequate method of cfDNAi analysis: a cheap and reproducible tool, robust and performable in all laboratories using a real-time PCR instrument.
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23
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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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24
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Park K, Woo M, Kim JE, Ahn JH, Jung KH, Roh J, Gong G, Kim SB. Efficacy of assessing circulating cell-free DNA using a simple fluorescence assay in patients with triple-negative breast cancer receiving neoadjuvant chemotherapy: a prospective observational study. Oncotarget 2017; 9:3875-3886. [PMID: 29423090 PMCID: PMC5790507 DOI: 10.18632/oncotarget.23520] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/15/2017] [Indexed: 12/31/2022] Open
Abstract
This study aims to assess cell-free DNA (CFD) by a fluorescence assay as a biomarker for early prediction of a pathologic complete response (pCR) and relapse in patients with triple-negative breast cancer (TNBC) undergoing neoadjuvant chemotherapy. Patients with clinical stage II or III TNBC scheduled for neoadjuvant chemotherapy were prospectively enrolled. All patients underwent four cycles of Adriamycin plus cyclophosphamide (AC), followed by four cycles of cisplatin or docetaxel chemotherapy and surgery. Blood samples were obtained before the initial chemotherapy (baseline-CFD) and after four AC neoadjuvant chemotherapy cycles (AC-CFD) to evaluate CFD levels. In total, 72 patients who met the inclusion criteria were enrolled. The mean baseline-CFD and AC-CFD levels were 239 ± 68 and 210 ± 66 ng/mL, respectively, with a significant decline in the CFD levels after AC neoadjuvant chemotherapy (P = 0.001). In the 33.6-month median follow-up, 18 cases of relapse were reported. A ROC curve analysis of baseline-CFD was performed to determine the predictive value for relapse, and an area under the curve of 0.62 (95% CI, 0.46–0.78) at 264 ng/mL was obtained. Patients with baseline-CFD >264 ng/mL were at a higher risk of relapse than those with baseline-CFD ≤264 ng/mL (HR, 2.84; 95% CI, 1.11–7.24; P = 0.029). Multivariate analysis established baseline-CFD as an independent predicting factor for relapse (HR, 3.74; 95% CI, 1.32–10.53; P = 0.013). In conclusion, baseline-CFD measured by a fluorescence assay might be a potential biomarker to predict relapse, which could be useful for risk stratification of TNBC.
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Affiliation(s)
- Kwonoh Park
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Medical Oncology and Hematology, Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan-si, Republic of Korea
| | - Miyoung Woo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jeong Eun Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jin-Hee Ahn
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kyung Hae Jung
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jin Roh
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Gyungyub Gong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sung-Bae Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
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25
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Wang R, Li X, Zhang H, Wang K, He J. Cell-free circulating tumor DNA analysis for breast cancer and its clinical utilization as a biomarker. Oncotarget 2017; 8:75742-75755. [PMID: 29088906 PMCID: PMC5650461 DOI: 10.18632/oncotarget.20608] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/17/2017] [Indexed: 01/05/2023] Open
Abstract
Circulating tumor DNA (ctDNA) in the blood of cancer patients contains much information on genetic and epigenetic profiles associated with cancer development, progression, and response to therapy. Analysis of ctDNA provides an opportunity for non-invasive sampling of tumor DNA repetitiously and therefore advance precision medicine. Recent development in massively parallel sequencing and digital genomic techniques support the analytical and clinical validity of ctDNA as a promising 'liquid biopsy' in human cancer. In this review, we discussed the current status of cell-free ctDNA including ctDNA biology, recently developed techniques for ctDNA detection, breast cancer specific detecting strategies, with a focus on clinical applications of ctDNA-based biomarkers in breast oncology.
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Affiliation(s)
- Ru Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, P.R. China
| | - Xiao Li
- Department of Breast Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, P.R. China
| | - Huimin Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, P.R. China
| | - Ke Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, P.R. China
| | - Jianjun He
- Department of Breast Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, P.R. China
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26
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Riethdorf S, Müller V, Loibl S, Nekljudova V, Weber K, Huober J, Fehm T, Schrader I, Hilfrich J, Holms F, Tesch H, Schem C, von Minckwitz G, Untch M, Pantel K. Prognostic Impact of Circulating Tumor Cells for Breast Cancer Patients Treated in the Neoadjuvant "Geparquattro" Trial. Clin Cancer Res 2017; 23:5384-5393. [PMID: 28679772 DOI: 10.1158/1078-0432.ccr-17-0255] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/03/2017] [Accepted: 06/26/2017] [Indexed: 11/16/2022]
Abstract
Purpose: This study aimed to evaluate the prognostic impact of circulating tumor cells (CTC) detected in patients with operable or locally advanced breast cancer before and after neoadjuvant therapy (NT) within the clinical trial GeparQuattro.Experimental Design: Data on CTCs enumerated with the CellSearch system were available for 213 and 207 patients before and after NT, respectively. Associations of CTCs with disease-free survival (DFS) and overall survival (OS) were analyzed by nonparametric Kaplan-Meier estimates and parametric Cox regression.Results: After a median follow-up of 67.1 months, the detection of ≥1 CTC/7.5 mL and ≥2 CTCs/7.5 mL before NT was associated with reduced DFS (P = 0.031 and P < 0.0001, respectively) and OS (P = 0.0057 and P < 0.0001, respectively), whereas CTCs detected after NT did not correlate with DFS or OS. In parametric univariate and multivariate Cox models, ≥1 CTC/7.5 mL, ≥2 CTCs/7.5 mL, and absolute CTC numbers before NT revealed to be independent prognostic parameters of DFS and OS. CTC-negative patients with pathologic complete response (pCR) exhibited the best prognosis, whereas those with CTCs and less tumor response were at high risk of tumor relapse. In HER2 (ERBB2)-positive and triple-negative patients, ≥2 CTCs/7.5 mL detected before NT also were significantly associated with worse DFS and OS.Conclusions: Detection of CTCs before NT is an independent prognostic factor of impaired clinical outcome, and combined with pCR, it could be helpful to stratify breast cancer patients for therapeutic interventions. Clin Cancer Res; 23(18); 5384-93. ©2017 AACR.
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Affiliation(s)
- Sabine Riethdorf
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Volkmar Müller
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | - Jens Huober
- Department of Gynecology and Obstetrics, University Medical Center, Ulm, Germany
| | - Tanja Fehm
- Department of Obstetrics and Gynecology, University Medical Center, Düsseldorf, Germany
| | | | | | - Frank Holms
- Department of Obstetrics and Gynecology, St. Barbara-Klinik, Hamm-Heessen, Germany
| | | | - Christian Schem
- Department of Gynecology and Obstetrics, University Medical Center, Kiel, Germany
| | | | - Michael Untch
- Department of Obstetrics and Gynecology, Heliosklinik Buch, Berlin, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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27
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Liquid biopsy: unlocking the potentials of cell-free DNA. Virchows Arch 2017; 471:147-154. [DOI: 10.1007/s00428-017-2137-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/20/2017] [Accepted: 04/26/2017] [Indexed: 01/02/2023]
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28
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Tadayyon H, Sannachi L, Gangeh MJ, Kim C, Ghandi S, Trudeau M, Pritchard K, Tran WT, Slodkowska E, Sadeghi-Naini A, Czarnota GJ. A priori Prediction of Neoadjuvant Chemotherapy Response and Survival in Breast Cancer Patients using Quantitative Ultrasound. Sci Rep 2017; 7:45733. [PMID: 28401902 PMCID: PMC5388850 DOI: 10.1038/srep45733] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/06/2017] [Indexed: 12/26/2022] Open
Abstract
Quantitative ultrasound (QUS) can probe tissue structure and analyze tumour characteristics. Using a 6-MHz ultrasound system, radiofrequency data were acquired from 56 locally advanced breast cancer patients prior to their neoadjuvant chemotherapy (NAC) and QUS texture features were computed from regions of interest in tumour cores and their margins as potential predictive and prognostic indicators. Breast tumour molecular features were also collected and used for analysis. A multiparametric QUS model was constructed, which demonstrated a response prediction accuracy of 88% and ability to predict patient 5-year survival rates (p = 0.01). QUS features demonstrated superior performance in comparison to molecular markers and the combination of QUS and molecular markers did not improve response prediction. This study demonstrates, for the first time, that non-invasive QUS features in the core and margin of breast tumours can indicate breast cancer response to neoadjuvant chemotherapy (NAC) and predict five-year recurrence-free survival.
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Affiliation(s)
- Hadi Tadayyon
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Lakshmanan Sannachi
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mehrdad J Gangeh
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Christina Kim
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Sonal Ghandi
- Division of Medical Oncology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Maureen Trudeau
- Division of Medical Oncology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Kathleen Pritchard
- Division of Medical Oncology, Department of Medicine, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - William T Tran
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Elzbieta Slodkowska
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Ali Sadeghi-Naini
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Gregory J Czarnota
- Physical Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada.,Department of Radiation Oncology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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29
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Perakis S, Auer M, Belic J, Heitzer E. Advances in Circulating Tumor DNA Analysis. Adv Clin Chem 2017; 80:73-153. [PMID: 28431643 DOI: 10.1016/bs.acc.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
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30
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Jiang P, Lo YD. The Long and Short of Circulating Cell-Free DNA and the Ins and Outs of Molecular Diagnostics. Trends Genet 2016; 32:360-371. [DOI: 10.1016/j.tig.2016.03.009] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/30/2016] [Indexed: 12/25/2022]
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31
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Canzoniero JV, Park BH. Use of cell free DNA in breast oncology. Biochim Biophys Acta Rev Cancer 2016; 1865:266-74. [PMID: 27012505 DOI: 10.1016/j.bbcan.2016.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/18/2016] [Accepted: 03/19/2016] [Indexed: 12/24/2022]
Abstract
Cell free DNA (cfDNA) are short fragments of nucleic acids present in circulation outside of cells. In patients with cancer, some portion of cfDNA is derived from tumor cells, termed circulating tumor DNA (ctDNA), and contains the same mutations and genetic changes as the cancer. The development of new, more effective methods to detect these changes has led to increased interest in developing ctDNA as a biomarker for cancer. Here we will review current literature on the use of ctDNA, with an emphasis on breast cancer, for cancer detection, prognosis, monitoring response to therapy, and tracking the rise of new mutant subclones.
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Affiliation(s)
- Jenna VanLiere Canzoniero
- Division of General Internal Medicine, Johns Hopkins, 600 N Wolfe St, Nelson 207, Baltimore, MD 21287, USA.
| | - Ben Ho Park
- The Sidney Kimmel Comprehensive Cancer Institute at Johns Hopkins, 1650 Orleans Street, CRBI, Baltimore, MD 21287, USA.
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32
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Abstract
As the release of tumor-associated DNA into blood circulation is a common event in patients with cancer, screening of plasma or serum DNA may provide information on genetic and epigenetic profiles associated with breast cancer development, progression, and response to therapy. Quantitative testing of circulating DNA can reflect tumor burden, and molecular characterization of circulating DNA can reveal important tumor characteristics relevant to the choice of targeted therapies in individual patients. Contrary to circulating DNA from blood that presents molecular changes in tumor DNA in real time, tissue biopsies can deliver only a spatially and temporally limited snapshot of the heterogeneous tumor. Analyses of circulating DNA might provide prognostic and predictive information and therefore advance personalized medicine. However, standardization of different technical platforms as well as the control of pre-analytical and analytical factors is mandatory before its introduction into clinical practice. In the present review, we discussed technical aspects and clinical relevance of the analyses of circulating plasma/serum DNA in patients with breast cancer.
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Affiliation(s)
- Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraβe 52, 20246, Hamburg, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraβe 52, 20246, Hamburg, Germany.
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33
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Iqbal S, Vishnubhatla S, Raina V, Sharma S, Gogia A, Deo SSV, Mathur S, Shukla NK. Circulating cell-free DNA and its integrity as a prognostic marker for breast cancer. SPRINGERPLUS 2015; 4:265. [PMID: 26090312 PMCID: PMC4469592 DOI: 10.1186/s40064-015-1071-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/28/2015] [Indexed: 12/14/2022]
Abstract
The aim of our study was to look for alternative predictive biomarkers for breast cancer management in limited resource setup. A comprehensive analysis of circulating cell-free DNA (CCFD) in serum at baseline was performed to assess its prognostic potential. Quantitative polymerase chain reaction (qPCR) of ALU sequences using ALU115 and ALU247 primers was carried out in patients (N: baseline 148, postoperative 47) and 51 healthy controls. Mean serum DNA integrity, levels of ALU 247 and levels of ALU 115 were significantly higher in patients than in healthy females. No significant differences were observed in the levels ALU 247 and ALU 115 between stage IV and earlier stages of the disease. The DNA integrity was significantly higher in stage IV than earlier stages. A significant decrease in DNA integrity was observed after surgery (pre: 0.55 ± 0.23 vs post: 0.43 ± 0.30; P = 0.002) while no such change could be observed for ALU 247 and ALU 115. Baseline DNA integrity was significantly higher in relapsed patients than in patients who were free of disease (P = 0.005). Higher baseline DNA integrity was also indicated, though statistically not significant, in patients who died (P = 0.14). In contrast, ALU 247 and ALU 115 levels were decreased in died patients as compared to survivors (24.8 ± 34.80 vs 73.5 ± 170.83, P = 0.02 for ALU 247 and 41.0 ± 47.99 vs 159.5 ± 299.54, P = 0.005 for ALU 115). Baseline levels of ALU 115 and ALU 247 were lower in relapsed patients, though statistically not significant. In univariate analysis, the only clinic-pathological parameter associated with disease prognosis was tumor size. The hazards of 5-year overall mortality was 3.60 (95 % CI: 1.03 12.53, P = 0.03) among patients with lower baseline serum levels of CCFD (ALU 247 < 21 and ALU 115 < 41). Similarly the 4 year hazards for recurrence was 2.30 (95 % CI: 0.96 5.52, P = 0.05) among patients with higher DNA integrity. Baseline serum levels of CCFD and its integrity were found to be potential prognostic biomarkers in patients of primary breast cancer at our centre.
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Affiliation(s)
- Sobuhi Iqbal
- Department of Medical Oncology, Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | | | - Vinod Raina
- Department of Medical Oncology, Hematology and Stem Cell Transplantation, Fortis Memorial Research Institute, Sector 44, Gurgoan, India
| | - Surabhi Sharma
- Department of Medical Oncology, Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Ajay Gogia
- Department of Medical Oncology, Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Suryanarayana S V Deo
- Department of Surgical Oncology, Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sandeep Mathur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Nutan Kumar Shukla
- Department of Surgical Oncology, Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
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34
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Abstract
Many methods have been developed for DNA integrity assessment including electrophoresis-based procedures, quantitative PCR, and, more recently, microfluidics-based procedures. DNA integrity evaluation can be employed for characterizing biological samples quality before extensive genomic analysis and also finds applications in reproductive medicine, prenatal diagnostics, or cancer research. In this chapter, we will focus on the assessment of DNA integrity in cancer research. In particular, we will present the application of the determination of DNA integrity for tracking of circulating tumor DNA. Finally, we will conclude by illustrating the potential innovative application of DNA integrity as a biomarker in clinical research, especially for prognostic purposes, patient follow-up, or early diagnosis.
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35
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Fleischhacker M, Schmidt B. Extracellular Nucleic Acids and Cancer. ADVANCES IN PREDICTIVE, PREVENTIVE AND PERSONALISED MEDICINE 2015. [DOI: 10.1007/978-94-017-9168-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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36
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Tug S, Helmig S, Menke J, Zahn D, Kubiak T, Schwarting A, Simon P. Correlation between cell free DNA levels and medical evaluation of disease progression in systemic lupus erythematosus patients. Cell Immunol 2014; 292:32-9. [PMID: 25243646 DOI: 10.1016/j.cellimm.2014.08.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/07/2014] [Accepted: 08/12/2014] [Indexed: 12/20/2022]
Abstract
High levels of cell free DNA (cfDNA) in human blood plasma have been described in patients with autoimmune diseases. The aim of this study was to determine the levels of cfDNA in systemic lupus erythematosus (SLE) patients and to assess fluctuations of cfDNA concentrations compared to the course of disease progression under standard treatment. Therefore, nuclear cfDNA concentrations in plasma were measured in 59 SLE patients and 59 healthy controls. Follow-up blood plasma was collected from 27 of the 59 SLE patients. Patients were characterised by clinical parameters (antinuclear antibodies (ANA), anti-dsDNA-antibodies, C3, C4, and CRP), SLE disease activity index (SLEDAI) and medical therapy. Our results showed that cfDNA concentrations were significantly higher in SLE patients compared to healthy individuals. Levels of cfDNA assessed in serial samples correlated significantly with the medical evaluation of disease activity in SLE patients. Our results could implicate cfDNA as a global marker for disease activity.
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Affiliation(s)
- Suzan Tug
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Susanne Helmig
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Julia Menke
- Department of Rheumatology and Clinical Immunology, University Medical Centre of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Daniela Zahn
- Institute of Psychology, Health Psychology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Thomas Kubiak
- Institute of Psychology, Health Psychology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Andreas Schwarting
- Department of Rheumatology and Clinical Immunology, University Medical Centre of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes Gutenberg-University Mainz, Mainz, Germany.
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37
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Elshimali YI, Khaddour H, Sarkissyan M, Wu Y, Vadgama JV. The clinical utilization of circulating cell free DNA (CCFDNA) in blood of cancer patients. Int J Mol Sci 2013; 14:18925-58. [PMID: 24065096 PMCID: PMC3794814 DOI: 10.3390/ijms140918925] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 08/26/2013] [Accepted: 08/30/2013] [Indexed: 02/06/2023] Open
Abstract
Qualitative and quantitative testing of circulating cell free DNA (CCFDNA) can be applied for the management of malignant and benign neoplasms. Detecting circulating DNA in cancer patients may help develop a DNA profile for early stage diagnosis in malignancies. The technical issues of obtaining, using, and analyzing CCFDNA from blood will be discussed.
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Affiliation(s)
- Yahya I. Elshimali
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
- Author to whom correspondence should be addressed; E-Mail: or ; Tel.: +1-818-515-7618; Fax: +1-818-994-9875
| | - Husseina Khaddour
- Laboratory Diagnostic Medicine, Faculty of Pharmacy, Mazzeh (17th April Street), Damascus University, Damascus, Syria; E-Mail:
| | - Marianna Sarkissyan
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
| | - Yanyuan Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
- David Geffen School of Medicine at UCLA, UCLA’s Jonsson Comprehensive Cancer Center, 8-684 Factor Building, Box 951781, Los Angeles, CA 90095-1781, USA
| | - Jaydutt V. Vadgama
- Division of Cancer Research and Training, Department of Internal Medicine, Charles Drew University of Medicine and Science, 1720 East 120th Street, Los Angeles, CA 90059, USA; E-Mails: (M.S.); (Y.W.); (J.V.V.)
- David Geffen School of Medicine at UCLA, UCLA’s Jonsson Comprehensive Cancer Center, 8-684 Factor Building, Box 951781, Los Angeles, CA 90095-1781, USA
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